Contacts of the helix formed by residues 72 - 93 (chain D) in PDB entry 2B5F
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 VAL 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.7 14.6 - - + -
75B LEU* 4.1 26.6 - - + +
78B ALA* 6.1 0.2 - - + -
211B LEU* 4.0 37.2 - - + +
214B ILE* 6.1 3.6 - - + -
215B PRO* 6.2 3.4 - - + -
58D THR* 4.5 13.0 - - + +
62D HIS* 5.2 3.4 - - + +
71D SER* 1.3 76.4 - - - +
73D GLY* 1.3 77.2 + - - +
75D LEU* 4.7 1.9 + - - +
76D GLY* 3.3 30.8 + - - -
77D ILE* 3.9 4.7 - - + +
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Residues in contact with GLY 73 (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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69C CYS 5.7 3.4 - - - -
70C GLY 5.5 0.9 - - - -
62D HIS* 3.7 20.1 + - - -
71D SER* 3.1 10.9 + - - -
72D VAL* 1.3 86.9 - - - +
74D LEU* 1.3 58.4 + - - -
75D LEU* 3.1 3.4 - - - -
76D GLY 2.6 24.9 + - - -
77D ILE* 3.1 2.4 + - - +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 5.7 3.8 - - - +
70C GLY* 3.0 32.9 + - - +
71C SER* 4.0 16.9 + - - +
72C VAL* 4.5 7.4 - - + +
62D HIS* 3.5 25.8 - - + +
73D GLY* 1.3 70.2 - - - -
75D LEU* 1.3 63.1 + - - +
77D ILE* 3.0 16.9 + - + +
78D ALA* 2.8 24.8 + - - +
214D ILE* 3.2 39.4 - - + +
215D PRO* 5.4 4.9 - - + -
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.6 22.0 - - + -
71C SER 4.8 0.2 + - - -
72C VAL* 3.5 28.8 + - - +
75C LEU* 3.5 39.5 - - + -
76C GLY* 4.1 11.2 - - - +
79C TRP* 4.5 5.8 - - + +
72D VAL 4.7 3.6 - - - +
73D GLY 3.0 1.0 + - - +
74D LEU* 1.3 78.4 - - - +
76D GLY* 1.3 62.3 + - - +
78D ALA* 3.3 2.1 + - - +
79D TRP* 3.1 26.6 + - + +
207D PHE* 3.9 17.3 - - + -
211D LEU* 3.9 22.9 - - + -
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.5 12.5 - - - +
211B LEU* 3.9 7.0 - - - +
58D THR* 4.4 1.2 - - - +
72D VAL* 3.3 27.0 + - - -
73D GLY 2.6 15.6 + - - -
75D LEU* 1.3 74.9 - - - +
77D ILE* 1.3 59.8 + - - -
79D TRP* 3.3 9.0 + - - +
80D ALA* 3.0 21.5 + - - +
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D THR* 3.9 24.5 - - + +
59D VAL* 3.6 33.4 - - + -
62D HIS* 3.8 35.2 - - + +
72D VAL* 3.9 1.8 - - + +
73D GLY 3.1 6.5 + - - +
74D LEU* 3.0 22.2 + - + +
76D GLY* 1.3 77.1 - - - +
78D ALA* 1.3 63.1 + - - +
80D ALA* 3.1 11.1 + - - +
81D PHE* 3.2 32.5 + - + -
214D ILE* 4.2 14.8 - - + -
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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
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74D LEU 2.8 15.8 + - - +
75D LEU 3.5 8.5 - - - +
77D ILE* 1.3 72.7 - - - +
79D TRP* 1.3 56.6 + - - +
81D PHE* 3.4 3.8 + - - +
82D GLY* 3.1 22.9 + - - -
207D PHE* 3.6 26.8 - - + -
210D HIS* 3.8 26.2 - - + +
211D LEU* 3.8 19.1 - - + -
214D ILE* 4.2 6.0 - - + +
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Residues in contact with TRP 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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75B LEU* 4.6 8.9 - - + +
79B TRP* 3.9 24.7 - + - +
204B PHE* 3.8 30.7 - + - -
207B PHE* 4.2 14.1 - + + -
208B MET* 3.4 6.6 - - + +
211B LEU* 4.1 12.3 - - + -
79C TRP* 3.7 30.8 - + - +
75D LEU* 3.1 32.5 + - + +
76D GLY* 3.5 9.2 - - - +
77D ILE 3.2 0.2 - - - -
78D ALA* 1.3 74.5 - - - +
80D ALA* 1.3 60.0 + - - +
82D GLY 4.5 0.9 - - - +
83D GLY* 2.8 35.8 + - - -
203D GLY 6.4 0.4 - - - -
204D PHE* 3.9 24.9 - + - -
207D PHE* 3.3 45.6 - + + -
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Residues in contact with ALA 80 (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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208B MET* 3.9 10.3 - - - -
