Contacts of the helix formed by residues 77 - 96 (chain B) in PDB entry 4G3I
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 ARG 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 6.4 2.0 - - - -
16B GLU* 3.0 34.8 + - - +
19B LEU* 3.7 27.3 - - - +
75B PRO* 3.8 11.4 - - + +
76B MET* 1.3 72.9 - - - +
78B LYS* 1.3 61.1 + - - +
79B GLU 3.4 3.9 + - - -
80B VAL* 3.4 26.5 + - + +
81B TYR* 2.9 41.1 + - + +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.8 24.9 - - + +
76B MET* 3.6 32.2 + - + +
77B ARG* 1.3 74.3 - - - +
79B GLU* 1.3 58.5 + - + +
80B VAL 3.2 0.2 - - - -
81B TYR* 3.7 9.8 - - + +
82B GLN* 3.0 26.7 + - + +
104B ILE* 4.7 12.6 - - + +
275B LYS* 6.1 1.2 - - - +
6F G 5.1 1.2 + - - -
7F C 3.6 32.1 + - - -
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 4.8 6.4 - - - +
36A ARG 4.9 12.1 - - - +
38A GLU* 6.1 0.7 - - - +
252A LYS* 5.2 4.3 + - - -
77B ARG 3.4 0.8 - - - -
78B LYS* 1.3 77.6 - - + +
80B VAL* 1.3 61.9 + - + +
82B GLN* 3.8 19.4 - - - +
83B GLN* 3.0 43.5 + - - +
274B TYR* 5.8 5.0 - - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG 6.0 2.7 - - - +
37A PHE* 6.6 0.4 - - - -
15B VAL* 4.1 10.5 - - + -
19B LEU* 4.0 27.1 - - + -
77B ARG* 3.7 35.7 - - + +
78B LYS 3.2 0.4 - - - -
79B GLU* 1.3 80.4 - - + +
81B TYR* 1.3 68.7 + - + +
83B GLN* 3.2 19.6 + - - +
84B VAL* 3.1 33.7 + - + +
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.5 16.7 - - + -
12B TYR* 3.4 68.2 - + + -
15B VAL* 4.0 22.0 - - + -
16B GLU* 2.6 37.3 + - + +
30B VAL* 3.6 12.2 - - + +
75B PRO 3.8 1.2 + - - -
76B MET* 4.0 6.5 - - - -
77B ARG* 2.9 45.1 + - + -
78B LYS* 3.7 10.1 - - - +
80B VAL* 1.3 78.5 - - + +
82B GLN* 1.3 56.9 + - - +
84B VAL 3.4 0.2 + - - -
85B SER* 2.8 30.6 + - - -
104B ILE* 4.3 2.9 - - + -
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 3.0 20.5 + - + +
79B GLU* 4.0 23.1 - - - +
80B VAL 3.2 0.2 - - - -
81B TYR* 1.3 73.1 - - - +
83B GLN* 1.3 66.8 + - - +
85B SER* 3.2 12.2 + - - -
86B SER* 3.0 41.3 + - - +
104B ILE* 3.3 24.0 - - + +
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Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 4.6 6.5 + - - -
36A ARG* 5.4 3.2 + - - +
252A LYS* 3.2 55.3 - - + +
253A ARG* 5.9 0.5 - - - +
79B GLU* 3.0 33.2 + - - +
80B VAL* 3.2 22.0 + - - +
82B GLN* 1.3 77.1 - - - +
84B VAL* 1.3 64.7 + - + +
86B SER* 3.4 6.3 + - - -
87B ARG* 3.1 43.2 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.2 13.9 - - + -
15B VAL* 4.3 20.4 - - + -
19B LEU* 6.4 1.1 - - + -
80B VAL* 3.1 22.5 + - + +
81B TYR 3.8 2.9 - - - +
83B GLN* 1.3 73.9 - - + +
85B SER* 1.3 60.9 + - - +
87B ARG* 3.3 26.6 + - - +
88B ILE* 3.0 44.8 + - + +
136B GLU* 4.0 13.7 - - - +
138B ILE* 4.4 8.7 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.4 6.5 - - - -
11B PHE* 4.0 9.2 - - - -
81B TYR 2.8 19.2 + - - -
82B GLN* 3.5 11.1 + - - -
84B VAL* 1.3 73.4 - - - +
86B SER* 1.3 59.2 + - - +
88B ILE* 3.4 2.8 + - - +
89B MET* 2.9 43.0 + - - +
104B ILE* 2.6 43.9 + - - +
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Residues in contact with SER 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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82B GLN* 3.0 28.8 + - - +
83B GLN* 3.5 9.8 - - - -
85B SER* 1.3 73.9 - - - +
87B ARG* 1.3 69.4 + - - +
89B MET* 2.9 17.6 + - - +
90B ASN* 2.9 25.5 + - - +
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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
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252A LYS* 5.6 5.7 - - - +
253A ARG* 6.1 5.3 - - - +
83B GLN* 3.1 31.0 + - - +
84B VAL* 3.6 25.9 - - - +
86B SER* 1.3 79.3 - - - +
88B ILE* 1.3 63.6 + - - +
90B ASN* 3.5 10.6 + - - +
91B LEU* 3.2 25.7 + - - +
