Contacts of the strand formed by residues 59 - 63 (chain B) in PDB entry 3VAS
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 ASN 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS* 2.8 28.1 + - - +
18B ASP 3.6 0.3 - - - +
19B ILE* 3.6 4.3 - - - +
20B ILE* 2.8 50.8 + - + +
57B LYS 5.1 1.1 - - - +
58B LEU* 1.3 74.8 - - - +
60B TYR* 1.3 68.8 + - - +
61B ILE* 3.5 24.0 - - - +
336B SER* 5.7 5.3 + - - -
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 4.9 2.5 - - - -
92A ASP* 4.1 11.2 - - - +
93A ILE* 3.7 51.2 + - + -
96A LYS* 3.2 27.9 + - + +
17B LEU* 3.9 26.0 - - + -
18B ASP 3.4 3.6 - - - +
19B ILE* 4.2 14.6 - - + -
53B GLN* 3.2 36.3 + - - -
58B LEU* 3.4 27.8 - - + +
59B ASN* 1.3 83.2 + - - +
61B ILE* 1.3 62.0 + - - +
94B GLN* 6.1 1.6 - - - -
97B TYR* 3.2 13.3 + - + -
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Residues in contact with ILE 61 (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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96A LYS* 3.5 10.8 - - - +
17B LEU* 3.6 6.2 - - - +
18B ASP* 2.7 50.5 + - + +
20B ILE* 4.2 16.8 - - + -
59B ASN* 3.5 26.7 - - - +
60B TYR* 1.3 80.0 - - - +
62B ALA* 1.3 73.9 + - - +
71B LYS* 5.0 2.5 - - - +
97B TYR* 4.5 2.7 - - - +
336B SER 5.6 4.0 - - - +
337B GLY* 6.4 1.1 - - - -
338B PHE* 3.6 29.6 - - + +
339B SER* 5.3 10.8 - - - -
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Residues in contact with ALA 62 (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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16B LEU 4.0 3.6 - - - -
17B LEU* 4.4 1.6 - - - -
18B ASP* 4.8 0.2 - - - +
61B ILE* 1.3 83.0 - - - +
63B GLY* 1.3 58.8 + - - +
67B LEU* 5.1 4.5 - - + -
68B ASN* 3.9 2.1 - - - +
71B LYS* 3.1 21.1 + - - +
97B TYR* 3.8 11.3 + - + -
98B ILE* 4.0 27.6 - - + -
101B ASP* 3.8 36.3 + - + +
102B CYS* 6.3 0.2 - - - -
338B PHE* 5.0 1.0 - - - +
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Residues in contact with GLY 63 (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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16B LEU 2.6 28.7 + - - +
18B ASP* 3.8 7.6 - - - -
61B ILE 3.4 1.4 + - - -
62B ALA* 1.3 75.0 - - - +
64B GLY* 1.3 63.7 + - - +
67B LEU* 3.5 24.5 - - - +
68B ASN* 3.6 10.8 - - - -
401B ADN 3.8 9.9 - - - -
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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