Contacts of the helix formed by residues 72 - 93 (chain B) in PDB entry 7A62
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 ASP 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLN* 3.8 7.7 - - - +
70B LEU 3.6 1.0 + - - -
71B THR* 1.3 89.8 - - - +
73B HIS* 1.3 66.8 + - - +
74B LYS* 3.4 7.3 + - - +
75B SER* 2.8 43.3 + - - -
76B GLN* 2.9 27.5 + - - +
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Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 4.3 29.0 + + - -
25B LEU* 4.3 14.6 - - + +
72B ASP* 1.3 74.5 - - - +
74B LYS* 1.3 62.8 + - + +
76B GLN* 3.0 15.0 + - - +
77B ARG* 2.8 69.6 + - + +
118B LEU* 4.1 19.5 - - + +
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.3 25.9 - - + +
26B PRO* 2.5 37.7 + - - +
27B ASN* 2.9 26.0 + - - +
29B GLN* 4.1 25.0 + - + +
72B ASP* 3.3 7.4 + - - +
73B HIS* 1.3 81.8 - - + +
75B SER* 1.3 63.0 + - - +
77B ARG* 3.3 6.9 + - - +
78B LEU* 3.0 24.3 + - - +
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 3.1 27.3 + - - +
32B LEU* 3.6 9.6 - - - +
33B PRO* 5.1 4.8 - - - +
70B LEU* 4.0 12.5 - - - +
71B THR* 4.1 14.3 + - - +
72B ASP* 2.8 38.7 + - - -
74B LYS* 1.3 77.8 - - - +
76B GLN* 1.3 57.8 + - - +
78B LEU 3.4 0.7 + - - -
79B ALA* 3.0 28.8 + - - +
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.1 22.5 + - + +
72B ASP* 2.9 16.9 + - - +
73B HIS* 3.4 21.0 + - - +
75B SER* 1.3 72.7 - - - +
77B ARG* 1.3 61.7 + - - +
79B ALA* 3.3 3.7 + - - +
80B ARG* 2.9 29.8 + - - +
114B LEU* 3.8 30.2 - - + +
117B ALA* 4.7 12.3 - - - +
118B LEU* 3.8 26.9 - - + +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE 5.7 0.6 + - - -
25B LEU* 3.9 36.0 - - + +
73B HIS* 2.8 54.6 + - + +
74B LYS 3.6 7.0 - - - +
76B GLN* 1.3 76.1 - - - +
78B LEU* 1.3 63.8 + - - +
80B ARG* 3.2 7.8 + - - +
81B LEU* 3.0 21.7 + - - +
118B LEU* 4.4 11.9 - - - -
120B LEU* 5.7 5.1 - - - +
127B ALA* 2.8 44.1 + - - +
128B ASP* 4.7 10.1 + - - +
131B LEU* 4.1 8.9 - - - +
132B ALA* 3.8 16.0 - - + +
300B PRO* 4.9 12.4 - - - +
303B HIS* 5.9 3.6 - - - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 3.4 21.1 - - + +
30B GLU 3.4 33.4 - - - +
31B ASN 3.5 19.7 - - - +
32B LEU* 3.8 15.3 - - + +
40B MET* 4.2 2.2 - - + -
74B LYS 3.0 17.4 + - - +
75B SER* 3.8 3.8 - - - +
77B ARG* 1.3 76.3 - - - +
79B ALA* 1.3 57.7 + - - +
81B LEU* 3.1 8.6 + - + +
82B VAL* 2.9 27.7 + - + +
132B ALA* 5.6 2.4 - - - +
151B LEU* 4.2 9.0 - - + -
152B PHE* 3.9 30.3 - - + -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.9 17.0 - - + +
39B TRP* 4.7 8.1 - - + -
70B LEU* 3.6 32.5 - - + -
75B SER 3.0 17.5 + - - +
76B GLN 3.8 0.7 - - - +
78B LEU* 1.3 77.1 - - - +
80B ARG* 1.3 62.6 + - - +
82B VAL* 3.4 2.0 + - - +
83B LEU* 3.0 29.1 + - - +
114B LEU* 3.7 10.5 - - + -
