Contacts of the helix formed by residues 77 - 91 (chain E) in PDB entry 6G2T
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 ASN 77 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ARG* 5.1 3.2 - - - +
67E LYS* 4.8 10.0 - - - +
69E PRO* 3.9 7.0 + - + +
75E VAL* 3.4 3.1 - - - +
76E THR* 1.3 89.2 + - - +
78E TRP* 1.3 66.4 + - - +
79E ASP* 2.7 35.4 + - - +
80E ASP* 3.1 28.2 + - + +
81E MET* 3.6 16.5 + - - +
204K GLY* 5.3 8.5 - - - -
205K GLN* 5.4 1.6 + - - +
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Residues in contact with TRP 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E VAL* 3.3 43.4 + - + +
76E THR 5.6 1.3 - - - -
77E ASN* 1.3 74.6 + - - +
79E ASP* 1.3 66.9 + - - +
81E MET* 3.1 13.2 + - + +
82E GLU* 3.0 21.0 + - - +
85E TRP* 4.7 7.6 - + - -
113E ALA* 4.4 1.1 - - + -
114E ASN* 3.5 34.3 - - + -
117E LYS* 3.3 43.4 - - + +
118E MET* 4.0 16.4 - - + -
121E ILE* 3.3 33.6 - - + +
201K SER 5.6 2.0 - - - -
203K VAL 5.6 6.7 - - - -
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Residues in contact with ASP 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ARG* 4.7 6.4 + - - -
77E ASN* 2.7 42.8 + - - +
78E TRP* 1.3 75.3 - - - +
80E ASP* 1.3 74.9 + - - +
82E GLU* 3.1 14.0 + - - +
83E LYS* 3.0 35.6 + - - +
204K GLY* 6.4 0.4 - - - -
205K GLN* 4.1 24.0 - - - +
206K HIS* 5.7 8.8 - - + -
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Residues in contact with ASP 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E VAL* 3.5 33.3 - - + +
36E ARG* 3.1 26.7 + - - -
67E LYS* 4.4 16.3 - - - +
69E PRO* 4.4 10.2 - - + +
77E ASN* 3.1 33.0 + - + +
78E TRP 3.3 0.4 - - - -
79E ASP* 1.3 86.0 + - - +
81E MET* 1.3 62.1 + - - +
83E LYS* 3.2 11.6 + - - +
84E ILE* 3.1 26.6 + - - +
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Residues in contact with MET 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASN* 4.1 13.9 - - - +
32E SER* 5.9 0.4 - - - -
69E PRO* 3.7 19.9 - - + +
70E ILE* 3.5 38.4 - - + -
75E VAL* 3.8 13.9 - - + -
77E ASN 3.6 8.7 + - - +
78E TRP* 3.1 17.2 + - + +
80E ASP* 1.3 80.6 - - - +
82E GLU* 1.3 56.2 + - - +
84E ILE* 3.2 13.6 + - + +
85E TRP* 2.8 74.8 + - + +
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Residues in contact with GLU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TRP 3.0 12.7 + - - +
79E ASP* 3.1 18.2 + - - +
81E MET* 1.3 77.6 - - - +
83E LYS* 1.3 65.4 + - - +
85E TRP* 3.4 12.3 + - - +
86E HIS* 2.8 40.4 + - - +
121E ILE* 4.9 8.5 - - + -
125E THR* 3.7 32.3 - - + +
126E PHE* 3.9 10.2 - - + -
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Residues in contact with LYS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E VAL* 5.2 1.6 - - + -
36E ARG* 3.8 20.7 - - - +
50E ASP* 4.9 3.8 + - - +
51E SER* 3.8 31.8 - - - +
53E VAL* 3.8 22.1 - - + +
79E ASP* 3.0 25.2 + - - +
80E ASP* 3.2 15.7 + - - +
82E GLU* 1.3 82.9 - - - +
84E ILE* 1.3 57.4 + - - +
86E HIS* 3.3 8.2 + - - +
87E HIS* 2.8 30.5 + - - +
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E CYS* 3.4 29.8 - - - -
30E PHE* 4.3 8.5 - - + -
32E SER* 4.3 15.7 - - - -
33E ILE 4.4 2.0 - - - +
34E VAL* 4.1 11.9 - - + -
