Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 2VSC
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 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 4.2 14.6 - - + -
30B ALA* 3.5 31.4 - - + -
32B ASN 4.0 8.7 - - - +
33B THR* 3.0 12.1 + - - +
35B GLU* 1.3 79.9 - - - +
37B TYR* 1.3 70.7 + - - +
38B VAL* 4.3 1.3 - - + -
50B PHE* 4.0 2.5 - - - -
52B GLY* 3.0 27.7 + - - -
53B ALA 4.6 0.3 + - - -
73B LEU* 3.5 38.1 - - + -
74B LEU* 4.2 8.3 - - + -
98B VAL* 4.4 3.1 - - + -
99B THR 3.4 7.2 - - - +
100B GLU* 4.7 2.9 - - + -
101B LEU* 5.3 1.5 - - - +
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Residues in contact with TYR 37 (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 GLU 4.1 0.2 + - - -
36B VAL* 1.3 75.8 - - - +
38B VAL* 1.3 81.8 + - - +
39B LYS* 4.1 26.9 - - + -
49B THR* 3.9 21.2 + - - +
50B PHE 3.4 8.5 - - - -
51B ASP* 3.6 40.3 + - + +
97B GLU* 3.8 6.4 - - - +
98B VAL* 3.4 4.7 - - - +
99B THR* 2.9 48.0 + - - +
101B LEU* 5.0 15.9 - - + -
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Residues in contact with VAL 38 (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 VAL* 4.3 2.7 - - + -
37B TYR* 1.3 84.2 - - - +
39B LYS* 1.3 65.6 + - - +
40B TRP* 3.9 28.3 - - + +
48B TYR* 4.8 2.7 - - + -
49B THR* 3.2 5.8 - - - -
50B PHE* 2.9 42.4 + - + +
68B ILE* 4.3 9.9 - - + -
73B LEU* 3.6 42.2 - - + -
78B ALA* 4.4 10.5 - - + -
96B CYS* 4.9 1.3 - - - -
97B GLU 3.4 7.9 - - - +
98B VAL* 4.4 9.4 - - + -
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Residues in contact with LYS 39 (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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37B TYR* 4.1 22.0 - - + -
38B VAL* 1.3 75.8 - - - +
40B TRP* 1.3 63.5 + - - +
41B LYS* 3.3 25.4 + - + +
46B ASP* 3.3 41.2 + - + +
48B TYR 3.4 3.6 - - - +
49B THR* 4.3 7.6 - - + -
95B THR 3.6 1.7 - - - +
96B CYS* 3.7 0.9 - - - -
97B GLU* 2.8 62.4 + - + +
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Residues in contact with TRP 40 (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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109A ILE* 3.8 10.8 - - + -
21B ILE* 3.5 40.8 - - + -
23B CYS* 3.5 18.6 - - + -
38B VAL* 3.9 18.3 - - + +
39B LYS* 1.3 73.1 - - - +
41B LYS* 1.3 60.6 + - - +
46B ASP* 3.4 5.2 - - - +
47B ILE* 2.8 43.0 + - + -
48B TYR* 2.9 21.4 + + + -
68B ILE* 4.0 3.4 - - + +
78B ALA 2.9 29.3 + - - -
80B LEU* 3.4 42.7 - - + +
94B TYR* 3.9 15.5 - + + -
95B THR 3.2 15.7 - - - -
96B CYS* 3.6 20.1 - - + -
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Residues in contact with LYS 41 (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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106A GLU* 5.4 5.1 + - - -
39B LYS* 3.3 32.6 - - + +
40B TRP* 1.3 78.5 - - - +
42B PHE* 1.3 61.5 + - - +
44B GLY* 5.0 10.3 - - - +
45B ARG 3.1 13.7 - - - +
46B ASP* 3.6 17.3 - - - +
47B ILE* 4.3 2.2 - - - -
93B ASN 4.1 0.2 - - - +
94B TYR* 3.3 9.0 - - - +
95B THR* 2.8 56.8 + - + +
97B GLU* 3.7 21.4 + - - -
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Residues in contact with PHE 42 (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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41B LYS* 1.3 74.5 - - - +
43B LYS* 1.3 100.1 + - + +
44B GLY 3.1 0.6 + - - -
45B ARG* 3.0 29.7 + - - +
47B ILE* 4.0 14.5 - - + +
63B PHE* 4.2 3.1 - + + -
89B SER 5.1 0.7 - - - -
90B HIS* 3.5 50.3 - + + -
91B THR 3.3 25.1 - - - -
92B GLY* 3.9 9.0 - - - -
93B ASN 3.7 13.5 - - - -
94B TYR* 3.5 35.9 - + + -
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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