Contacts of the strand formed by residues 92 - 99 (chain R) in PDB entry 2A3W
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 VAL 92 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38R ARG* 3.4 7.1 - - - +
39R ALA* 2.9 47.9 + - + +
65R LYS* 6.1 0.9 - - - +
71R TYR* 3.7 21.5 - - - +
86R GLU* 4.3 5.6 - - + +
90R ALA* 4.4 5.6 - - + +
91R PRO* 1.3 75.6 - - - +
93R HIS* 1.3 65.8 + - - +
94R ILE* 3.7 24.4 + - + -
109R ILE* 3.7 26.0 - - + -
110R ASN* 3.5 10.5 - - - +
203R TRP* 4.8 0.4 - - - -
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Residues in contact with HIS 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R CYS* 4.1 11.5 - - + +
37R PHE* 3.7 17.1 + - - -
38R ARG* 3.8 32.3 - - + +
92R VAL* 1.3 73.5 - - - +
94R ILE* 1.3 62.7 + - - +
95R CYS* 3.3 32.6 + - - -
108R TRP* 3.5 4.1 + - - +
109R ILE* 3.5 2.8 - - - -
110R ASN* 2.8 38.8 + - - +
111R GLY 4.8 3.2 + - - -
156R ASP* 5.4 3.6 + - + +
169R ILE* 4.4 0.7 - - + -
172R ALA* 3.6 13.1 + - - +
173R TYR* 3.5 51.6 - + + +
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Residues in contact with ILE 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R LEU 3.7 0.2 - - - +
36R CYS* 3.1 3.6 - - - -
37R PHE* 2.8 77.2 + - + +
39R ALA* 4.6 3.1 - - + -
49R LEU* 4.4 9.9 - - + -
63R VAL* 4.9 2.2 - - + -
71R TYR* 3.7 21.3 - - + -
92R VAL* 3.7 24.2 - - + +
93R HIS* 1.3 79.7 - - - +
95R CYS* 1.3 75.3 + - - +
96R VAL* 4.7 1.1 - - + +
107R PHE* 4.3 21.5 - - + -
108R TRP 3.5 2.5 - - - -
109R ILE* 3.9 15.5 - - + -
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Residues in contact with CYS 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34R THR* 4.9 0.4 - - + -
35R LEU 3.1 3.1 - - - -
36R CYS* 2.0 46.0 - - - -
93R HIS* 3.3 23.3 - - - -
94R ILE* 1.3 73.7 - - - +
96R VAL* 1.3 60.2 + - - +
106R GLU 4.2 0.9 - - - -
107R PHE* 3.4 5.9 - - - -
108R TRP* 2.7 48.7 + - + +
169R ILE* 3.9 32.8 - - + -
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Residues in contact with VAL 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R PHE* 3.8 9.9 - - + -
34R THR* 3.3 2.4 - - - -
35R LEU* 2.7 58.0 + - + +
37R PHE* 5.5 0.7 - - + -
63R VAL* 4.0 26.9 - - + -
73R LEU* 3.9 26.7 - - + -
94R ILE* 5.3 2.5 - - + -
95R CYS* 1.3 76.4 - - - +
97R SER* 1.3 64.7 + - - +
106R GLU 3.2 9.6 - - - +
107R PHE* 3.7 33.4 - - + -
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Residues in contact with SER 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R PHE* 3.1 12.8 - - - -
34R THR* 3.4 19.3 - - - -
96R VAL* 1.3 78.3 - - - +
98R TRP* 1.3 62.8 + - - +
104R ILE 3.9 0.7 + - - +
105R ALA* 3.3 4.3 - - - +
106R GLU* 2.8 55.0 + - - +
108R TRP* 5.6 1.3 - - - -
163R VAL* 3.7 23.3 - - - +
164R LEU 4.9 1.6 - - - -
169R ILE* 5.6 2.9 - - - -
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Residues in contact with TRP 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R LEU 4.2 2.2 - - - -
31R GLN 3.5 20.4 - - - -
32R ASN* 3.4 5.0 - - - -
33R PHE* 3.0 55.0 + + + -
73R LEU* 4.2 4.9 - - + -
75R ILE* 3.7 26.7 - - + +
97R SER* 1.3 77.2 - - - +
99R GLU* 1.3 65.6 + - - +
100R SER* 3.7 10.8 - - - -
103R GLY 3.3 17.9 + - - -
104R ILE 3.4 11.2 - - - -
105R ALA* 4.0 2.5 - - + -
119R LEU* 3.0 37.2 + - + +
120R ARG 3.2 22.7 - - - -
123R TYR 3.1 28.3 - - - -
125R VAL* 3.6 27.6 - - + -
163R VAL* 3.6 5.9 - - - +
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Residues in contact with GLU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Q LYS* 2.7 33.3 + - - -
32R ASN* 3.6 17.9 - - - +
98R TRP* 1.3 81.0 - - - +
100R SER* 1.3 54.9 + - - +
101R SER* 3.7 18.6 + - - +
102R SER* 2.7 22.2 + - - +
103R GLY* 2.7 36.6 + - - -
104R ILE* 3.2 9.3 + - + +
163R VAL* 3.8 21.7 - - + +
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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
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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