Contacts of the helix formed by residues 78 - 116 (chain D) in PDB entry 4CKH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 78 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D PRO* 3.1 15.1 + - + +
77D ALA* 1.4 75.9 - - + +
79D CYS* 1.4 72.6 + - - +
80D LEU 3.5 0.4 - - - -
81D GLU* 3.2 5.3 + - - +
82D LYS* 2.9 45.5 + - + +
216D TYR* 4.1 11.3 + - - +
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Residues in contact with CYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C MET* 4.1 0.9 - - + -
74D PRO 4.6 1.8 - - - -
75D MET* 3.0 28.0 + - - +
78D GLU* 1.4 84.6 - - - +
80D LEU* 1.3 61.3 + - - +
82D LYS* 3.0 3.9 + - - +
83D PHE* 2.9 30.7 + - + -
216D TYR* 3.5 35.2 - - + +
220D LEU* 3.9 34.5 - - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.7 23.8 - - + -
189C MET* 3.9 38.8 - - + +
192C VAL* 3.8 32.3 - - + -
63D ILE* 5.1 4.9 - - + +
67D ALA* 3.7 30.3 - - + +
75D MET 3.1 6.3 + - - -
76D MET* 3.3 30.5 + - + +
78D GLU 3.5 0.2 - - - -
79D CYS* 1.3 75.8 - - - +
81D GLU* 1.3 60.8 + - - +
83D PHE* 3.6 4.2 + - - +
84D THR* 3.2 32.3 + - + +
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D MET 3.7 4.6 + - - +
77D ALA 3.5 23.9 - - - +
78D GLU* 3.2 4.1 + - - +
79D CYS 3.2 0.2 - - - -
80D LEU* 1.3 77.4 - - - +
82D LYS* 1.3 62.6 + - + +
84D THR* 3.3 5.3 + - - +
85D VAL* 3.1 51.3 + - + +
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLU* 2.9 42.1 + - + +
79D CYS 3.0 4.0 + - - +
81D GLU* 1.3 75.0 - - + +
83D PHE* 1.3 63.0 + - - +
85D VAL* 4.2 6.8 - - + +
86D SER* 3.2 24.6 + - - -
213D LEU* 4.9 4.3 - - + +
216D TYR* 4.3 19.1 - - + +
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C MET* 4.0 12.6 - - - -
192C VAL* 3.5 29.6 - - + -
193C LEU* 3.7 28.7 - - + -
196C VAL* 3.7 34.9 - - + +
79D CYS* 2.9 29.4 + - + +
80D LEU* 4.0 5.2 - - - +
81D GLU 3.2 0.2 - - - -
82D LYS* 1.3 79.3 - - - +
84D THR* 1.3 60.7 + - - +
86D SER* 3.6 5.6 - - - -
87D LEU* 3.2 26.0 + - - +
213D LEU* 4.0 22.2 - - + -
216D TYR* 3.6 33.2 - + - -
217D ARG* 4.2 7.0 - - - -
220D LEU* 4.3 10.3 - - + -
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C VAL* 4.8 8.5 - - + -
60D VAL* 3.7 6.1 - - + +
63D ILE* 3.8 29.8 - - + -
64D CYS* 3.7 28.7 - - - +
80D LEU* 3.2 20.9 + - + +
81D GLU* 3.3 9.0 + - - +
82D LYS 3.4 0.2 - - - -
83D PHE* 1.3 75.9 - - - +
85D VAL* 1.3 62.6 + - - +
87D LEU* 3.1 16.9 + - + +
88D ASN* 3.1 31.0 + - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLU* 3.1 39.4 + - + +
82D LYS* 4.2 7.4 - - + +
84D THR* 1.3 74.7 - - - +
86D SER* 1.3 65.8 + - - +
88D ASN* 3.2 9.7 + - - +
89D HIS* 3.0 54.8 + - + +
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Residues in contact with SER 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLN* 5.3 0.6 + - - -
82D LYS 3.2 17.3 + - - -
83D PHE 3.6 6.1 - - - -
85D VAL* 1.3 79.1 - - - +
87D LEU* 1.3 56.6 + - - -
89D HIS* 3.4 8.3 - - - +
90D LYS* 3.1 46.5 + - - +
209D GLU* 6.1 0.5 - - - +
210D LEU* 4.5 4.5 - - - +
213D LEU* 3.7 30.1 - - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C VAL* 5.4 2.7 - - + -
195C LEU* 5.2 10.3 - - + -
196C VAL* 4.1 24.7 - - + +