136B GLU* 2.9 42.4 + - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.0 48.5 - - + -
11B PHE* 4.6 1.6 - - + -
84B VAL* 3.0 29.5 + - + +
85B SER 3.6 7.0 - - - +
86B SER 3.1 0.2 - - - -
87B ARG* 1.3 78.1 - - - +
89B MET* 1.3 61.6 + - - +
91B LEU* 3.1 19.5 + - + +
92B LEU* 3.1 14.2 + - + +
132B ILE* 4.0 24.5 - - + -
136B GLU* 4.0 16.2 - - + -
138B ILE* 3.7 32.8 - - + -
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.4 30.7 - - + -
85B SER* 2.9 26.1 + - - +
86B SER* 2.9 8.0 + - - +
88B ILE* 1.3 76.7 - - - +
90B ASN* 1.3 56.8 + - - +
92B LEU* 3.2 15.1 + - - +
93B ARG* 3.1 42.1 + - - +
99B ILE* 4.2 2.9 - - - +
101B ILE* 4.0 23.3 - - + -
103B SER 4.2 6.3 - - - +
104B ILE 3.7 10.1 - - - +
106B GLU 3.6 27.4 - - - +
107B ALA* 3.8 22.4 - - - -
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B SER* 2.9 21.6 + - - +
87B ARG* 3.7 11.3 - - - +
89B MET* 1.3 72.8 - - - +
91B LEU* 1.3 66.9 + - + +
93B ARG* 3.0 40.3 + - - +
94B GLU* 3.2 15.1 + - - +
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Residues in contact with LEU 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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87B ARG 3.2 14.9 + - - +
88B ILE* 3.1 14.6 + - - +
90B ASN* 1.3 75.4 - - + +
92B LEU* 1.3 62.3 + - + +
94B GLU* 3.1 41.1 + - - +
95B TYR* 3.4 14.4 - - + -
131B LYS* 4.5 15.9 - - + +
132B ILE* 4.2 30.5 - - + -
135B LYS* 3.9 41.7 - - + -
136B GLU* 4.7 6.7 - - + +
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Residues in contact with LEU 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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6B VAL* 3.9 20.9 - - + -
8B PHE* 4.6 2.0 - - + -
88B ILE* 3.1 19.9 + - + +
89B MET* 3.4 22.9 - - - +
90B ASN 3.2 0.2 - - - -
91B LEU* 1.3 75.3 - - - +
93B ARG* 1.3 61.8 + - - +
95B TYR* 3.4 5.3 + - + +
96B SER 3.3 20.7 + - - +
99B ILE* 3.7 11.9 - - + -
107B ALA* 3.8 26.9 - - + -
109B LEU* 3.6 24.4 - - + +
128B ILE* 3.7 32.1 - - + -
132B ILE* 4.4 6.7 - - + -
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Residues in contact with ARG 93 (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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86B SER* 6.2 0.2 - - - +
89B MET* 3.1 20.6 + - - +
90B ASN* 3.0 37.8 + - - +
92B LEU* 1.3 73.6 - - - +
94B GLU* 1.3 67.0 - - - +
96B SER 3.4 18.9 + - - +
97B GLU* 4.0 6.2 + - - +
99B ILE* 4.1 24.3 - - + +
101B ILE* 3.6 29.7 - - - +
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Residues in contact with GLU 94 (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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90B ASN 3.2 11.2 + - - +
91B LEU* 3.1 33.7 + - - +
93B ARG* 1.3 77.3 - - - +
95B TYR* 1.3 68.5 + - + +
96B SER* 3.4 0.7 + - - -
97B GLU* 5.6 1.0 - - - +
131B LYS* 5.6 5.2 - - - +
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Residues in contact with TYR 95 (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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91B LEU* 3.4 21.3 - - + -
92B LEU* 3.4 9.3 + - + +
93B ARG 3.3 0.6 - - - -
94B GLU* 1.3 85.0 - - + +
96B SER* 1.3 62.5 + - - +
109B LEU* 4.2 11.7 - - + -
111B ILE* 5.3 2.9 - - + +
114B LYS* 4.0 21.1 - - - +
124B LEU* 4.3 25.2 - - + +
127B GLU* 3.2 40.8 + - + +
128B ILE* 3.7 37.7 - - + -
131B LYS* 3.5 32.3 - - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU 3.3 11.4 + - - +
93B ARG* 3.4 18.5 + - - +
94B GLU 4.4 0.7 - - - -
95B TYR* 1.3 81.9 - - - +
97B GLU* 1.4 73.0 + - - +
98B LYS* 3.4 15.4 + - - +
99B ILE* 4.1 9.9 - - - +
109B LEU* 4.3 14.8 - - - +
110B ASP 3.3 23.2 + - - -
111B ILE* 4.4 8.7 - - - -
114B LYS* 5.0 7.7 - - - +
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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