Contacts of the strand formed by residues 134 - 139 (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 MET 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B LEU* 5.2 0.9 - - - +
37B ASN 2.9 15.5 + - - +
38B ILE* 3.5 33.1 - - + -
39B VAL* 3.1 26.5 + - - +
123B VAL* 3.7 24.7 - - + -
124B ALA 3.3 2.9 - - - -
125B VAL* 4.1 21.5 - - + -
132B ARG* 5.4 3.4 - - + -
133B SER* 1.3 80.4 + - - +
135B VAL* 1.3 64.5 + - - +
136B THR 4.1 0.2 - - - -
169B PHE* 6.3 0.4 - - + -
298B ASN* 3.7 27.4 - - + -
401B ADN 4.0 34.3 - - + +
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Residues in contact with VAL 135 (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 LEU* 3.6 41.1 - - + -
39B VAL* 3.5 7.0 - - + +
40B LEU 5.1 0.2 - - - -
41B ALA* 3.9 19.3 - - + -
45B HIS* 4.0 22.4 - - + -
48B ILE* 3.9 15.9 - - + -
49B TYR* 2.9 21.6 + - + +
123B VAL* 3.4 1.2 - - - -
124B ALA* 2.8 43.4 + - + +
126B LEU* 5.4 0.2 - - + -
133B SER 5.4 0.4 - - - +
134B MET* 1.3 77.0 - - - +
136B THR* 1.3 60.5 + - - +
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Residues in contact with THR 136 (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 17.9 - - + -
38B ILE* 3.8 7.0 - - - +
39B VAL 2.9 15.8 + - - -
40B LEU* 3.7 11.0 - - + +
41B ALA* 2.8 26.7 + - - +
49B TYR* 3.3 4.7 - - - -
122B LYS 3.7 2.7 - - - +
123B VAL* 3.6 12.7 - - + +
135B VAL* 1.3 71.7 - - - +
137B TYR* 1.3 63.4 + - - +
138B LEU* 4.0 14.4 + - + +
401B ADN 2.9 48.3 + - - +
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Residues in contact with TYR 137 (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* 4.2 0.7 - - - +
41B ALA* 4.6 1.6 - - + -
46B MET* 3.9 35.9 - - + -
49B TYR* 3.1 25.8 + + + +
118B LEU* 4.8 9.5 - - + +
119B MET* 5.2 7.4 - - + -
120B THR 5.4 0.9 - - - -
121B GLY* 3.2 4.0 - - - -
122B LYS* 2.8 60.1 + - + +
136B THR* 1.3 72.3 - - - +
138B LEU* 1.3 62.5 + - - +
139B GLY* 3.7 23.3 - - - -
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Residues in contact with LEU 138 (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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14B ASN* 3.8 24.0 - - + +
16B LEU* 4.2 9.6 - - + -
40B LEU* 4.1 21.1 - - + -
121B GLY* 3.2 12.9 - - - -
136B THR* 3.9 13.1 + - + +
137B TYR* 1.3 73.7 - - - +
139B GLY* 1.3 65.6 + - - +
141B ALA* 3.0 19.8 + - + +
142B CYS* 3.7 20.9 - - - -
169B PHE 5.8 0.2 - - - +
172B ASN* 4.6 15.0 - - + +
173B THR* 3.9 17.7 - - + -
401B ADN 3.7 24.7 - - + +
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Residues in contact with GLY 139 (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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118B LEU* 3.9 18.1 - - - +
119B MET 3.8 5.8 - - - -
121B GLY* 4.3 0.9 - - - -
137B TYR* 3.3 30.5 - - - -
138B LEU* 1.3 75.6 - - - +
140B ALA* 1.3 63.6 + - - -
141B ALA 3.0 1.7 + - - -
142B CYS* 3.1 22.2 + - - +
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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