Contacts of the strand formed by residues 46 - 53 (chain B) in PDB entry 1WSQ
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B VAL* 3.2 7.1 - - - +
39B PHE* 2.8 41.8 + - + +
44B GLN 3.9 10.1 - - - +
45B GLN* 1.3 80.8 - - - +
47B THR* 1.3 62.3 + - - +
63B VAL* 3.8 16.8 - - + -
64B ARG 3.3 13.2 - - - +
65B THR* 4.2 14.4 - - + -
73B LEU* 3.8 31.4 - - + -
123B LEU* 6.2 0.7 - - + -
125B LEU* 4.2 24.9 - - + -
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Residues in contact with THR 47 (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 GLY* 3.9 23.3 - - - +
37B ARG 3.5 3.4 - - - +
38B VAL* 3.6 15.9 - - + +
45B GLN* 5.6 0.5 - - - +
46B VAL* 1.3 74.4 - - - +
48B VAL* 1.3 71.1 + - - +
49B ASP* 4.3 2.2 - - - +
63B VAL* 3.2 6.2 - - - -
64B ARG* 2.9 64.1 + - - +
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Residues in contact with VAL 48 (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 TYR 3.3 29.4 - - - +
35B ILE* 4.1 5.0 - - + +
36B GLY* 3.0 25.3 + - - -
37B ARG 2.8 17.2 + - - +
39B PHE* 3.4 36.1 - - + -
46B VAL 5.6 0.2 - - - +
47B THR* 1.3 74.3 - - - +
49B ASP* 1.3 64.5 + - - +
50B GLU 3.7 18.4 - - - +
61B PHE* 3.6 30.1 - - + -
62B LEU 3.8 4.0 - - - +
63B VAL* 4.1 4.0 - - + -
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Residues in contact with ASP 49 (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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77A PHE* 5.4 3.5 - - - -
35B ILE* 3.5 23.4 - - - +
47B THR* 3.5 3.0 + - - +
48B VAL* 1.3 79.1 - - - +
50B GLU* 1.3 71.7 + - + +
62B LEU* 2.7 23.4 + - + +
63B VAL 4.6 0.2 - - - -
64B ARG* 3.1 50.5 + - - +
70B LYS* 3.5 14.0 - - - +
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Residues in contact with GLU 50 (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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34A TYR* 5.2 1.0 + - - -
37A ARG* 3.0 39.0 + - - -
75A ARG* 3.0 34.6 + - - -
77A PHE* 4.0 14.1 - - + -
114A VAL* 3.9 13.8 - - + +
35B ILE* 3.8 7.6 - - - -
48B VAL* 3.7 4.5 - - - +
49B ASP* 1.3 89.6 - - + +
51B VAL* 1.3 68.0 + - - +
52B LEU* 4.9 4.1 - - + +
61B PHE* 3.4 6.1 - - - +
62B LEU* 2.8 38.0 + - + +
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Residues in contact with VAL 51 (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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114A VAL* 3.1 24.0 + - - +
115A SER* 3.7 33.2 - - - +
116A SER* 5.1 6.5 - - - +
34B TYR* 4.0 13.9 - - + -
35B ILE* 4.2 1.3 - - + +
50B GLU* 1.3 77.2 - - - +
52B LEU* 1.3 63.6 + - - +
53B ALA* 4.0 12.3 - - - +
54B GLU* 5.0 4.3 - - + +
59B ILE* 3.8 24.2 - - + -
60B VAL 3.9 3.1 - - - +
61B PHE* 3.8 24.2 - - + -
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Residues in contact with LEU 52 (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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37A ARG* 4.8 10.3 - - - +
50B GLU* 3.8 4.9 + - + +
51B VAL* 1.3 75.5 - - - +
53B ALA* 1.3 62.0 + - - +
60B VAL* 2.7 27.8 + - + +
61B PHE 3.8 7.6 - - - +
62B LEU* 3.7 36.3 - - + +
72B ALA* 4.4 4.7 - - + -
128B PHE* 3.9 35.4 - - + -
133B GLN* 5.1 1.6 + - - -
404B KSA 4.0 37.5 - - + -
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Residues in contact with ALA 53 (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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51B VAL* 3.7 6.0 - - - -
52B LEU* 1.3 81.4 - - - +
54B GLU* 1.3 61.8 + - - +
55B GLY 3.9 0.9 - - - -
59B ILE* 3.5 4.3 - - - +
60B VAL* 2.9 28.9 + - - +
133B GLN* 4.5 4.9 - - - +
404B KSA 3.4 50.0 - - + +
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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