199C GLN* 3.4 32.1 - - + +
60D VAL* 3.9 23.3 - - + -
63D ILE* 5.0 11.2 - - + -
83D PHE* 3.2 18.1 + - + +
84D THR* 3.1 22.2 + - + +
86D SER* 1.3 76.7 - - - +
88D ASN* 1.3 60.7 + - - +
90D LYS* 3.7 4.3 + - - +
91D LEU* 3.3 27.9 + - - +
213D LEU* 5.7 0.2 - - + -
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Residues in contact with ASN 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 3.4 33.8 + - - +
60D VAL* 3.4 30.9 - - - +
61D VAL* 5.5 0.5 + - - +
64D CYS* 5.0 5.5 - - - -
84D THR 3.1 21.9 + - - -
85D VAL* 3.2 9.7 + - - +
87D LEU* 1.3 74.2 - - - +
89D HIS* 1.4 57.4 + - - +
91D LEU* 3.3 5.5 + - - +
92D ASP* 2.8 38.9 + - - +
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Residues in contact with HIS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D VAL* 3.0 44.3 + - + +
86D SER* 3.4 10.5 - - - +
88D ASN* 1.4 74.6 - - - +
90D LYS* 1.4 68.5 + - + +
92D ASP* 3.4 9.4 + - - +
93D SER* 3.0 29.2 + - - -
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Residues in contact with LYS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLN* 4.5 24.5 - - - +
203C PHE* 5.1 8.3 - - + -
86D SER* 3.1 26.4 + - - +
87D LEU 4.0 5.2 - - - +
88D ASN 3.4 0.2 - - - -
89D HIS* 1.4 88.1 - - - +
91D LEU* 1.4 62.8 + - - +
93D SER* 3.3 10.8 + - - -
94D HIS* 3.0 25.7 + - - +
202D HIS* 4.7 6.1 - - + -
205D GLN 5.4 0.2 + - - -
206D GLY* 4.3 16.6 - - - -
209D GLU* 2.8 31.7 + - - +
210D LEU* 4.0 29.6 - - + -
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.7 33.3 - - + +
56D SER* 3.5 24.7 - - - +
57D ARG* 3.6 57.6 + - + +
60D VAL* 4.7 4.5 - - + -
87D LEU 3.3 17.7 + - - +
88D ASN* 3.3 13.6 + - - +
90D LYS* 1.4 75.3 - - + +
92D ASP* 1.3 57.6 + - - +
94D HIS* 3.5 1.1 + - + -
95D ALA* 2.9 27.7 + - - +
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 2.7 33.5 + - - -
88D ASN* 2.8 19.8 + - - +
89D HIS* 3.4 12.6 + - - +
91D LEU* 1.3 74.9 - - - +
93D SER* 1.4 57.4 + - - +
95D ALA* 3.4 10.0 - - - +
96D GLU* 3.2 28.3 + - - +
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D HIS 3.0 17.5 + - - -
90D LYS* 3.3 13.5 + - - +
92D ASP* 1.4 74.0 - - - +
94D HIS* 1.3 57.6 + - - +
96D GLU* 3.0 29.7 + - - +
97D LEU 3.1 10.0 + - - -
202D HIS* 3.4 22.3 + - - -
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Residues in contact with HIS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C TYR* 3.0 36.3 + + - -
52D TYR* 5.6 3.0 - + - -
53D LEU* 3.8 26.2 - - + -
90D LYS 3.0 18.0 + - - +
91D LEU 3.9 4.0 - - - +
93D SER* 1.3 74.5 - - - +
95D ALA* 1.4 62.2 + - - +
97D LEU* 3.1 26.9 + - + +
98D LEU* 3.0 25.1 + - + +
202D HIS* 3.0 30.3 + + + +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ARG* 3.7 20.8 + - - +
53D LEU* 3.6 13.5 - - + +
57D ARG* 5.3 3.4 - - - +
91D LEU 2.9 18.9 + - - +
92D ASP* 3.4 14.4 - - - +
94D HIS* 1.4 73.0 - - - +
96D GLU* 1.4 56.9 + - + +
98D LEU* 3.2 4.4 + - - +
99D ASP* 2.9 34.7 + - - +
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ASP 3.2 12.9 + - - +
93D SER* 3.0 21.9 + - - +
95D ALA* 1.4 73.6 - - - +
97D LEU* 1.4 56.9 + - - +
99D ASP* 3.3 8.9 + - - +
