Contacts of the strand formed by residues 57 - 67 (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 ARG 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ASN* 3.5 8.6 - - - +
54B THR* 2.9 46.2 + - - +
55B GLN 3.5 8.7 - - - +
56B GLY* 1.3 84.4 - - - +
58B ASP* 1.3 63.3 + - - +
60B GLU* 3.4 14.2 + - - +
77B ARG* 3.3 30.1 - - - +
123B TYR* 2.8 36.7 + - - -
124B PHE 4.8 0.6 + - - -
126B GLU* 3.7 24.5 + - + +
139B SER 6.4 0.4 - - - -
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Residues in contact with ASP 58 (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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53B ASN* 2.9 12.3 + - - +
56B GLY 4.2 1.0 + - - -
57B ARG* 1.3 72.9 - - - +
59B ASN* 1.3 78.1 + - - +
60B GLU 3.2 0.2 - - - -
77B ARG* 2.9 35.7 + - + +
137B GLN 2.8 11.8 - - - +
138B ASP* 3.3 21.1 - - - +
304B CA 2.4 31.1 - - - -
342B CPJ 3.2 6.9 - - - +
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Residues in contact with ASN 59 (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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53B ASN* 2.9 12.4 + - - -
58B ASP* 1.3 77.9 + - - +
60B GLU* 1.3 63.7 + - - +
61B LEU* 3.3 3.8 + - - +
62B LEU* 3.9 13.0 - - + -
74B TYR* 3.9 29.2 - - + +
76B GLY 3.5 0.7 + - - -
77B ARG* 2.8 27.6 + - + +
136B GLU* 2.8 10.3 - - - +
304B CA 2.3 27.6 - - - -
342B CPJ 2.9 37.9 + - - +
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Residues in contact with GLU 60 (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 TYR* 3.4 26.9 + - + +
54B THR* 3.8 30.3 - - - +
57B ARG* 3.4 11.6 + - - +
58B ASP 3.1 2.7 + - - -
59B ASN* 1.3 77.2 - - - +
61B LEU* 1.3 60.5 + - - +
75B ILE* 3.4 7.3 - - - +
76B GLY* 2.7 21.9 + - - +
77B ARG* 3.1 20.8 + - - +
123B TYR* 2.6 30.8 + - - -
125B VAL* 3.2 9.9 - - + +
126B GLU* 2.8 30.7 + - - +
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Residues in contact with LEU 61 (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* 3.5 45.3 - - + -
35B LEU* 5.3 0.4 - - + -
50B PHE* 3.9 14.9 - - + +
52B TYR* 2.9 61.7 + - + +
60B GLU* 1.3 78.4 - - - +
62B LEU* 1.3 66.0 + - - +
63B VAL* 4.7 3.1 - - + -
73B LEU* 3.8 14.4 - - + -
74B TYR 3.2 5.8 - - - +
75B ILE* 4.7 3.4 - - + -
125B VAL* 4.5 10.8 - - + -
159B MET* 3.8 23.6 - - + -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 3.2 28.3 - - - +
50B PHE 3.4 11.4 - - - +
51B SER* 4.0 7.4 - - - +
52B TYR 5.2 0.2 - - - +
53B ASN* 5.9 0.2 - - - +
59B ASN* 3.8 15.3 - - - +
61B LEU* 1.3 76.8 - - - +
63B VAL* 1.3 66.1 + - - +
64B TYR* 3.9 8.2 + - + -
72B SER 3.6 0.9 - - - +
73B LEU* 3.3 6.7 - - - +
74B TYR* 2.8 65.3 + - + -
136B GLU* 3.5 27.8 - - + +
342B CPJ 3.6 20.9 - - + -
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Residues in contact with VAL 63 (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* 3.9 19.3 - - + -
37B PHE* 4.4 9.9 - - + -
48B SER* 3.8 2.8 + - - -
49B LEU* 2.8 46.4 + - + -
50B PHE* 3.0 22.5 + - + +
61B LEU* 4.7 1.1 - - + -
62B LEU* 1.3 74.3 - - - +
64B TYR* 1.3 62.5 + - - +
71B TYR* 5.2 2.2 - - + -
72B SER 3.5 5.4 - - - +
73B LEU* 4.1 10.5 - - + -
94B ILE* 5.0 2.5 - - + -
96B VAL* 3.9 24.7 - - + -
107B PHE* 4.0 24.0 - - + -
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Residues in contact with TYR 64 (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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46B ALA* 3.5 31.8 - - + +
47B TYR 3.7 19.7 - - - -
48B SER* 3.9 14.6 - - - -
49B LEU* 4.8 2.0 - - - -
62B LEU* 4.0 7.6 - - + -
63B VAL* 1.3 74.4 - - - +
65B LYS* 1.3 59.9 + - - +
66B GLU* 3.6 29.1 + - + -
71B TYR* 3.9 1.3 - - - +
72B SER* 2.8 37.3 + - - +
74B TYR* 3.9 31.4 - + + -
136B GLU* 4.5 2.2 - - + -
148B GLN* 3.1 41.3 + - + +
342B CPJ 4.0 23.8 - - + -
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Residues in contact with LYS 65 (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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43B LEU 6.0 0.2 + - - -
45B ARG 4.4 1.4 - - - +
46B ALA* 3.1 2.1 - - - -
47B TYR* 2.9 74.1 + - + +
49B LEU* 3.9 9.7 - - + +
64B TYR* 1.3 71.2 - - - +
66B GLU* 1.3 66.4 + - - +
67B ARG 3.3 26.7 - - - +
68B VAL* 3.9 13.5 - - - +
69B GLY 4.1 0.4 - - - +
70B GLU 3.6 8.3 - - - +
71B TYR* 3.4 39.3 + - + -
86B GLU* 2.7 29.9 + - - -
88B PHE* 5.8 3.2 - - - -
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Residues in contact with GLU 66 (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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44B SER 4.9 0.3 - - - +
45B ARG 4.4 0.2 - - - -
46B ALA* 3.3 29.2 + - - +
64B TYR* 3.6 27.8 + - + -
65B LYS* 1.3 72.5 - - - +
67B ARG* 1.3 85.8 + - - +
70B GLU* 3.7 23.1 + - + +
72B SER* 4.2 16.2 - - - +
74B TYR* 5.8 0.7 - - - -
79B LYS* 4.5 16.6 + - - -
81B THR* 5.7 1.8 - - + +
342B CPJ 5.8 2.6 - - - +
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Residues in contact with ARG 67 (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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44B SER 4.4 12.3 - - - +
45B ARG 5.4 1.3 - - - -
65B LYS* 3.3 12.9 - - - +
66B GLU* 1.3 103.3 + - - +
68B VAL* 1.3 72.5 + - - +
70B GLU* 2.9 64.4 + - - +
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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