Contacts of the strand formed by residues 92 - 99 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ARG* 3.3 7.9 - - - +
39B ALA* 2.9 47.8 + - + +
71B TYR* 3.6 22.2 - - - +
86B GLU* 4.4 4.9 - - + +
90B ALA 4.3 4.7 - - - +
91B PRO* 1.3 75.6 - - - +
93B HIS* 1.3 66.3 + - - +
94B ILE* 3.7 26.0 + - + -
109B ILE* 3.7 20.9 - - + -
110B ASN* 3.5 13.5 - - - +
203B TRP* 4.8 0.6 - - - -
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Residues in contact with HIS 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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36B CYS* 4.1 9.9 - - + +
37B PHE* 3.6 16.4 + - - -
38B ARG* 3.8 34.5 - - + +
92B VAL* 1.3 74.6 - - - +
94B ILE* 1.3 64.2 + - - +
95B CYS* 3.3 33.2 + - - -
108B TRP 3.5 1.5 + - - +
109B ILE* 3.4 4.9 - - - -
110B ASN* 2.8 39.7 + - - +
111B GLY 4.9 3.4 + - - -
156B ASP* 5.1 3.7 + - + +
169B ILE* 5.7 0.6 - - + +
172B ALA* 3.7 12.4 + - - +
173B TYR* 3.5 51.3 - + + +
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Residues in contact with ILE 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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35B LEU 3.8 0.5 - - - +
36B CYS* 3.1 3.5 - - - +
37B PHE* 2.8 79.2 + - + +
39B ALA* 4.8 1.6 - - + -
49B LEU* 4.1 10.1 - - + -
63B VAL* 5.0 2.2 - - + -
71B TYR* 3.5 28.7 - - + -
92B VAL* 3.7 25.8 - - + +
93B HIS* 1.3 77.7 - - - +
95B CYS* 1.3 67.3 + - - +
96B VAL* 4.8 1.3 - - + +
107B PHE* 4.1 30.1 - - + -
108B TRP 3.5 2.0 - - - -
109B ILE* 4.1 6.5 - - + -
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Residues in contact with CYS 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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34B THR* 4.9 0.2 - - + -
35B LEU 3.2 3.4 - - - -
36B CYS* 2.0 46.0 - - - -
93B HIS* 3.3 23.3 - - - -
94B ILE* 1.3 75.6 - - - +
96B VAL* 1.3 60.5 + - - +
106B GLU 4.3 0.7 - - - -
107B PHE* 3.4 5.2 - - - -
108B TRP* 2.6 48.9 + - + +
169B ILE* 3.7 34.1 - - + -
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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
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33B PHE* 3.9 10.4 - - + -
34B THR* 3.3 3.3 - - - -
35B LEU* 2.7 56.6 + - + +
37B PHE* 5.7 0.7 - - + -
63B VAL* 3.9 27.6 - - + -
73B LEU* 4.0 20.4 - - + -
94B ILE* 5.2 2.5 - - + -
95B CYS* 1.3 74.8 - - - +
97B SER* 1.3 68.7 + - - +
105B ALA* 5.2 0.4 - - + -
106B GLU 3.2 11.7 - - - +
107B PHE* 3.7 32.8 - - + -
169B ILE* 6.1 0.2 - - - -
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Residues in contact with SER 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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33B PHE* 3.1 14.1 - - - -
34B THR* 3.4 18.8 - - - -
96B VAL* 1.3 77.5 - - - +
98B TRP* 1.3 62.0 + - - +
104B ILE 4.4 1.3 + - - -
105B ALA* 3.3 5.7 - - - +
106B GLU* 2.9 51.2 + - - +
108B TRP* 5.2 2.2 + - - -
163B VAL* 3.6 23.0 - - - +
164B LEU 4.8 2.3 + - - -
169B ILE* 5.6 3.1 - - - -
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Residues in contact with TRP 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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30B LEU 3.9 6.7 - - - -
31B GLN 3.6 17.7 - - - -
32B ASN* 3.5 4.2 - - - -
33B PHE* 3.0 56.3 + + + -
73B LEU* 4.1 5.6 - - + -
75B ILE* 3.8 26.4 - - + +
97B SER* 1.3 75.8 - - - +
99B GLU* 1.3 67.8 + - - +
100B SER* 3.6 10.8 - - - -
103B GLY 3.4 17.6 + - - -
104B ILE 3.3 10.8 - - - -
105B ALA* 4.2 2.5 - - + -
119B LEU* 3.0 36.6 + - + +
120B ARG 3.3 22.2 - - - -
123B TYR 3.2 26.9 - - - -
125B VAL* 3.6 26.0 - - + -
163B VAL* 3.5 5.4 - - - +
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Residues in contact with GLU 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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199A LYS* 2.6 28.7 + - - -
32B ASN* 3.6 15.5 - - - +
98B TRP* 1.3 81.5 - - - +
100B SER* 1.3 53.6 + - - +
101B SER* 3.6 21.1 + - - +
102B SER* 2.5 27.2 + - - +
103B GLY* 2.7 36.7 + - - -
104B ILE* 3.1 10.3 + - + +
163B VAL* 3.8 19.8 - - + +
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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