100D ALA* 2.8 30.1 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D SER 3.1 9.5 + - - +
94D HIS* 3.1 39.7 + - + +
96D GLU* 1.4 75.0 - - - +
98D LEU* 1.4 60.6 + - + +
100D ALA* 3.3 7.0 + - + +
101D THR* 2.8 37.1 + - - +
195D LEU 5.7 0.2 - - - +
198D ALA* 3.6 37.5 - - + +
199D GLN* 4.2 14.1 - - + +
202D HIS* 4.0 21.5 - - + +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C TYR* 3.6 24.0 - - + +
45D LEU* 4.9 2.9 - - + +
46D LEU* 3.3 41.0 - - + +
49D GLY* 3.6 31.4 - - - -
50D ARG* 3.7 22.9 - - + +
53D LEU* 3.8 19.5 - - + -
94D HIS* 3.0 17.3 + - + +
95D ALA 3.7 6.7 - - - +
97D LEU* 1.4 74.1 - - + +
99D ASP* 1.3 65.0 + - - +
101D THR* 4.4 3.8 - - + +
102D GLN* 3.2 21.5 + - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ARG* 2.6 28.4 + - - +
95D ALA* 2.9 18.8 + - - +
96D GLU* 3.6 11.6 - - - +
98D LEU* 1.3 75.2 - - - +
100D ALA* 1.3 61.7 + - - +
102D GLN* 3.3 18.3 + - - +
103D HIS* 3.1 20.6 + - - +
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLU 2.8 20.4 + - - +
97D LEU* 3.9 11.2 - - + +
98D LEU 3.3 0.2 - - - -
99D ASP* 1.3 73.2 - - - +
101D THR* 1.4 60.9 + - - +
103D HIS* 3.2 9.1 + - - +
104D THR* 3.0 28.3 + - - +
198D ALA* 5.4 9.6 - - + -
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 5.8 6.1 - - + -
42D GLY* 5.3 3.1 - - - +
45D LEU* 5.5 10.5 - - + -
46D LEU* 3.7 23.1 - - + -
97D LEU* 2.8 31.1 + - - +
98D LEU* 4.4 4.6 - - + +
100D ALA* 1.4 69.4 - - - +
102D GLN* 1.3 55.5 + - - +
104D THR* 3.4 2.1 + - - -
105D LEU* 2.9 33.7 + - + +
191D PHE* 5.5 1.1 - - + -
195D LEU* 3.6 30.2 - - + +
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Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.8 26.0 - - + +
50D ARG* 4.8 5.0 + - - -
98D LEU 3.2 13.3 + - - +
99D ASP* 3.3 26.9 + - - +
101D THR* 1.3 74.1 - - - +
103D HIS* 1.4 53.4 + - - +
105D LEU* 3.6 4.0 - - + +
106D GLN* 2.7 55.7 + - + +
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Residues in contact with HIS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASP 3.1 9.8 + - - +
100D ALA* 3.2 12.3 + - - +
102D GLN* 1.4 77.5 - - - +
104D THR* 1.3 57.3 + - - +
106D GLN* 3.6 7.8 - - + +
107D GLN* 2.7 63.5 + - + +
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Residues in contact with THR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA 3.0 16.3 + - - -
101D THR 3.5 6.1 - - - -
103D HIS* 1.3 81.2 + - - +
105D LEU* 1.3 54.2 + - - +
107D GLN* 3.7 9.7 - - - +
108D GLN* 3.2 30.9 + - + +
191D PHE* 3.6 26.2 - - + -
194D ARG* 3.6 34.2 - - + +
195D LEU* 3.9 18.3 - - + +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 5.3 3.6 - - + -
38D LEU 4.5 2.7 - - - +
39D LEU* 4.2 19.7 - - + +
42D GLY* 3.5 41.3 - - - +
43D THR* 3.7 12.1 - - - +
46D LEU* 4.0 14.6 - - + -
101D THR* 2.9 23.2 + - + +
102D GLN* 3.6 3.8 - - + +
104D THR* 1.3 72.3 - - - +
106D GLN* 1.4 60.5 + - - +
109D ILE* 3.0 49.5 + - + +
110D GLN* 3.1 12.1 + - - +
191D PHE* 3.9 17.9 - - + -
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLN* 2.7 41.1 + - + +
103D HIS* 3.7 7.4 - - + +
105D LEU* 1.4 69.6 - - - +
107D GLN* 1.3 62.8 + - - +
110D GLN* 3.7 38.1 + - - +
111D THR* 3.2 20.4 + - - -
