Contacts of the strand formed by residues 169 - 174 (chain B) in PDB entry 1VAV
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 LEU 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY 3.8 0.2 - - - +
164B VAL* 3.3 3.0 - - - -
165B SER* 2.8 44.5 + - - +
167B SER* 3.5 5.5 - - - +
168B GLY* 1.3 77.2 - - - +
170B LEU* 1.3 67.3 + - - +
171B SER* 3.3 28.9 + - - +
180B GLU* 3.9 24.0 - - + +
181B GLN* 3.4 27.8 - - - +
182B GLN* 3.5 20.0 - - + +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 4.1 13.5 - - + -
116B LEU* 4.1 3.4 - - + -
117B VAL* 3.5 25.8 - - + -
134B VAL* 4.1 17.0 - - + -
163B GLY 3.2 18.2 - - - +
164B VAL* 3.8 13.7 - - + -
168B GLY 3.6 2.2 + - - -
169B LEU* 1.3 72.9 - - - +
171B SER* 1.3 64.2 + - - +
172B VAL* 3.8 21.3 - - + -
179B LEU* 3.6 1.7 - - + +
180B GLU* 3.2 6.6 - - - -
181B GLN* 2.7 50.7 + - + +
183B LEU* 3.6 26.7 - - + -
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TRP* 3.7 29.4 - - - -
161B ARG 3.7 1.6 - - - +
162B ILE* 3.3 3.3 - - - -
163B GLY 2.9 34.0 + - - +
169B LEU* 3.3 25.2 + - - +
170B LEU* 1.3 72.8 + - - +
172B VAL* 1.3 64.1 + - - +
173B SER* 6.4 0.2 - - - -
178B ALA* 5.8 3.8 - - - -
179B LEU 3.4 6.1 - - - -
180B GLU* 3.8 12.5 + - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 4.0 19.7 - - + -
119B LEU* 4.8 0.4 - - + -
132B ALA* 3.9 14.4 - - + -
134B VAL* 5.2 0.2 - - + -
148B LEU* 3.9 10.5 - - + +
161B ARG 3.4 4.5 - - - -
162B ILE* 3.8 17.9 - - + -
170B LEU* 3.8 23.3 - - + -
171B SER* 1.3 80.1 - - - +
173B SER* 1.3 61.5 + - - +
178B ALA* 3.3 1.3 - - - +
179B LEU* 2.8 66.1 + - + +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TRP* 5.9 0.7 - - - -
119B LEU* 5.2 1.0 - - - +
148B LEU* 3.9 4.1 - - - +
160B TYR* 3.1 7.7 - - - +
161B ARG* 2.8 55.0 + - - +
162B ILE* 4.7 0.6 - - - +
171B SER* 6.4 0.2 - - - -
172B VAL* 1.3 76.1 - - - +
174B VAL* 1.3 66.1 + - - +
175B ASN 4.3 0.2 - - - -
176B GLY* 4.2 11.6 + - - -
177B SER 3.1 17.0 - - - -
178B ALA* 3.4 15.9 - - - -
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Residues in contact with VAL 174 (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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119B LEU* 5.1 1.6 - - + -
130B VAL* 3.5 33.2 - - + -
148B LEU* 3.8 18.6 - - + +
149B MET* 3.5 32.0 - - + +
152B ILE* 5.5 0.2 - - + -
158B PHE* 4.1 18.6 - - + -
159B SER 3.2 10.1 - - - +
160B TYR* 4.2 9.4 - - + -
173B SER* 1.3 80.8 - - - +
175B ASN* 1.3 73.2 + - - +
176B GLY 3.0 2.9 - - - -
177B SER* 2.9 25.0 + - - -
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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