Contacts of the strand formed by residues 76 - 82 (chain B) in PDB entry 2WA2
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 GLY 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LYS* 1.3 75.7 - - - +
77B THR* 1.3 59.4 + - - -
78B VAL 3.6 0.3 + - - -
97B ASN 2.9 15.1 + - - -
98B VAL* 3.8 2.1 - - - +
99B ARG* 2.8 41.2 + - - -
100B GLU 3.3 8.8 + - - +
142B ASP* 3.4 11.9 - - - -
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Residues in contact with THR 77 (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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76B GLY* 1.3 70.3 - - - -
78B VAL* 1.3 65.9 + - - +
99B ARG* 5.6 0.9 - - - +
100B GLU* 2.7 40.4 + - + +
102B LYS* 4.7 9.9 - - + -
139B PHE* 5.0 3.8 - - + -
140B GLN* 3.9 22.6 + - - +
141B ALA* 3.7 7.5 - - + -
142B ASP* 2.8 46.4 + - - -
143B THR 3.1 6.2 + - - -
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Residues in contact with VAL 78 (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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74B LEU* 5.0 1.3 - - + -
75B LYS 3.7 19.7 - - - +
77B THR* 1.3 74.3 - - - +
79B VAL* 1.3 71.9 + - - +
92B ALA* 4.3 9.9 - - + -
98B VAL* 3.7 33.0 - - + -
100B GLU 2.9 9.8 + - - +
101B VAL* 3.3 12.0 - - + +
102B LYS* 2.8 26.2 + - - +
143B THR* 3.4 16.2 - - + +
145B LEU* 3.6 33.7 - - + -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 5.0 1.8 - - + -
78B VAL* 1.3 76.7 - - - +
80B ASP* 1.3 57.3 - - - +
81B LEU* 4.3 12.6 - - + -
102B LYS* 3.3 10.5 - - + +
104B TYR* 5.0 0.7 - - + -
139B PHE* 3.6 38.1 - - + -
141B ALA* 3.7 13.0 - - + -
143B THR 2.9 9.7 + - - +
144B VAL* 3.8 30.3 - - + -
145B LEU* 2.8 35.2 + - - +
172B TRP* 3.8 22.9 - - + -
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Residues in contact with ASP 80 (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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78B VAL 4.2 0.2 + - - -
79B VAL* 1.3 72.7 - - - +
81B LEU* 1.3 68.7 + - - +
82B GLY 3.7 1.2 + - - +
83B CYS* 3.2 24.5 - - - +
86B GLY 4.7 0.2 - - - +
88B TRP* 3.6 24.5 + - - +
89B SER* 2.6 42.4 + - - +
101B VAL* 4.6 5.6 - - + -
102B LYS 2.9 9.1 + - - +
103B ALA* 3.4 4.6 - - - -
104B TYR* 3.0 27.2 + - - +
145B LEU* 3.6 15.2 - - + +
147B ASP 4.9 1.2 + - - -
1267B SAM 4.9 1.4 + - - -
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Residues in contact with LEU 81 (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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79B VAL* 4.3 9.2 - - + -
80B ASP* 1.3 72.1 - - - +
82B GLY* 1.3 63.7 + - - +
104B TYR* 4.1 13.7 - - + -
133B VAL* 4.1 11.7 - - + -
136B MET* 3.4 31.9 - - + -
144B VAL* 4.3 5.4 - - + -
145B LEU 2.9 16.9 + - - +
146B CYS* 3.4 13.6 - - - -
147B ASP 3.4 22.0 + - - -
148B ILE* 4.1 2.5 - - - -
168B VAL* 4.8 7.0 - - + -
169B ILE* 3.9 25.1 - - + -
172B TRP* 3.6 35.7 - - + +
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Residues in contact with GLY 82 (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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80B ASP* 4.5 1.4 - - - +
81B LEU* 1.3 74.8 - - - +
83B CYS* 1.3 62.8 + - - -
84B GLY 3.3 3.6 - - - -
104B TYR 2.8 14.5 + - - -
133B VAL* 4.1 4.2 - - - +
147B ASP 4.5 2.9 + - - +
148B ILE* 3.6 12.8 - - - +
1267B SAM 3.3 52.1 + - - +
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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