Contacts of the helix formed by residues 76 - 92 (chain B) in PDB entry 3G33
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 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU* 2.8 23.0 + - + +
75B GLU* 1.3 79.5 + - - +
77B VAL* 1.3 66.5 + - - +
79B PRO* 3.3 3.7 - - - +
80B LEU* 3.2 19.8 + - - +
114B ARG* 3.1 43.6 + - + +
156B ILE* 3.3 16.6 - - + +
158B HIS* 3.2 38.1 + - + -
159B ASP* 4.5 5.7 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B CYS* 4.2 14.8 - - - -
73B CYS* 4.1 7.9 - - + -
74B GLU* 3.0 18.0 + - + +
76B GLU* 1.3 76.2 - - - +
78B PHE* 1.3 54.2 + - - +
80B LEU* 3.0 9.0 + - - +
81B ALA* 2.7 34.3 + - + +
107B MET* 4.1 9.0 - - + +
110B ALA* 3.5 22.2 - - + +
111B SER* 3.8 17.0 - - - +
114B ARG* 4.8 4.3 - - + +
115B GLU* 3.4 37.5 - - + +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 3.2 30.1 - - + -
64B MET* 3.6 21.1 - - + -
65B LEU* 3.6 32.8 - - + -
68B CYS* 4.1 21.4 - - + +
74B GLU 4.6 0.8 + - - -
75B GLU 4.3 3.2 + - - +
77B VAL* 1.3 77.7 - - - +
79B PRO* 1.3 74.6 - - + +
81B ALA* 3.0 8.8 + - + +
82B MET* 2.9 42.8 + - + +
187B ALA* 3.6 18.4 - - + -
190B ALA* 3.4 21.5 - - + -
191B THR* 3.6 15.3 - - + -
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU 3.4 14.8 - - - +
76B GLU* 3.3 11.2 - - - +
78B PHE* 1.3 103.7 - - + +
80B LEU* 1.3 56.0 + - - +
82B MET* 3.3 3.9 + - + +
83B ASN* 2.9 27.2 + - - +
156B ILE* 3.9 22.2 - - + +
157B ALA* 6.0 1.8 - - + +
158B HIS* 5.3 8.5 - - + +
186B LEU* 4.8 14.6 - - + +
187B ALA* 5.3 0.7 - - - -
190B ALA* 4.1 21.1 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU 3.2 9.9 + - - +
77B VAL* 3.0 9.8 + - - +
79B PRO* 1.3 77.7 - - - +
81B ALA* 1.3 64.9 + - - +
83B ASN* 2.9 19.2 + - + +
84B TYR* 3.0 59.5 + - + +
110B ALA* 4.0 20.9 - - + +
113B LEU* 4.4 5.6 - - + -
114B ARG* 3.3 37.7 - - + +
152B LEU 4.0 4.9 - - - +
154B ALA* 4.3 13.9 - - + -
156B ILE* 3.8 14.2 - - + +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 4.5 12.1 - - - -
77B VAL* 2.7 15.4 + - + +
78B PHE* 3.3 12.1 - - - +
80B LEU* 1.3 73.5 - - - +
82B MET* 1.3 57.2 + - - +
84B TYR* 3.2 4.4 + - - -
85B LEU* 2.9 23.8 + - - +
106B CYS* 3.4 38.9 - - + +
107B MET* 3.8 12.1 - - + +
110B ALA* 3.6 9.3 - - + +
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Residues in contact with MET 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 3.4 40.8 - - - +
61B ALA* 4.0 16.2 - - + -
64B MET* 3.6 28.3 - - - +
78B PHE* 2.9 37.9 + - + +
79B PRO* 3.5 9.6 - - + +
81B ALA* 1.3 73.2 - - - +
83B ASN* 1.3 65.3 - - - +
85B LEU* 3.3 22.5 + - + +
86B ASP* 3.0 30.2 + - - +
190B ALA* 3.7 21.5 - - + +
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.1 26.8 + - - +
40B PRO* 4.2 9.4 - - - +
79B PRO 2.9 12.3 + - - +
80B LEU* 3.0 15.9 - - + +
82B MET* 1.3 77.7 - - - +
84B TYR* 1.3 63.5 + - - +
86B ASP* 3.5 4.5 + - - +
87B ARG* 3.0 63.3 + - - +
154B ALA* 3.4 15.9 - - - +
156B ILE* 4.3 12.1 - - + +
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.0 40.2 + - + +
81B ALA* 3.5 6.5 - - - +
83B ASN* 1.3 84.6 - - - +
85B LEU* 1.3 63.7 + - - +
87B ARG* 3.3 7.6 + - - +
88B TYR* 2.9 25.6 + - - +
106B CYS* 3.7 30.5 - - - -
