Contacts of the helix formed by residues 82 - 98 (chain B) in PDB entry 2G5W
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 SER 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 1.3 92.7 + - - +
83B ASP* 1.3 63.9 + - - +
84B GLU* 3.8 9.2 + - - +
85B GLN* 3.0 39.6 + - - +
86B VAL* 3.2 22.5 + - - +
174B ASN* 4.2 2.9 - - - -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR 4.3 0.4 + - - -
82B SER* 1.3 71.5 - - - +
84B GLU* 1.3 64.9 + - - +
86B VAL* 3.3 6.7 + - - +
87B GLU* 3.2 28.3 + - + +
174B ASN* 4.4 2.9 + - - -
177B ARG* 3.2 34.3 + - - +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.8 34.2 - - + +
82B SER* 3.3 8.8 + - - +
83B ASP* 1.3 76.9 - - - +
85B GLN* 1.3 64.4 + - + +
87B GLU* 3.2 10.4 + - - +
88B ALA* 3.1 20.3 + - - +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN 5.4 0.4 + - - -
40B GLY* 3.4 26.4 + - - +
41B VAL* 4.7 6.9 - - + +
42B PRO* 3.9 9.6 - - + +
66B MET* 3.9 4.0 - - - +
79B GLY* 3.2 33.5 - - - +
80B ILE* 4.3 1.6 - - - -
81B TYR* 3.1 34.0 + - - -
82B SER* 3.0 39.3 + - - +
84B GLU* 1.3 80.2 - - + +
86B VAL* 1.3 60.6 + - - +
88B ALA* 3.3 3.7 + - - +
89B TRP* 3.0 30.6 + - - -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 4.0 12.6 - - + +
82B SER 3.2 7.7 + - - +
83B ASP 3.5 8.1 - - - +
84B GLU 3.3 0.4 - - - -
85B GLN* 1.3 77.0 - - - +
87B GLU* 1.3 68.1 + - - +
89B TRP* 3.4 11.7 + - - +
90B LYS* 3.6 12.7 + - - +
174B ASN* 3.4 52.7 - - + +
177B ARG* 3.5 33.4 - - + +
178B ALA* 3.7 18.2 - - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 3.2 14.8 + - + +
84B GLU* 3.2 10.1 + - - +
86B VAL* 1.3 82.8 - - - +
88B ALA* 1.3 62.1 + - - +
90B LYS* 3.2 49.4 + - - +
91B GLN* 4.3 2.3 + - - +
177B ARG* 4.5 9.0 + - - -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.8 9.0 - - + -
42B PRO* 3.3 49.5 - - + +
84B GLU* 3.1 14.9 + - + +
85B GLN 3.3 0.8 + - - +
87B GLU* 1.3 75.7 - - - +
89B TRP* 1.3 57.9 + - - +
90B LYS 3.4 0.2 - - - -
91B GLN* 3.3 30.7 + - - +
92B VAL* 3.9 1.6 - - - +
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Residues in contact with TRP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.5 11.3 - - + +
46B LEU* 4.1 13.5 - - + -
50B TYR* 4.8 4.5 - + - -
62B SER* 4.5 5.8 - - - -
63B GLU* 4.5 9.0 - - + -
65B THR* 3.7 18.7 - - + +
78B PRO* 3.4 33.4 - - + -
79B GLY 3.1 19.6 + - - -
80B ILE* 3.4 23.1 - - + +
85B GLN 3.0 24.3 + - - -
86B VAL 3.7 8.7 - - - +
87B GLU 3.2 1.0 - - - -
88B ALA* 1.3 78.5 - - - +
90B LYS* 1.3 63.1 + - - +
91B GLN 3.3 0.9 - - - -
92B VAL* 2.9 38.7 + - + +
93B VAL* 2.9 24.4 + - - +
103B ILE* 5.7 0.4 - - + -
105B CYS* 5.1 0.4 - - - -
178B ALA* 3.7 12.6 - - + -
180B PHE* 3.5 33.7 - + + -
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.6 11.4 + - - +
87B GLU* 3.2 43.2 + - - +
89B TRP* 1.3 79.5 - - - +
91B GLN* 1.3 53.7 + - - +
93B VAL* 3.3 1.2 + - - +
94B GLU* 2.7 58.3 + - - +
177B ARG 3.7 19.3 - - - -
178B ALA* 3.4 22.7 - - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO 4.3 2.2 + - - -
