Contacts of the helix formed by residues 77 - 102 (chain D) in PDB entry 3H90
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 LYS 77 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 3.2 21.8 - - - +
205B LEU 3.5 21.0 + - - +
206B LEU* 3.9 17.5 - - + -
207B ASP* 3.5 13.7 + - - +
74D GLY 5.2 0.9 - - - -
75D HIS 3.2 0.8 - - - -
76D GLY* 1.3 72.2 - - - +
78D ALA* 1.3 62.1 + - - +
79D GLU 2.9 7.1 + - - -
80D SER* 3.0 21.4 + - - +
81D LEU* 3.1 11.8 + - - +
204D SER* 3.3 24.5 - - - +
205D LEU* 3.7 15.7 + - + +
207D ASP* 2.8 25.5 + - - -
237D ARG* 5.3 0.2 - - - +
238D GLN 4.5 4.0 - - - +
239D SER* 3.7 30.4 + - - +
240D GLY 4.8 0.2 - - - +
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 3.6 17.6 - - + +
59D VAL* 3.5 18.9 - - + +
62D TYR* 4.0 23.1 - - + -
63D SER* 4.3 7.2 - - - -
75D HIS 3.1 16.6 + - - +
77D LYS* 1.3 76.4 - - - +
79D GLU* 1.3 56.5 + - - +
81D LEU* 3.6 6.3 - - - +
82D ALA* 3.0 28.8 + - - +
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ARG* 2.5 30.6 + - - -
14D ILE* 4.7 3.1 - - - -
59D VAL* 5.4 0.7 - - - -
60D VAL* 5.1 3.6 - - + -
63D SER* 3.3 27.0 + - - +
76D GLY 3.0 10.9 + - - +
77D LYS 2.9 2.4 + - - -
78D ALA* 1.3 77.6 - - - +
80D SER* 1.3 53.7 + - - +
82D ALA* 3.0 6.1 + - - +
83D ALA* 2.7 36.2 + - - +
144D SER* 2.9 37.1 + - - -
145D GLN* 3.7 6.4 + - + +
146D ALA* 3.6 23.4 - - + +
240D GLY* 4.6 7.6 - - - -
241D PRO* 3.7 10.4 - - - +
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLY 4.8 0.9 + - - -
77D LYS* 3.0 15.6 + - - +
79D GLU* 1.3 78.0 - - - +
81D LEU* 1.3 57.0 + - - +
83D ALA* 3.5 4.4 - - - +
84D LEU* 2.8 30.7 + - - +
145D GLN* 2.9 26.5 + - - -
201D ALA* 3.6 21.3 - - - +
204D SER* 3.7 11.7 - - - -
205D LEU* 4.1 12.9 - - - +
240D GLY* 4.9 6.8 + - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.5 9.4 - - + -
202B VAL* 3.9 27.4 - - + -
205B LEU* 3.9 22.7 - - + -
206B LEU* 3.4 31.0 - - + -
77D LYS 3.1 12.0 + - - +
78D ALA* 3.6 7.4 - - - +
80D SER* 1.3 75.4 - - - +
82D ALA* 1.3 59.5 + - - +
84D LEU* 3.2 8.8 + - + +
85D ALA* 2.9 28.1 + - - +
205D LEU* 3.5 29.4 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASN* 4.4 16.4 - - - +
59D VAL* 3.8 22.0 - - + +
78D ALA 3.0 15.3 + - - +
79D GLU* 3.4 9.0 - - - +
81D LEU* 1.3 71.2 - - - +
83D ALA* 1.3 61.5 + - - +
85D ALA* 3.2 8.7 + - - +
86D GLN* 2.8 40.3 + - + +
146D ALA* 5.1 4.0 - - + -
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLU 2.7 18.8 + - - +
80D SER* 3.5 7.9 - - - +
82D ALA* 1.3 74.1 - - - +
84D LEU* 1.3 56.6 + - - +
86D GLN* 3.4 2.4 + - - +
87D SER* 2.9 29.6 + - - -
145D GLN* 3.8 34.5 - - + +
146D ALA* 4.9 1.7 - - - +
149D ALA* 3.8 16.9 - - + +
197D MET* 4.1 8.7 - - + +
201D ALA* 4.4 7.9 - - + -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.3 10.8 - - + -
84B LEU* 5.6 5.4 - - + -
80D SER 2.8 17.6 + - - +
81D LEU* 3.4 9.9 - - + +
82D ALA 3.2 0.2 - - - -
83D ALA* 1.3 73.9 - - - +
85D ALA* 1.3 65.4 + - - +
87D SER* 3.1 15.4 + - - +
88D MET* 3.2 39.3 + - + +
198D GLY* 3.4 29.8 - - - +
