Contacts of the strand formed by residues 47 - 53 (chain B) in PDB entry 2W3B
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 GLN 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B THR 5.9 0.2 - - - -
41B SER* 4.7 3.1 - - - -
45B GLY 6.0 0.2 - - - -
46B LYS* 1.3 78.3 - - - +
48B ASN* 1.3 69.9 + - - +
69B GLY* 3.5 34.8 + - - +
70B ARG 3.7 18.2 - - - +
71B ILE* 3.7 17.1 - - + +
87B HIS* 6.0 0.2 - - - -
108B LYS 3.0 6.0 + - - +
109B VAL* 3.3 7.8 - - - -
110B ASP* 2.9 21.4 + - - -
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Residues in contact with ASN 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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38B THR 2.9 30.6 + - - +
39B THR 3.6 3.3 + - - +
40B THR 3.0 28.4 + - - -
41B SER* 3.4 17.5 - - - -
47B GLN* 1.3 75.9 - - - +
49B LEU* 1.3 60.0 - - - +
69B GLY 4.6 2.8 + - - -
70B ARG* 3.4 9.5 - - + -
71B ILE* 2.9 25.8 + - - +
110B ASP* 3.5 0.3 - - - +
111B MET* 3.0 38.2 + - - +
113B TRP* 3.6 16.4 - - + +
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Residues in contact with LEU 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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47B GLN 3.9 0.8 + - - -
48B ASN* 1.3 72.8 - - - +
50B VAL* 1.3 61.1 + - - +
51B ILE* 3.9 28.5 - - + -
71B ILE* 3.4 36.3 - - + +
73B LEU* 3.9 28.0 - - + -
88B PHE* 5.4 0.2 - - + -
96B ALA 4.9 0.9 - - - +
97B LEU* 5.4 0.4 - - + -
100B THR* 3.6 29.8 - - + -
105B LEU* 5.4 3.8 - - + -
109B VAL* 3.9 18.8 - - + +
111B MET 2.8 8.0 + - - +
112B VAL* 3.5 10.6 - - + +
113B TRP* 2.9 30.1 + - - +
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Residues in contact with VAL 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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38B THR* 4.0 18.4 - - - +
48B ASN 4.1 0.4 + - - -
49B LEU* 1.3 75.9 - - - +
51B ILE* 1.3 61.3 + - - +
52B MET* 4.0 12.2 - - + +
67B LEU* 4.2 10.3 - - + -
70B ARG* 4.0 28.3 - - + -
71B ILE 2.8 20.1 + - - +
72B ASN* 3.8 25.4 - - - +
73B LEU* 2.9 30.5 + - - +
113B TRP* 3.3 6.7 - - + +
115B VAL* 4.1 21.1 - - + -
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Residues in contact with ILE 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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49B LEU* 3.9 20.2 - - + -
50B VAL* 1.3 77.5 - - - +
52B MET* 1.3 62.4 + - - +
73B LEU* 3.4 12.8 - - + -
75B LEU* 3.9 34.5 - - + -
93B LEU* 3.8 26.5 - - + -
96B ALA* 3.8 15.9 - - + -
97B LEU* 4.1 4.0 - - + -
112B VAL* 3.7 25.6 - - + -
113B TRP 2.9 9.6 + - - +
114B ILE* 3.6 8.1 - - + +
115B VAL* 3.0 25.9 + - - +
116B GLY 4.2 0.5 + - - -
120B VAL* 4.4 5.2 - - + -
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Residues in contact with MET 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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50B VAL* 4.0 23.6 - - + +
51B ILE* 1.3 75.8 - - - +
53B GLY* 1.3 69.4 + - - +
56B THR* 3.9 7.2 - - + -
57B TRP* 3.6 38.6 - - + -
60B ILE* 3.7 21.5 - - + -
67B LEU* 4.3 2.5 - - + -
72B ASN* 3.9 24.0 - - + +
73B LEU 3.0 11.5 + - - +
74B VAL* 3.3 4.5 - - + -
75B LEU* 2.8 26.8 + - - -
115B VAL* 3.6 17.9 - - + -
116B GLY 3.1 12.1 - - - +
120B VAL* 4.4 5.2 - - - -
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Residues in contact with GLY 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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52B MET* 1.3 78.2 - - - +
54B LYS* 1.3 65.6 + - - -
55B LYS 3.4 2.9 - - - -
56B THR* 3.3 1.7 + - - -
57B TRP* 3.1 18.7 + - - +
74B VAL* 4.3 0.7 - - - -
75B LEU* 3.9 5.8 - - - -
116B GLY 2.8 14.1 + - - -
120B VAL* 3.7 9.8 - - - +
201B NDP 3.5 27.8 - - - -
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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