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN 2.9 14.5 + - - +
77B ARG* 3.5 7.9 - - - +
79B ALA* 1.3 78.5 - - - +
81B LEU* 1.3 57.4 + - - +
83B LEU* 4.7 2.5 - - - +
84B GLY* 2.9 26.3 + - - -
111B TYR* 4.2 11.5 + - + -
114B LEU* 3.6 17.9 - - + +
115B SER* 3.0 25.4 + - - +
118B LEU* 3.8 22.9 - - + -
120B LEU* 3.5 30.2 - - - +
121B PRO 2.9 21.8 + - - -
123B ILE 2.7 23.6 + - - -
125B VAL* 3.6 13.1 - - - +
128B ASP* 2.7 44.4 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG 3.0 11.9 + - - +
78B LEU* 3.5 14.1 - - + +
80B ARG* 1.3 74.5 - - - +
82B VAL* 1.3 65.2 + - - +
84B GLY* 3.4 0.5 + - - -
85B CYS* 3.0 44.9 + - - -
124B LEU* 4.2 3.4 - - + -
128B ASP* 3.3 37.1 + - + +
129B CYS* 3.9 9.4 - - - -
132B ALA* 3.9 10.8 - - + +
133B ASN* 3.7 29.8 - - + +
151B LEU* 4.3 1.6 - - + -
152B PHE* 3.5 31.9 - - + -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.3 4.5 - - + -
39B TRP* 3.8 36.3 - - + +
40B MET* 3.7 22.0 - - + +
43B ALA* 3.8 18.9 - - + +
78B LEU* 2.9 20.8 + - + +
79B ALA* 3.7 6.7 - - - +
81B LEU* 1.3 76.6 - - - +
83B LEU* 1.3 64.1 + - - +
85B CYS* 3.3 2.8 + - - +
86B ILE* 3.1 27.2 + - + +
152B PHE* 3.6 28.3 - - + -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 3.6 51.1 - - + -
67B ILE* 5.6 0.2 - - + -
79B ALA 3.0 20.3 + - - +
82B VAL* 1.3 75.0 - - + +
84B GLY* 1.3 60.5 + - - +
86B ILE* 3.4 5.7 + - + +
87B THR* 2.8 34.3 + - - +
107B ILE* 3.8 27.7 - - + +
110B PRO 4.4 1.1 - - - -
111B TYR* 3.7 49.6 - - + +
114B LEU* 4.3 12.3 - - + -
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG 2.9 17.3 + - - -
81B LEU 3.8 0.7 - - - -
83B LEU* 1.3 77.9 - - - +
85B CYS* 1.3 56.3 + - - +
87B THR* 3.2 3.2 + - - -
88B MET* 2.9 33.6 + - - +
111B TYR* 3.4 23.2 - - - -
124B LEU* 4.0 17.9 - - - -
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Residues in contact with CYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA* 5.1 3.1 - - + -
46B LEU* 3.9 18.8 - - + -
81B LEU* 3.0 40.7 + - - +
82B VAL* 3.8 4.3 - - - +
84B GLY* 1.3 76.0 - - - +
86B ILE* 1.3 59.4 + - - +
88B MET 3.4 0.3 + - - -
89B ALA* 2.9 30.8 + - - +
124B LEU* 4.2 6.7 - - - -
129B CYS* 5.7 1.6 - - - -
133B ASN* 5.9 0.9 - - - -
152B PHE* 4.0 21.5 - - + -
153B SER 5.8 0.7 - - - -
154B PHE* 3.6 28.6 - - + -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 3.6 33.7 - - + +
42B ILE* 4.0 20.6 - - + -
43B ALA* 4.1 10.3 - - + -
46B LEU* 4.7 3.4 - - + -
55B LEU* 4.5 0.7 - - + +
59B VAL* 3.7 29.4 - - + -
62B LEU* 5.5 0.7 - - + -
82B VAL* 3.1 26.6 + - + +
83B LEU* 3.8 7.4 - - - +
85B CYS* 1.3 75.4 - - - +
87B THR* 1.3 59.5 + - - +
89B ALA* 3.3 5.8 + - - +
90B TYR* 2.8 29.0 + - + +
103B LEU* 6.3 0.2 - - + -
107B ILE* 4.4 23.1 - - + -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU 2.8 20.4 + - - -
84B GLY 3.6 3.8 - - - -