201D ALA* 3.9 6.0 - - + +
202D VAL* 3.6 17.0 - - + -
205D LEU* 3.5 25.1 - - + -
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 6.1 5.2 - - + -
81D LEU 2.9 12.8 + - - +
82D ALA* 3.5 10.5 - - - +
84D LEU* 1.3 76.2 - - - +
86D GLN* 1.3 63.8 + - + +
88D MET* 3.5 13.3 + - - +
89D PHE* 3.5 26.8 - - + -
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ALA 6.1 0.4 - - - -
56D ASN* 3.0 43.4 + - - +
82D ALA* 2.8 25.1 + - + +
83D ALA 3.5 4.7 - - - +
85D ALA* 1.3 73.4 - - + +
87D SER* 1.3 66.9 + - - +
88D MET 3.1 0.5 + - - -
89D PHE* 3.2 6.8 + - - +
90D ILE* 3.0 36.8 + - + +
146D ALA 3.6 9.3 + - - -
149D ALA* 3.6 11.3 - - + +
150D ASP* 3.3 30.3 + - - +
153D HIS* 5.3 1.7 - - - +
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Residues in contact with SER 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ALA 2.9 18.2 + - - -
84D LEU* 3.1 8.5 + - - +
86D GLN* 1.3 77.8 - - - +
88D MET* 1.3 57.2 + - - +
90D ILE* 4.6 6.5 - - - -
91D SER* 2.9 31.6 + - - -
152D LEU* 6.1 0.2 - - - -
194D ALA* 2.6 29.9 + - - +
195D LEU* 4.8 1.2 - - - +
197D MET* 4.2 9.0 - - - -
198D GLY* 3.1 26.9 - - - -
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Residues in contact with MET 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 6.1 4.9 - - + -
88B MET* 4.1 35.7 - - + +
89B PHE* 6.6 0.2 - - - -
84D LEU* 3.2 40.4 + - + +
85D ALA* 3.8 10.5 - - - +
86D GLN 3.1 0.6 - - - -
87D SER* 1.3 75.9 - - - +
89D PHE* 1.3 65.1 + - + +
91D SER* 3.0 6.9 + - - -
92D GLY* 2.6 34.1 + - - -
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 6.5 1.1 - - - -
85D ALA* 3.5 17.3 - - + +
86D GLN* 3.2 9.1 + - - +
88D MET* 1.3 81.5 - - + +
90D ILE* 1.3 53.9 + - + +
92D GLY* 3.0 2.6 + - - +
93D SER* 2.8 40.7 + - - +
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Residues in contact with ILE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN* 3.0 34.3 + - + +
87D SER* 4.0 5.6 - - - +
89D PHE* 1.3 76.9 - - + +
91D SER* 1.3 60.9 + - - +
93D SER* 3.3 8.4 + - - -
94D ALA* 3.1 23.2 + - - +
149D ALA* 3.4 26.2 - - - +
152D LEU* 4.0 17.9 - - + -
153D HIS* 3.8 33.4 - - + +
156D SER* 5.8 1.1 - - - -
190D ILE* 4.0 16.3 - - + +
194D ALA* 3.8 17.3 - - + -
197D MET* 6.3 0.4 - - + -
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Residues in contact with SER 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D SER* 2.9 21.3 + - - -
88D MET* 3.0 7.8 + - - -
90D ILE* 1.3 76.3 - - - +
92D GLY* 1.3 58.0 + - - +
94D ALA* 3.4 1.1 + - - -
95D LEU* 3.2 24.3 + - - +
191D LEU* 3.3 32.5 - - - +
194D ALA* 3.7 13.6 - - - +
195D LEU* 3.5 25.1 - - - +
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Residues in contact with GLY 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D MET 2.6 18.9 + - - -
89D PHE* 3.0 4.5 + - - -
91D SER* 1.3 71.7 - - - +
93D SER* 1.3 62.2 + - - +
95D LEU* 3.8 7.4 + - - +
96D PHE* 3.2 22.7 + - - +
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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 PHE* 2.8 23.1 + - - +