211B LEU* 4.2 5.6 - - + +
54D ILE* 4.8 5.8 - - + -
55D THR* 3.6 21.2 - - + +
58D THR* 4.0 23.8 - - + +
76D GLY 3.0 13.1 + - - +
77D ILE* 3.1 9.6 + - - +
79D TRP* 1.3 75.0 - - - +
81D PHE* 1.3 63.5 - - + +
84D MET* 3.1 31.4 + - - +
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Residues in contact with PHE 81 (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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51D PHE* 3.8 17.4 - + - -
52D LEU* 5.7 0.2 - - + -
55D THR* 3.4 36.8 - - + -
56D VAL* 4.9 2.5 - - + -
59D VAL* 3.8 11.2 - - + -
77D ILE* 3.2 42.0 + - + -
78D ALA 3.8 4.5 - - - +
79D TRP 3.2 0.4 - - - -
80D ALA* 1.3 78.2 - - + +
82D GLY* 1.3 62.5 + - - +
85D ILE* 3.3 28.6 + - - +
206D VAL* 3.8 4.5 - - + -
210D HIS* 3.1 43.3 - + + +
218D GLY 5.5 2.7 - - - -
225D ARG* 3.6 47.8 - - + -
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Residues in contact with GLY 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 ALA 3.1 13.8 + - - -
79D TRP* 4.0 1.3 - - - -
81D PHE* 1.3 75.7 - - - +
83D GLY* 1.3 55.9 + - - +
85D ILE* 3.3 2.3 + - - +
86D PHE 3.1 22.9 + - - -
203D GLY* 3.1 34.3 - - - -
206D VAL* 3.8 5.9 - - - +
207D PHE* 3.7 15.9 - - - -
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Residues in contact with GLY 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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204B PHE* 4.3 19.1 - - - -
208B MET* 3.7 14.6 - - - -
79D TRP* 2.8 26.5 + - - +
82D GLY* 1.3 70.0 - - - -
84D MET* 1.3 58.1 + - - +
86D PHE* 3.5 6.3 + - - +
87D VAL* 3.0 32.6 + - - +
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Residues in contact with MET 84 (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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174B VAL* 4.7 14.1 - - + -
208B MET* 3.8 19.3 - - - -
50D LEU* 3.2 29.6 - - + +
51D PHE* 4.0 17.3 - - + +
54D ILE* 3.5 38.8 - - + -
55D THR* 4.8 2.2 - - + -
80D ALA 3.1 25.4 + - - +
81D PHE 4.1 0.2 - - - +
83D GLY* 1.3 73.1 - - - +
85D ILE* 1.3 61.0 + - - +
87D VAL* 4.4 7.9 - - + -
88D LEU* 2.9 63.1 + - + +
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Residues in contact with ILE 85 (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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51D PHE* 3.2 40.8 - - + -
81D PHE 3.3 10.4 + - - +
82D GLY 3.7 6.7 - - - +
84D MET* 1.3 76.8 - - - +
86D PHE* 1.3 57.1 + - - +
88D LEU* 4.6 0.9 - - + -
89D VAL* 2.9 46.1 + - + +
99D HIS 5.4 1.1 - - - +
100D ILE* 4.1 28.7 - - + +
101D ASN* 6.1 0.9 - - + -
202D ILE* 3.1 36.6 - - + -
206D VAL* 4.0 16.4 - - + -
222D ASN* 5.2 2.2 - - - +
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Residues in contact with PHE 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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200B LEU* 3.7 26.5 - - + -
201B PRO* 3.5 29.8 - - + -
204B PHE* 4.0 29.8 - + + -
82D GLY 3.1 7.3 + - - +
83D GLY* 3.5 8.7 - - - +
85D ILE* 1.3 76.0 - - - +
87D VAL* 1.3 65.7 + - + +
89D VAL* 5.0 0.2 - - - -
90D TYR* 3.0 28.9 + + + +
199D PRO* 3.2 43.1 - - + +
200D LEU* 3.4 35.0 - - + -
203D GLY* 3.5 23.5 - - - +
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Residues in contact with VAL 87 (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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174B VAL* 5.2 8.3 - - + -
177B TYR* 6.4 0.4 - - + -
178B THR* 3.7 31.0 - - + +
201B PRO* 4.1 9.9 - - - +
