Contacts of the strand formed by residues 87 - 94 (chain B) in PDB entry 2W9F
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 ILE 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.4 15.9 - - + -
37B VAL 3.5 1.9 - - - +
38B ARG* 3.4 4.9 - - - -
39B VAL* 2.8 44.2 + - + +
40B PRO 4.7 2.0 - - - +
41B ASN* 3.5 35.2 - - + +
48B GLY* 4.5 1.8 - - - +
49B LEU* 4.0 32.8 - - + +
50B PRO* 4.8 2.0 - - + -
79B ALA* 3.9 26.5 - - + -
80B THR 4.4 1.8 - - - +
81B SER 3.1 18.2 - - - +
82B ARG* 5.2 0.2 - - - -
86B GLU* 1.3 81.0 - - - +
88B LYS* 1.3 65.3 + - - +
89B VAL* 3.9 3.6 - - + -
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Residues in contact with LYS 88 (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 SER* 5.8 7.0 - - - -
37B VAL 3.7 4.3 - - - +
38B ARG* 3.2 53.9 - - + +
78B CYS 3.7 0.9 - - - +
79B ALA* 3.3 1.4 - - - -
80B THR* 2.9 44.3 + - - +
81B SER* 3.7 23.8 - - - +
86B GLU* 4.9 5.4 - - - +
87B ILE* 1.3 76.3 - - - +
89B VAL* 1.3 63.1 + - - +
90B THR* 3.7 2.5 + - - +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 4.1 23.8 - - + -
36B SER* 3.3 4.5 - - - -
37B VAL* 3.0 45.9 + - + +
39B VAL* 4.1 24.2 - - + -
49B LEU* 5.1 1.1 - - + -
53B THR* 4.6 5.8 - - + -
57B VAL* 5.1 4.9 - - + -
77B VAL* 3.5 31.0 - - + -
78B CYS 3.6 4.3 - - - +
79B ALA* 4.0 13.5 - - + +
87B ILE* 4.6 3.6 - - + +
88B LYS* 1.3 73.2 - - - +
90B THR* 1.3 60.4 + - - +
91B LEU* 3.6 9.1 + - + +
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Residues in contact with THR 90 (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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5B ARG* 5.8 7.1 + - - +
6B TYR* 6.1 1.3 - - + -
34B LEU* 4.2 30.3 - - + -
35B LYS 3.4 11.9 - - - +
36B SER* 4.1 9.4 + - - +
77B VAL* 3.4 5.2 - - - +
78B CYS* 2.6 49.7 + - + +
80B THR* 4.5 9.8 + - - +
88B LYS* 4.4 5.7 + - - +
89B VAL* 1.3 70.8 - - - +
91B LEU* 1.3 63.2 + - - +
92B VAL* 3.7 5.8 + - + +
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Residues in contact with LEU 91 (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 ALA 3.3 5.5 - - - +
34B LEU* 3.5 2.8 - - - -
35B LYS* 2.9 41.7 + - + +
37B VAL* 4.9 7.9 - - + -
57B VAL* 4.8 10.1 - - + -
74B LEU* 4.3 8.3 - - + -
76B ASP 4.3 0.4 - - - -
77B VAL* 3.5 34.3 - - + -
89B VAL* 3.6 12.5 + - + +
90B THR* 1.3 71.4 - - - +
92B VAL* 1.3 60.7 + - - +
93B PHE* 3.1 25.9 - - + -
161B LEU* 3.4 33.7 - - + -
164B ILE* 5.3 2.9 - - + -
165B TYR* 4.3 15.5 - - + +
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Residues in contact with VAL 92 (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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6B TYR* 3.7 32.3 - - + +
32B VAL* 3.0 28.9 - - + -
33B ALA 3.7 2.7 - - - -
34B LEU* 3.4 20.2 - - + -
74B LEU* 3.0 7.8 - - - +
75B MET* 2.9 32.5 + - + -
76B ASP* 3.1 32.8 + - + +
77B VAL 5.0 0.2 - - - +
78B CYS* 5.7 2.7 - - + +
90B THR* 3.7 11.6 + - + +
91B LEU* 1.3 71.2 - - - +
93B PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 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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32B VAL* 3.1 24.8 - - - +
33B ALA* 2.8 25.5 + - + +
35B LYS* 3.8 24.7 - - + -
60B LEU* 6.3 3.1 - - + -
72B VAL* 4.1 25.6 - - + -
73B ARG 3.5 5.4 - - - -
74B LEU* 4.1 27.4 - - + -
75B MET* 4.2 5.5 - - - +
91B LEU* 3.1 49.4 - - + -
92B VAL* 1.3 73.6 - - - +
94B GLU* 1.3 69.4 + - - +
157B ALA 4.6 8.3 - - - -
158B ASP* 4.8 1.6 - - - -
159B PHE* 5.2 9.4 - + - -
161B LEU* 4.2 17.9 - - + -
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Residues in contact with GLU 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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31B PHE 4.9 0.9 - - - -
33B ALA* 4.4 3.9 - - - +
71B VAL 3.9 2.1 - - - +
72B VAL* 3.5 23.2 - - + +
73B ARG* 2.9 68.3 + - + +
75B MET* 4.4 8.1 - - - -
93B PHE* 1.3 81.2 - - - +
95B HIS* 1.3 67.8 + - - +
96B VAL* 3.9 3.9 + - + -
147B LEU* 4.9 3.5 - - - +
155B LYS* 3.0 35.0 + - - +
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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