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Residues in contact with GLN 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D HIS* 2.7 48.4 + - + +
104D THR* 3.7 8.9 - - - +
106D GLN* 1.3 73.0 - - - +
108D GLN* 1.3 87.2 + - - +
111D THR* 2.9 23.5 + - - +
190D GLU* 4.8 5.9 - - - +
194D ARG* 5.1 11.8 + - - +
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D THR* 3.2 17.1 + - + +
107D GLN* 1.3 111.1 - - - +
109D ILE* 1.3 66.0 + - + +
110D GLN 3.5 0.4 - - - -
111D THR* 3.9 0.7 - - - -
112D LEU* 2.8 35.5 + - + +
187D ASP* 3.5 46.4 + - + +
190D GLU* 2.7 32.6 + - + +
191D PHE* 4.1 22.7 - - + +
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.6 50.0 - - + +
38D LEU* 4.1 9.9 - - + -
39D LEU* 3.9 17.3 - - + +
105D LEU* 3.0 19.3 + - + +
108D GLN* 1.3 83.6 - - + +
110D GLN* 1.3 56.9 + - - +
112D LEU* 3.9 5.0 - - + +
113D VAL* 3.0 28.3 + - + +
187D ASP 5.6 0.4 - - - +
188D ILE* 4.4 8.1 - - + -
191D PHE* 3.4 51.1 - - + -
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Residues in contact with GLN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.7 28.0 - - + +
105D LEU* 3.1 11.1 + - - +
106D GLN* 3.7 52.1 + - - +
109D ILE* 1.3 73.8 - - - +
111D THR* 1.3 59.7 - - - +
113D VAL* 3.5 1.7 + - - +
114D LYS* 2.9 38.1 + - + +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLN 3.2 9.3 + - - -
107D GLN* 2.9 26.7 + - - +
108D GLN 3.6 1.3 + - - -
109D ILE 3.5 0.4 - - - -
110D GLN* 1.3 76.2 - - - +
112D LEU* 1.3 60.3 + - - +
114D LYS* 4.6 1.3 - - - -
115D GLU* 2.9 60.5 + - + +
116D GLY* 3.2 5.7 + - - +
183D LYS* 5.6 6.5 - - - +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 5.7 3.8 - - + -
35D LEU* 4.3 34.8 - - + -
108D GLN* 2.8 21.0 + - + +
109D ILE* 3.9 5.6 - - + +
110D GLN 3.3 0.2 - - - -
111D THR* 1.3 78.9 - - - +
113D VAL* 1.3 63.2 + - - +
116D GLY* 3.0 33.1 + - - +
117D LEU* 3.9 16.5 + - + +
180D ILE* 6.3 1.8 - - + -
183D LYS* 3.8 29.6 - - + +
184D ARG* 5.8 3.8 - - - +
187D ASP* 3.7 38.8 - - + +
188D ILE* 5.1 7.6 - - + -
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLU* 4.7 19.0 - - + +
35D LEU* 3.7 31.4 - - + -
36D GLU* 3.5 46.0 - - + +
39D LEU* 3.9 13.7 - - + -
109D ILE 3.0 18.4 + - - +
110D GLN 3.9 2.9 - - - +
112D LEU* 1.3 77.4 - - - +
114D LYS* 1.4 61.4 + - + +
116D GLY 5.0 0.2 + - - -
117D LEU* 5.1 8.7 - - - +
121D ARG* 5.8 0.5 + - - -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D GLN* 2.9 28.5 + - + +
111D THR* 4.2 2.0 - - - +
113D VAL* 1.4 76.6 - - + +
115D GLU* 1.3 80.4 + - + +
118D ARG* 4.9 15.3 + - - +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D THR* 2.9 37.6 + - + +
114D LYS* 1.3 95.9 + - + +
116D GLY* 1.4 62.7 + - - +
117D LEU 3.6 2.2 - - - -
118D ARG* 3.7 37.6 + - - +
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Residues in contact with GLY 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D THR* 3.2 6.8 + - - -
112D LEU* 3.0 18.7 + - - +
115D GLU* 1.4 78.2 - - - +
117D LEU* 1.3 64.9 + - - +
118D ARG 3.5 2.4 + - - -
119D GLY 5.4 0.8 + - - -
120D PHE* 5.7 0.5 - - - +
180D ILE* 5.0 5.4 - - - +
183D LYS* 3.7 35.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il