204B PHE* 4.1 25.6 - - + -
205B ALA* 4.2 9.9 - - + +
208B MET* 4.6 5.6 - - + -
83D GLY 3.0 19.2 + - - +
84D MET* 3.8 9.9 - - - +
85D ILE 3.4 0.2 - - - -
86D PHE* 1.3 78.2 - - + +
88D LEU* 1.3 66.5 + - + +
90D TYR* 3.3 8.9 + - - +
91D CYS* 2.9 32.0 + - - -
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Residues in contact with LEU 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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174B VAL* 6.5 0.2 - - + -
177B TYR* 4.8 17.9 - - + -
46D ILE 5.4 0.2 - - - +
47D ALA* 3.4 37.0 - - + +
50D LEU* 4.8 7.6 - - + -
51D PHE* 3.5 26.7 - - + +
84D MET* 2.9 44.9 + - + +
85D ILE* 4.2 2.7 - - - +
87D VAL* 1.3 80.3 - - + +
89D VAL* 1.3 66.2 + - - +
91D CYS* 3.2 3.5 + - + +
92D THR* 2.9 29.8 + - + +
100D ILE* 4.0 18.4 - - + -
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Residues in contact with VAL 89 (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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85D ILE* 2.9 41.0 + - + +
86D PHE* 4.3 1.6 - - - +
88D LEU* 1.3 72.1 - - - +
90D TYR* 1.3 55.5 + - - +
92D THR* 3.8 6.1 - - - -
93D ALA* 2.7 36.2 + - - +
97D GLY 4.4 2.9 - - - +
98D GLY 3.4 25.6 - - - +
99D HIS 5.2 0.9 - - - +
100D ILE* 4.3 9.4 - - + -
197D LEU* 3.9 33.2 - - + +
198D ALA 4.1 10.8 - - - +
199D PRO* 4.6 5.6 - - + -
202D ILE* 4.6 11.9 - - + -
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Residues in contact with TYR 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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178B THR* 4.9 3.1 - - + -
181B SER* 3.3 35.0 + - - -
182B ALA* 3.9 8.5 - - - +
184B ASP* 3.8 14.6 + - - -
198B ALA 4.7 8.1 + - - -
201B PRO* 4.0 35.3 - - + +
86D PHE* 3.0 23.0 + + + +
87D VAL* 3.3 6.7 - - - +
88D LEU 3.2 0.2 - - - -
89D VAL* 1.3 78.2 - - - +
91D CYS* 1.3 71.6 + - - +
93D ALA* 3.5 15.4 - - + +
199D PRO* 4.2 24.0 - - + +
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Residues in contact with CYS 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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177B TYR* 3.5 38.8 + - + +
178B THR* 4.1 19.1 - - - -
181B SER* 3.8 30.2 + - - +
87D VAL* 2.9 30.3 + - - +
88D LEU* 3.2 7.3 + - - +
90D TYR* 1.3 83.9 - - - +
92D THR* 1.3 60.6 + - + +
95D ILE* 4.7 6.4 - - - +
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Residues in contact with THR 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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177B TYR* 4.2 11.7 - - + +
43D ALA* 4.1 28.5 - - + +
44D GLU* 4.9 0.9 - - - +
47D ALA* 4.3 12.8 - - + -
88D LEU* 2.9 16.8 + - + +
89D VAL* 3.7 0.5 + - - -
91D CYS* 1.3 79.8 - - + +
93D ALA* 1.3 51.9 + - - +
94D GLY 2.5 4.3 + - - -
95D ILE* 2.5 43.8 + - + +
96D SER* 3.4 18.8 + - - +
97D GLY 4.3 1.1 - - - -
98D GLY* 2.8 26.4 - - - -
100D ILE* 4.2 3.2 - - + +
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Residues in contact with ALA 93 (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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89D VAL 2.7 24.9 + - - +
90D TYR* 3.5 15.7 - - + +
92D THR* 1.3 69.2 + - - +
94D GLY* 1.3 57.5 + - - +
95D ILE 3.5 0.4 - - - -
97D GLY* 3.2 31.7 - - - +
195D PRO 5.1 0.2 - - - -
196D ILE* 3.1 25.4 - - + +
197D LEU 4.3 15.5 - - - +
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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
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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