53E VAL* 3.6 20.4 - - + -
54E GLY 5.6 0.2 - - - +
69E PRO* 3.4 35.4 - - + -
80E ASP 3.1 14.3 + - - +
81E MET* 3.4 17.5 - - + +
83E LYS* 1.3 77.4 - - - +
85E TRP* 1.3 59.3 + - + +
87E HIS* 3.1 3.1 + - - +
88E THR* 2.8 37.7 + - + +
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Residues in contact with TRP 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 4.2 18.3 - - + +
11E ASN* 2.8 31.0 - - + +
78E TRP* 4.7 4.9 - + - -
81E MET* 2.8 50.3 + - + +
82E GLU* 3.7 7.0 - - - +
84E ILE* 1.3 78.9 - - + +
86E HIS* 1.3 62.1 + - - +
88E THR* 2.8 22.7 + - + -
89E PHE* 2.8 20.6 + - + -
104E LEU* 4.4 6.2 - - + +
118E MET* 3.7 38.6 - - + -
121E ILE* 3.7 37.9 - - + -
122E MET* 3.3 29.4 - - + +
126E PHE* 4.0 12.6 - + + -
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Residues in contact with HIS 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLU* 2.8 28.6 + - - +
83E LYS* 3.4 9.3 + - - +
85E TRP* 1.3 76.2 - - - +
87E HIS* 1.3 61.4 + - - +
90E TYR* 3.0 76.3 + + + +
91E ASN* 5.0 4.3 + - - -
126E PHE* 3.7 17.2 - + + -
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Residues in contact with HIS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E PHE* 3.5 26.5 - + - -
53E VAL* 3.0 43.3 + - + -
54E GLY* 4.3 3.1 - - - -
55E ASP* 4.7 6.4 + - - -
56E GLU* 5.0 7.8 + - - +
83E LYS 2.8 16.9 + - - +
84E ILE 3.3 4.3 - - - +
86E HIS* 1.3 80.4 + - - +
88E THR* 1.3 59.8 + - - +
91E ASN* 3.1 44.0 + - - +
92E GLU* 2.9 46.9 + - - +
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Residues in contact with THR 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 4.3 10.1 - - + +
16E CYS* 4.6 7.9 - - + -
18E ALA* 4.6 17.2 - - + +
30E PHE* 3.2 29.8 - - + -
84E ILE* 2.8 31.1 + - + +
85E TRP* 2.8 24.5 + - + -
87E HIS* 1.3 73.6 - - - +
89E PHE* 1.3 66.9 + - - +
92E GLU* 3.9 9.2 + - - +
93E LEU* 3.1 35.2 + - - +
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Residues in contact with PHE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 3.5 33.2 - - + -
9E ILE* 3.5 33.0 - - + -
85E TRP* 2.8 38.5 + - + +
88E THR* 1.3 83.4 + - - +
90E TYR* 1.3 71.2 + - + +
93E LEU* 3.2 11.4 - - + +
94E ARG 2.8 27.4 + - - -
95E VAL* 3.3 22.3 + - + +
97E PRO* 4.5 24.2 - - + -
102E VAL* 4.1 14.6 - - + -
122E MET* 4.4 13.5 - - + -
126E PHE* 4.6 13.0 - + + -
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Residues in contact with TYR 90 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E HIS* 3.0 57.7 + + + +
89E PHE* 1.3 88.0 - - + +
91E ASN* 1.3 70.4 + - - +
94E ARG* 3.8 13.6 - - - +
95E VAL 4.8 6.5 - - - -
96E ALA* 6.1 1.3 - - - -
97E PRO* 4.7 16.2 - - + +
98E GLU* 5.6 1.4 + - - -
126E PHE* 4.1 20.1 - + - -
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Residues in contact with ASN 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E HIS* 4.4 5.3 + - - +
87E HIS* 3.1 50.6 + - + +
90E TYR* 1.3 83.3 + - - +
92E GLU* 1.3 73.5 + - - +
94E ARG* 3.5 19.1 + - - +
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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
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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