109B LEU* 4.0 13.0 - - + -
110B ALA* 3.4 30.8 - - + -
113B LEU* 3.5 5.7 - - - +
144B VAL* 5.2 1.1 - - + -
148B LEU* 3.9 19.1 - - + +
152B LEU* 2.7 58.0 + - + +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 4.4 19.1 - - + +
60B LEU* 4.1 28.7 - - + -
64B MET* 4.1 6.7 - - + -
81B ALA 2.9 12.9 + - - +
82B MET* 3.4 40.8 - - + +
84B TYR* 1.3 77.7 - - - +
86B ASP* 1.3 59.2 + - - +
88B TYR* 3.1 3.2 + - - +
89B LEU* 2.9 45.7 + - + +
99B LEU* 4.9 1.3 - - + -
102B LEU* 3.6 34.3 - - + -
103B GLY 4.9 0.4 - - - +
106B CYS* 3.6 9.5 - - - -
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 3.5 22.4 - - + +
44B TYR* 2.7 41.6 + - + -
57B ARG* 2.7 35.0 + - - +
82B MET 3.0 15.5 + - - +
83B ASN* 4.0 2.9 - - - +
85B LEU* 1.3 80.6 - - - +
87B ARG* 1.3 57.1 + - - +
89B LEU 3.3 1.9 + - - -
90B SER* 2.6 34.5 + - - -
193B TYR* 4.4 0.2 - - - -
196B ALA* 3.8 16.1 - - - +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG 5.1 4.3 + - - -
38B TYR* 3.5 28.9 - - - +
39B VAL 5.3 0.7 - - - -
40B PRO* 4.4 19.5 - - + -
83B ASN* 3.0 49.5 + - - +
84B TYR* 3.7 10.9 - - - +
86B ASP* 1.3 75.7 - - - +
88B TYR* 1.3 62.1 + - - +
90B SER* 3.4 19.2 + - - -
91B CYS* 3.7 12.3 - - - -
148B LEU* 3.6 34.7 + - + +
151B ASP* 2.6 42.0 + - - +
154B ALA* 3.7 4.4 - - - +
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR 2.9 17.9 + - - +
85B LEU 3.5 3.4 - - - +
87B ARG* 1.3 76.1 - - - +
89B LEU* 1.3 58.0 + - + +
90B SER 3.1 1.8 - - - -
91B CYS* 3.5 3.1 + - - -
92B VAL* 3.0 56.4 + - + +
94B THR* 4.1 11.7 - - - -
102B LEU* 3.6 39.5 - - + -
140B TRP* 3.7 19.5 - + - -
143B LEU* 3.8 14.1 - - - +
144B VAL* 4.1 31.2 - - + -
147B LYS* 3.8 33.9 - - + +
148B LEU* 3.8 10.0 - - + +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.0 56.5 - - + +
47B CYS* 4.8 1.7 - - - +
48B VAL* 3.9 7.7 - - + +
52B ILE* 4.3 20.2 - - + -
57B ARG* 4.9 4.3 - - + -
85B LEU* 2.9 39.0 + - + +
86B ASP 3.7 2.9 - - - +
88B TYR* 1.3 74.5 - - + +
90B SER* 1.3 60.4 + - - +
91B CYS 3.4 0.4 + - - -
92B VAL 3.8 11.1 + - - +
94B THR* 3.2 26.7 - - - +
99B LEU* 5.0 11.4 - - + -
102B LEU* 3.8 16.8 - - + -
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 4.1 8.5 - - - +
41B ARG* 4.3 13.3 + - - -
42B ALA* 3.8 14.9 + - - +
44B TYR* 3.7 17.0 - - - +
47B CYS* 4.2 17.7 - - - -
86B ASP 2.6 21.0 + - - -
87B ARG* 3.4 13.1 - - - -
88B TYR 3.1 0.4 - - - -
89B LEU* 1.3 79.8 - - - +
91B CYS* 1.3 59.1 + - - +
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 6.3 1.6 - - - -
87B ARG 3.7 16.6 - - - -
88B TYR* 3.9 2.9 - - - -
90B SER* 1.3 77.9 - - - +
92B VAL* 1.3 77.0 + - - +
93B PRO* 3.6 8.8 - - - +
147B LYS* 4.4 19.9 + - - -
148B LEU* 5.7 0.4 - - - -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 6.1 0.4 - - - -
48B VAL* 4.5 0.3 - - - +
88B TYR* 3.0 52.1 + - + +
89B LEU* 3.8 13.8 - - - +
91B CYS* 1.3 91.5 - - - +
93B PRO* 1.3 69.7 - - + +
94B THR* 3.1 15.5 + - - +
147B LYS* 3.6 42.6 - - + +
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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) + - + + + + + -
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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