Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 2G8N
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 ASP 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ARG* 2.9 25.0 + - - +
74B THR* 3.2 19.0 - - + +
75B LEU* 2.9 25.8 + - - +
94B PHE* 4.3 0.7 - - - +
95B GLU* 1.3 81.2 - - + +
97B ILE* 1.3 65.0 + - - +
98B THR* 3.9 1.9 + - - -
150B ARG 3.9 1.8 - - - -
152B LYS* 3.4 13.2 - - + +
153B ARG* 2.8 46.3 + - - -
172B PRO* 3.8 9.2 - - - +
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Residues in contact with ILE 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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75B LEU* 3.5 18.8 - - + +
87B LEU* 3.9 31.0 - - + -
91B CYS* 3.8 37.5 - - + +
94B PHE* 3.9 19.7 - - + +
96B ASP* 1.3 81.0 + - - +
98B THR* 1.3 73.6 + - - +
99B MET* 4.1 0.4 + - + -
147B LEU* 4.3 9.6 - - + -
150B ARG* 2.9 21.6 + - + +
151B VAL* 3.4 12.4 - - + -
152B LYS* 2.8 29.3 + - - +
153B ARG 3.8 2.6 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 3.0 6.7 + - - +
76B ILE* 3.5 22.4 - - + +
77B ASP* 2.8 29.3 + - - +
96B ASP* 3.9 1.7 + - - -
97B ILE* 1.3 72.8 - - - +
99B MET* 1.3 72.2 + - - +
100B THR* 3.8 10.3 - - + -
153B ARG* 2.7 35.1 + - + +
155B LEU* 3.7 27.1 - - + -
165B LEU* 5.4 0.2 - - + -
171B ALA* 4.2 5.0 - - + +
172B PRO* 4.1 8.3 - - - +
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Residues in contact with MET 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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77B ASP* 3.9 2.9 - - - +
80B SER* 3.6 19.5 - - - +
83B THR 3.6 24.0 - - - +
84B VAL* 4.2 10.5 - - + -
87B LEU* 3.5 31.4 - - + -
97B ILE* 4.1 0.9 - - + -
98B THR* 1.3 75.7 - - - +
100B THR* 1.3 69.8 + - - +
110B LEU* 4.1 22.7 - - + -
113B TRP* 6.4 0.2 - - - -
114B LEU* 5.4 4.9 - - - -
147B LEU* 5.9 0.4 - - - -
151B VAL* 3.8 34.1 - - + -
153B ARG 3.0 12.4 + - - +
154B VAL* 3.3 13.6 - - + -
155B LEU 2.9 22.7 + - - -
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 4.2 6.5 - - + -
77B ASP 2.7 21.5 + - - +
78B ILE* 3.5 3.1 - - - -
79B GLY 3.1 12.3 + - - -
80B SER* 2.6 42.1 + - - -
98B THR* 3.8 18.4 - - + -
99B MET* 1.3 81.3 - - - +
101B ASP* 1.3 60.7 + - - +
107B ARG* 5.2 1.6 - - - -
110B LEU* 5.5 0.9 - - - -
154B VAL* 5.1 2.0 - - - -
155B LEU* 3.0 15.0 - - + +
157B ILE* 3.5 15.4 - - + +
165B LEU* 3.9 21.8 - - + -
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 3.5 6.5 - - - -
80B SER* 5.2 0.2 - - - -
81B GLY* 2.8 20.5 + - - +
100B THR* 1.3 75.6 - - - +
102B PHE* 1.3 57.5 + - - +
103B LEU 3.0 15.6 + - - +
106B ASN* 2.9 23.8 - - + +
107B ARG* 2.7 34.5 + - + +
110B LEU* 5.6 0.7 - - + -
155B LEU 2.9 5.9 + - - -
156B PRO* 3.2 9.9 - - - +
157B ILE* 3.5 11.0 - - - +
3002B SAH 2.7 49.3 + - - -
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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
------------------------------------------------------------
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