86B ILE* 1.3 74.7 - - - +
88B MET* 1.3 82.7 + - + +
90B TYR* 3.0 2.4 + - - +
91B VAL* 2.9 26.1 + - + +
103B LEU* 3.6 35.6 - - + +
107B ILE* 3.8 6.4 - - - +
111B TYR* 3.5 25.1 - - + -
122B PRO 5.2 0.4 - - - +
237B TRP* 4.1 15.9 - - + -
247B LEU* 4.5 1.1 - - + -
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLY 2.9 21.9 + - - +
85B CYS 3.9 3.1 - - - +
87B THR* 1.3 83.1 - - + +
89B ALA* 1.3 63.5 + - - +
91B VAL* 4.8 1.3 - - - -
92B TRP* 3.0 34.2 + - + +
123B ILE* 3.6 10.1 - - + -
124B LEU* 3.5 45.3 - - + +
154B PHE* 3.9 9.2 - - + -
233B TYR* 3.3 29.2 - - + +
234B LEU* 5.2 2.5 - - - +
235B SER 4.1 7.9 - - - +
237B TRP* 3.5 34.8 - - + -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.8 21.1 - - + -
50B ILE* 3.9 13.5 - - + -
55B LEU* 3.4 22.9 - - + +
85B CYS 2.9 18.4 + - - +
86B ILE 3.7 2.2 - - - +
88B MET* 1.3 77.7 - - - +
90B TYR* 1.3 58.2 + - - +
93B GLY* 2.8 30.0 + - - +
154B PHE* 4.5 2.8 - - + -
233B TYR* 4.4 11.0 - - - -
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.6 7.1 - - + +
56B ARG* 2.9 60.2 + - + +
59B VAL* 3.9 20.6 - - + -
60B GLU* 2.9 28.7 + - + +
86B ILE* 2.8 22.0 + - + +
87B THR* 3.0 6.5 + - - +
89B ALA* 1.3 74.3 - - - +
91B VAL* 1.3 65.2 + - + +
100B ARG* 3.7 28.1 - - + +
102B VAL 3.4 23.2 + - - -
103B LEU* 4.0 13.7 - - + -
104B PRO* 3.4 30.0 - - + +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 2.9 15.2 + - - -
87B THR* 2.9 21.9 + - + +
88B MET 4.0 2.5 - - - +
90B TYR* 1.3 82.8 - - + +
92B TRP* 1.3 83.7 + - + +
99B VAL* 3.2 5.4 - - - -
100B ARG 3.1 30.9 + - - +
103B LEU* 5.1 1.6 - - + -
237B TRP* 3.9 21.5 - - + -
243B LEU* 4.3 9.4 - - + -
247B LEU* 3.9 35.0 - - + -
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Residues in contact with TRP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 3.6 2.5 - - - -
88B MET* 3.0 24.3 + - - +
91B VAL* 1.3 81.7 - - + +
93B GLY* 1.3 65.8 + - - +
94B LYS 3.1 0.7 + - - -
95B GLY* 2.9 16.5 + - - -
96B HIS 4.5 1.0 + - - -
97B GLY 5.2 1.0 + - - -
98B ASP 3.9 7.4 - - - +
99B VAL* 3.8 18.5 - - + +
232B ILE* 3.4 38.7 + - + -
233B TYR* 3.9 21.1 + - + -
235B SER* 2.8 35.2 + - - -
236B GLY 3.5 11.2 - - - -
237B TRP* 3.8 14.7 - + - -
240B ASN* 3.5 19.7 - - - -
242B GLN* 3.9 20.9 - - - -
243B LEU* 3.5 30.7 - - + -
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.5 12.6 - - - +
55B LEU* 5.7 0.2 - - - -
56B ARG* 3.2 26.3 - - - +
89B ALA 2.8 21.4 + - - +
92B TRP* 1.3 75.2 - - - +
94B LYS* 1.3 52.8 + - - -
98B ASP 4.5 0.2 - - - -
233B TYR* 2.7 31.2 + - - -
502B GOL 4.6 7.4 - - - -
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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
------------------------------------------------------------
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