Contacts of the helix formed by residues 87 - 99 (chain B) in PDB entry 3G2S
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 LYS 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B ASP* 3.4 22.4 - - - +
84B GLU* 2.4 46.6 + - - +
85B VAL 3.1 2.8 + - - +
86B GLY* 1.3 80.8 - - - +
88B PHE* 1.3 61.6 + - - +
89B ARG* 4.2 22.7 - - + +
90B PHE* 3.0 7.8 + - - +
91B LEU* 2.9 27.3 + - - +
131B LYS* 4.2 5.8 - - - +
3D GLY* 3.9 17.8 + - - -
4D PHE* 5.4 1.6 - - - +
5D SER 4.8 8.2 + - - +
7D ASP* 3.5 20.4 - - + +
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Residues in contact with PHE 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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87B LYS* 1.3 67.9 - - - +
89B ARG* 1.3 60.2 + - - +
91B LEU* 4.0 15.9 - - + +
92B ASN* 2.8 49.1 + - - +
95B ILE* 5.4 0.2 - - + -
131B LYS* 3.6 47.3 - - + +
134B GLU* 3.5 24.2 - - + -
135B ALA* 4.4 1.8 - - + -
7D ASP* 2.7 21.3 + - - +
8D VAL* 3.3 27.6 - - - +
9D PRO* 4.2 0.7 - - + +
10D MET* 3.6 48.9 - - + -
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Residues in contact with ARG 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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105A SER* 5.5 2.6 + - - -
106A ARG* 4.3 40.2 + - - +
49B ARG* 5.9 5.2 - - + +
84B GLU* 5.5 4.6 + - - -
87B LYS* 4.4 19.5 - - + +
88B PHE* 1.3 76.3 - - - +
90B PHE* 1.3 57.0 + - - +
92B ASN* 4.8 1.0 - - - +
93B GLU* 3.8 19.8 + - - +
3D GLY* 6.1 0.8 - - - -
5D SER* 4.2 16.7 + - - -
6D ASP 2.6 31.1 + - - -
7D ASP* 3.0 26.1 + - - +
8D VAL* 3.7 22.4 - - + +
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Residues in contact with PHE 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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48B THR* 3.4 44.9 - - - +
51B LEU* 4.5 2.7 - - + -
52B ALA* 4.0 22.0 - - + -
55B ILE* 4.5 3.8 - - + -
70B LEU* 3.9 30.1 - - + -
84B GLU 3.7 15.3 - - - +
85B VAL* 3.6 35.9 - - + +
87B LYS* 3.0 8.7 + - - +
89B ARG* 1.3 78.3 - - - +
91B LEU* 1.3 66.4 + - + +
92B ASN 3.1 2.2 - - - -
93B GLU* 2.9 22.1 + - + +
94B LEU* 3.6 35.8 + - + +
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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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85B VAL* 3.3 24.0 - - + +
86B GLY 4.2 2.0 - - - -
87B LYS 2.9 23.0 + - - +
88B PHE* 4.0 20.2 - - + -
90B PHE* 1.3 74.8 - - + +
92B ASN* 1.3 58.2 + - - +
94B LEU* 3.1 16.5 + - + +
95B ILE* 2.9 31.0 + - + +
119B LEU* 4.0 27.6 - - + -
122B TRP* 5.2 0.2 - - + -
131B LYS* 3.5 37.0 - - + +
132B ILE* 3.8 13.2 - - + +
135B ALA* 4.2 10.8 - - + -
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Residues in contact with ASN 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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88B PHE* 2.8 31.8 + - - +
89B ARG* 4.8 1.3 - - - +
91B LEU* 1.3 71.8 - - - +
93B GLU* 1.3 63.9 + - - +
95B ILE* 3.3 9.0 + - - +
96B LYS* 3.0 36.8 + - + +
8D VAL* 3.7 13.3 - - - +
9D PRO 3.0 24.2 + - - -
10D MET* 3.5 6.8 - - - +
11D VAL* 2.9 46.6 + - + +
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Residues in contact with GLU 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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103A LEU* 4.3 22.4 - - - +
106A ARG* 4.4 7.2 + - - +
