Contacts of the strand formed by residues 82 - 90 (chain A) in PDB entry 2XWB
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 LYS 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PHE 5.4 4.0 - - - +
74A PHE* 3.0 56.7 + - + -
75A LYS* 3.1 25.0 - - - +
78A LYS* 6.6 0.2 - - - +
79A GLY 5.6 5.8 - - - -
81A ASN* 1.3 80.2 - - - +
83A PHE* 1.3 66.4 + - - +
100A LEU* 3.7 3.0 - - - +
101A VAL* 3.0 36.9 + - + +
103A LEU* 3.7 33.5 - - + +
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASP* 4.1 1.0 - - - +
40A PHE* 3.2 48.5 + + + +
74A PHE* 4.9 3.6 - - - -
81A ASN* 3.8 16.8 - - + -
82A LYS* 1.3 73.7 - - - +
84A VAL* 1.3 68.9 + - - +
98A VAL* 3.6 22.7 - - + -
99A VAL 3.5 6.7 - - - +
100A LEU* 3.4 43.1 - - + -
101A VAL* 3.9 1.6 - - - -
634A GLN* 5.9 0.7 - - + -
635A ARG 3.7 18.6 - - - -
636A ALA* 4.5 6.5 - - + -
1013B GLU* 3.4 42.2 - - + -
1017B LEU* 4.7 14.1 - - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.6 27.6 - - + -
37A VAL* 4.1 4.5 - - + -
38A HIS 3.2 17.5 - - - +
39A ASP* 4.1 2.5 - - - -
40A PHE* 4.7 0.2 - - - -
47A LEU* 3.8 17.3 - - + -
68A ILE* 4.3 10.8 - - + -
74A PHE* 4.3 12.8 - - + -
83A PHE* 1.3 81.1 - - - +
85A THR* 1.3 57.6 + - - +
86A VAL* 3.2 9.1 + - + -
98A VAL* 3.6 4.7 - - - -
99A VAL 3.0 29.5 + - - +
101A VAL* 3.5 24.0 - - + -
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR 3.7 1.9 - - - +
37A VAL* 4.6 0.2 - - - -
38A HIS* 3.0 43.2 + - - +
39A ASP 3.0 18.6 + - - -
40A PHE* 3.7 17.5 - - - -
42A GLY 4.7 2.5 + - - -
84A VAL* 1.3 68.2 - - - +
86A VAL* 1.3 65.1 + - - +
87A GLN* 3.3 6.9 + - + +
96A GLU* 4.5 21.1 - - + +
97A LYS 4.4 3.4 - - - +
98A VAL* 4.4 12.3 - - + +
1021B GLN* 6.1 0.4 - - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 5.5 1.1 - - + -
8A THR* 4.8 9.2 - - + +
12A LEU* 3.7 23.6 - - + -
20A MET* 3.5 35.4 - - + -
36A THR 4.3 1.8 - - - -
37A VAL* 4.4 17.0 - - + -
66A PHE* 5.1 2.7 - - + -
84A VAL* 3.2 9.3 + - + +
85A THR* 1.3 69.4 - - - +
87A GLN* 1.3 59.4 + - - +
95A VAL 4.5 0.3 - - - +
96A GLU* 3.6 1.0 - - - +
97A LYS* 2.9 42.7 + - + +
99A VAL* 3.7 24.2 - - + -
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR 5.9 0.2 - - - +
35A VAL* 3.4 9.6 - - - +
36A THR* 2.8 42.7 + - - +
38A HIS* 3.1 30.1 + - - -
43A LYS* 6.0 1.2 - - - +
85A THR* 3.3 7.9 + - + +
86A VAL* 1.3 77.7 - - - +
88A ALA* 1.3 65.1 + - - +
89A THR* 4.4 5.7 + - - +
94A VAL* 3.2 30.5 - - + +
95A VAL 3.8 2.5 - - - -
96A GLU* 4.1 20.8 + - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 5.0 5.2 - - + -
20A MET* 4.2 13.2 - - + -
22A LEU* 4.4 7.2 - - + -
33A VAL* 4.8 1.1 - - + -
34A THR 4.0 4.0 - - - -
35A VAL* 4.1 17.7 - - + +
87A GLN* 1.3 78.5 - - - +
89A THR* 1.3 62.5 + - - +
90A PHE* 3.8 19.8 - - + -
95A VAL* 2.9 41.2 + - + +
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.2 8.9 - - - +
34A THR* 3.1 46.4 + - - +
87A GLN* 4.4 6.8 + - - +
88A ALA* 1.3 73.3 - - - +
90A PHE* 1.3 62.9 + - - +
91A GLY 3.5 26.4 + - - +
92A THR* 4.1 13.7 - - - +
93A GLN 3.9 4.3 - - - +
94A VAL* 3.8 17.0 - - + +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.5 53.9 + + + -
5A SER 3.7 15.9 - - - -
6A ILE* 5.2 0.9 - - + -
22A LEU* 3.6 31.9 - - + -
23A GLU 3.7 15.7 - - - -
31A VAL* 4.3 9.7 - - + +
32A PRO 3.7 7.4 - - - -
33A VAL* 3.6 20.6 - - + -
54A LEU* 4.5 8.1 - - + -
88A ALA* 3.8 24.2 - - + -
89A THR* 1.3 69.9 - - - +
91A GLY* 1.3 58.4 + - - +
92A THR 3.0 8.3 + - - -
93A GLN* 2.9 25.8 + - - +
95A VAL* 4.0 15.7 - - + -
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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