43B ASN* 3.4 31.7 - - - +
44B ALA* 3.6 20.1 - - - +
47B ALA* 4.0 7.2 - - + +
87B GLU 4.3 1.4 + - - +
88B ALA* 3.3 24.9 + - - +
90B LYS* 1.3 77.3 - - - +
92B VAL* 1.3 67.6 + - + +
94B GLU* 3.9 10.0 + - - +
95B ALA* 3.0 26.2 + - - +
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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
----------------------------------------------------------
42B PRO* 4.4 3.1 - - + -
43B ASN 3.9 11.4 - - - +
46B LEU* 4.0 7.4 - - + -
47B ALA* 3.7 29.7 - - - +
50B TYR* 3.8 26.9 - - + -
88B ALA 3.9 12.1 - - - +
89B TRP* 2.9 42.5 + - + +
91B GLN* 1.3 77.9 - - + +
93B VAL* 1.3 64.1 + - + +
95B ALA* 3.6 3.3 + - - +
96B VAL* 3.3 21.8 + - - +
103B ILE* 5.1 6.3 - - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 2.9 20.0 + - + +
90B LYS 3.9 2.9 - - - +
92B VAL* 1.3 77.0 - - + +
94B GLU* 1.3 61.5 + - + +
96B VAL* 3.3 3.5 + - - +
97B HIS* 3.0 42.1 + - + +
103B ILE* 4.1 14.8 - - + -
178B ALA 4.0 10.1 - - - +
179B GLY* 3.3 32.8 - - - +
180B PHE* 3.8 41.5 - - + +
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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
----------------------------------------------------------
90B LYS* 2.7 48.0 + - - +
91B GLN* 4.0 7.5 - - - +
93B VAL* 1.3 70.9 - - + +
95B ALA* 1.3 59.5 + - - +
97B HIS* 3.9 8.6 - - + +
98B ALA* 3.0 29.1 + - - +
178B ALA 5.5 0.3 - - - +
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Residues in contact with ALA 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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47B ALA* 3.9 12.8 - - + +
51B ALA* 3.9 22.4 - - + +
91B GLN 3.0 18.4 + - - +
92B VAL 3.7 6.3 - - - +
94B GLU* 1.3 75.4 - - - +
96B VAL* 1.3 62.2 + - - +
98B ALA* 3.6 7.8 - - - +
99B LYS* 3.6 26.9 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 4.0 15.5 - - + -
51B ALA 4.5 0.4 - - - +
54B THR* 3.6 29.7 + - + -
60B LEU* 3.8 20.0 - - + -
92B VAL 3.3 15.7 - - - +
93B VAL 3.3 7.5 + - - +
95B ALA* 1.3 76.2 - - - +
97B HIS* 1.3 64.1 + - - +
98B ALA 3.2 0.2 - - - -
99B LYS* 3.1 12.3 + - - +
100B GLY 3.2 0.2 + - - -
101B GLY* 3.0 44.5 + - - +
102B PHE 4.1 0.2 - - - +
103B ILE* 4.1 22.9 - - + -
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.0 37.7 + - + +
94B GLU* 4.2 7.4 - - + +
96B VAL* 1.3 75.3 - - - +
98B ALA* 1.3 61.0 + - - +
100B GLY* 3.1 12.6 + - - +
101B GLY 3.1 18.6 + - - +
102B PHE* 4.6 1.5 - + - -
103B ILE* 4.7 3.8 - - + -
179B GLY* 3.2 22.9 + - - -
181B ASP* 3.0 37.1 + - - -
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Residues in contact with ALA 98 (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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94B GLU 3.0 20.4 + - - +
95B ALA* 3.6 10.5 - - - +
96B VAL 3.2 0.2 - - - -
97B HIS* 1.3 76.7 - - - +
99B LYS* 1.3 62.1 + - + +
100B GLY 3.4 0.8 + - - -
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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