Contacts of the strand formed by residues 163 - 167 (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 VAL 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.0 29.1 + - + +
9B VAL* 3.3 15.8 - - + +
10B PHE 2.8 25.1 + - - -
161B ALA* 3.6 1.1 - - - +
162B GLN* 1.3 85.5 - - + +
164B TYR* 1.3 74.6 + - - +
165B TYR* 6.0 0.4 - - + -
191B LEU* 3.4 22.7 - - + +
193B CYS* 4.5 1.6 - - - -
309B ILE* 4.1 15.7 - - + -
313B ILE* 3.7 33.4 - - + -
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Residues in contact with TYR 164 (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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9B VAL* 5.5 0.2 - - - -
10B PHE* 3.3 26.0 - + + +
158B VAL* 2.4 41.7 + - + -
161B ALA* 3.8 14.6 - - + -
163B VAL* 1.3 77.9 - - - +
165B TYR* 1.3 57.9 + - - +
166B ILE* 4.3 2.0 - - + -
181B ILE* 3.8 15.0 - - + -
184B HIS* 3.1 20.7 - + - -
185B SER* 3.5 33.0 - - - -
190B LYS* 3.1 30.1 + - + -
191B LEU 2.8 13.4 + - - +
192B PHE* 3.6 21.1 - + + -
193B CYS* 2.8 36.9 + - - +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.4 2.8 - - + +
10B PHE 3.0 7.5 + - - +
11B GLY* 3.3 18.7 - - - -
65B ALA* 4.6 1.6 - - - +
66B THR* 3.4 27.8 - - + +
69B THR* 3.5 39.7 + - + -
70B VAL* 4.4 11.7 - - + -
73B ILE* 5.2 4.0 - - + -
163B VAL* 6.0 0.4 - - + -
164B TYR* 1.3 73.9 - - - +
166B ILE* 1.3 68.0 + - - +
167B ALA* 4.4 11.1 - - + +
193B CYS* 3.4 14.8 - - + -
195B ASN* 3.0 37.4 + - + +
220B PHE* 4.2 12.1 - + - -
302B ASP* 4.8 4.2 + - - -
305B ALA* 3.6 19.5 - - + +
309B ILE* 3.5 26.2 - - + -
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Residues in contact with ILE 166 (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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10B PHE* 5.4 1.6 - - + +
11B GLY* 5.2 0.4 - - - -
12B MET* 3.5 33.4 - - + +
66B THR* 4.0 3.1 - - - -
164B TYR* 5.2 1.6 - - + -
165B TYR* 1.3 86.1 - - - +
167B ALA* 1.3 73.9 + - - +
170B VAL* 3.7 14.4 - - + -
178B MET* 3.8 34.8 - - + -
181B ILE* 4.3 14.1 - - + -
192B PHE* 3.8 33.8 - - + -
193B CYS 3.2 6.7 + - - -
194B PHE* 3.4 20.1 - - - -
195B ASN 3.6 6.9 + - - -
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Residues in contact with ALA 167 (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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65B ALA* 4.1 16.4 - - + -
66B THR* 3.0 24.6 + - - +
165B TYR* 4.4 5.8 - - + +
166B ILE* 1.3 78.2 - - - +
168B GLY* 1.3 65.4 + - - +
169B PHE* 3.0 5.6 - - + +
170B VAL* 3.0 19.4 + - - +
178B MET* 4.0 2.1 - - - +
194B PHE* 4.3 0.7 - - - -
195B ASN* 4.2 11.9 - - + -
197B SER* 3.4 12.6 - - - +
402B CL 4.1 10.1 - - + -
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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