52B ALA* 3.8 29.6 - - + -
55B ILE* 6.3 0.2 - - - -
56B GLN* 2.7 46.3 + - - +
89B ARG 3.8 19.5 - - - +
90B PHE* 2.9 10.3 + - + +
92B ASN* 1.3 84.2 - - - +
94B LEU* 1.3 62.7 + - + +
96B LYS* 3.6 20.7 + - - +
97B VAL* 3.4 18.4 + - - +
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Residues in contact with LEU 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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52B ALA* 5.9 0.9 - - - -
55B ILE* 4.0 38.4 - - + -
70B LEU* 4.7 5.8 - - + -
90B PHE* 3.7 35.7 - - + +
91B LEU* 3.1 13.1 + - + +
93B GLU* 1.3 77.2 - - + +
95B ILE* 1.3 64.8 + - + +
97B VAL* 3.1 15.6 + - - +
98B VAL* 3.3 18.1 + - - +
115B ILE* 4.2 25.1 - - + +
119B LEU* 4.3 26.5 - - + -
122B TRP* 4.4 10.8 - - + -
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Residues in contact with ILE 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* 2.9 20.0 + - + +
92B ASN* 3.3 21.5 + - - +
94B LEU* 1.3 74.9 - - + +
96B LYS* 1.3 57.9 + - + +
98B VAL* 3.2 9.9 + - - +
99B SER* 3.0 28.7 + - - -
102B TYR* 5.5 2.0 - - + -
119B LEU* 6.1 1.3 - - + -
135B ALA* 4.1 16.8 - - + -
138B MET* 3.4 32.3 - - + -
139B LEU* 4.6 10.1 - - + -
10D MET* 4.0 8.7 - - + -
11D VAL* 3.5 29.2 - - + +
12D ILE 4.6 0.4 - - - -
13D ALA* 4.1 18.2 - - + -
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Residues in contact with LYS 96 (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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96A LYS* 6.1 5.8 - - - +
102A TYR* 4.7 22.5 - - - -
56B GLN* 4.5 5.2 - - - +
92B ASN* 3.0 22.0 + - - +
93B GLU* 3.8 29.4 - - - +
94B LEU 3.2 0.4 - - - -
95B ILE* 1.3 75.7 - - - +
97B VAL* 1.3 61.1 + - - +
98B VAL 3.6 0.2 + - - -
99B SER 3.9 1.0 + - - -
102B TYR* 3.3 50.5 - - + +
103B LEU* 2.9 37.1 + - + +
104B GLY 3.7 1.0 + - - -
11D VAL* 3.8 27.0 - - + +
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Residues in contact with VAL 97 (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 ILE* 4.2 19.7 - - + +
56B GLN* 3.5 25.6 - - + -
93B GLU 3.4 15.5 - - - +
94B LEU* 3.1 9.2 + - - +
96B LYS* 1.3 78.5 - - - +
98B VAL* 1.3 56.6 + - - +
103B LEU* 4.2 9.6 - - + -
104B GLY* 3.2 20.6 + - - -
107B THR* 3.5 29.9 + - + +
111B VAL* 4.0 7.4 - - + -
112B LYS* 3.8 5.7 - - + +
115B ILE* 3.5 22.9 - - + -
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Residues in contact with VAL 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 LEU 3.8 7.2 - - - +
95B ILE* 3.2 10.1 + - - +
97B VAL* 1.3 79.5 - - - +
99B SER* 1.3 64.2 + - - +
100B PRO* 3.8 5.5 - - - +
104B GLY* 4.1 5.6 - - - -
112B LYS* 4.0 31.1 + - + +
115B ILE* 3.8 37.0 - - + -
116B LEU* 4.8 5.6 - - + -
139B LEU* 3.8 33.7 - - + -
144B ILE* 4.1 23.5 - - + +
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Residues in contact with SER 99 (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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95B ILE* 3.0 17.3 + - - -
96B LYS 3.9 0.4 + - - -
97B VAL 3.5 0.6 - - - -
98B VAL* 1.3 78.6 - - - +
100B PRO* 1.3 65.3 - - - +
101B LYS* 3.1 18.7 + - - +
102B TYR* 3.0 20.3 + - - -
103B LEU 3.5 1.2 + - - -
104B GLY* 2.9 22.2 + - - -
144B ILE* 4.7 0.4 - - - -
13D ALA* 2.7 42.9 + - - -
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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