90D ILE* 3.6 9.7 - - - -
91D SER 3.3 0.2 - - - -
92D GLY* 1.3 73.6 - - - +
94D ALA* 1.3 59.0 + - - +
96D PHE* 3.4 12.0 - - - +
97D LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ILE 3.1 16.3 + - - +
91D SER 3.8 1.3 - - - +
92D GLY 3.3 0.2 - - - -
93D SER* 1.3 76.2 - - - +
95D LEU* 1.3 60.4 + - - +
97D LEU* 3.3 6.2 + - - +
98D PHE* 2.9 23.0 + - - +
187D GLY* 3.4 17.5 - - - +
190D ILE* 3.8 13.2 - - + -
191D LEU* 3.4 37.7 - - + +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D SER 3.2 15.6 + - - +
92D GLY* 4.2 7.2 - - - +
93D SER 3.4 0.2 - - - -
94D ALA* 1.3 72.3 - - - +
96D PHE* 1.3 63.4 + - + +
97D LEU 3.1 0.2 - - - -
98D PHE* 4.4 5.4 - - - +
99D LEU* 3.0 54.3 + - + +
191D LEU* 4.5 20.1 - - + +
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Residues in contact with PHE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLY 3.2 17.8 + - - +
93D SER* 3.4 11.2 - - - +
95D LEU* 1.3 84.6 - - + +
97D LEU* 1.3 63.3 + - + +
99D LEU* 4.0 3.2 - - - +
100D THR* 2.6 44.2 + - + -
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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
----------------------------------------------------------
93D SER 3.0 16.3 + - - +
94D ALA* 3.8 7.6 - - - +
95D LEU 3.1 0.4 - - - -
96D PHE* 1.3 89.0 - - + +
98D PHE* 1.3 59.5 + - - +
99D LEU 3.4 0.2 - - - -
100D THR* 3.5 9.0 + - - -
101D GLY* 2.9 18.9 + - - -
156D SER* 5.8 2.7 - - - +
183D ALA* 3.1 39.3 - - + +
186D ILE* 4.0 28.5 - - + -
187D GLY* 4.2 3.8 - - - +
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ALA 2.9 16.8 + - - +
95D LEU* 4.1 4.9 - - - +
97D LEU* 1.3 76.0 - - - +
99D LEU* 1.3 77.4 + - + +
100D THR 3.2 1.6 - - - -
101D GLY* 3.0 13.3 + - - +
102D ILE* 3.1 35.3 + - + +
183D ALA 4.5 1.3 - - - -
184D LEU* 3.7 31.2 - - + -
187D GLY* 3.9 14.3 - - - +
188D ILE* 3.6 34.5 - - + -
191D LEU* 5.7 7.6 - - + -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 3.0 47.6 + - + +
96D PHE* 4.0 2.9 - - - +
98D PHE* 1.3 93.3 - - + +
100D THR* 1.3 59.4 + - - +
102D ILE* 3.7 25.1 - - + +
103D GLN* 3.2 23.2 + - - +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 2.6 38.5 + - + -
97D LEU* 3.5 11.1 + - + -
98D PHE 3.2 0.4 - - - -
99D LEU* 1.3 76.9 - - - +
101D GLY* 1.3 63.0 + - - +
102D ILE 3.5 0.4 - - - -
103D GLN* 3.5 19.2 + - - +
104D HIS* 3.3 48.5 + - + +
183D ALA* 5.5 2.0 - - + -
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU 2.9 15.0 + - - -
98D PHE 3.0 7.2 + - - -
100D THR* 1.3 79.9 - - - +
102D ILE* 1.3 57.5 + - - +
104D HIS 4.0 0.5 - - - -
105D LEU* 3.7 6.9 + - - +
180D ALA* 3.7 25.9 - - - +
183D ALA* 4.3 6.1 - - - -
184D LEU* 3.8 28.7 - - - +
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.1 32.3 + - + +
99D LEU* 3.7 27.4 - - + -
101D GLY* 1.3 72.5 - - - +
103D GLN* 1.3 66.3 + - - +
104D HIS 3.6 0.2 - - - -
105D LEU* 3.4 28.0 - - + +
107D SER* 4.0 3.5 + - - -
184D LEU* 3.5 21.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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