Contacts of the strand formed by residues 191 - 195 (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 LEU 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLN 2.9 15.2 + - - +
163B VAL* 3.4 9.1 - - + +
164B TYR* 2.8 27.9 + - - +
185B SER* 4.0 1.8 - - - -
190B LYS* 1.3 71.3 - - - +
192B PHE* 1.3 60.0 + - - +
193B CYS* 3.9 23.3 - - - -
217B ASN* 3.6 22.9 - - + +
218B ILE* 4.1 18.2 - - + -
309B ILE* 5.4 0.7 - - + -
312B TYR* 4.5 15.5 - - + -
313B ILE* 3.9 28.0 - - + -
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 3.6 22.0 - + + -
166B ILE* 3.8 33.9 - - + -
181B ILE* 4.1 2.2 - - + -
182B ALA* 3.9 26.9 - - + -
185B SER* 3.5 16.8 - - - +
190B LYS 3.7 0.6 + - - -
191B LEU* 1.3 71.2 - - - +
193B CYS* 1.3 71.9 + - - +
194B PHE* 4.1 8.1 - + + -
212B MET* 3.4 33.7 - - + -
215B TYR 3.6 18.8 - - - +
216B SER* 3.4 25.7 - - - -
217B ASN* 2.7 37.0 + - - +
218B ILE 3.2 6.6 + - - -
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Residues in contact with CYS 193 (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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163B VAL* 4.5 3.4 - - - -
164B TYR 2.8 21.0 + - - +
165B TYR* 3.4 20.4 - - + -
166B ILE 3.2 25.8 + - - +
191B LEU* 3.9 27.8 - - - -
192B PHE* 1.3 81.3 - - - +
194B PHE* 1.3 60.3 + - - +
218B ILE* 3.4 21.8 - - - +
220B PHE* 4.4 6.5 - - + -
309B ILE* 3.9 20.4 - - + -
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Residues in contact with PHE 194 (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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165B TYR* 5.1 0.7 - - - -
166B ILE 3.4 13.2 - - - -
168B GLY* 3.7 31.0 - - - -
171B ILE* 4.2 11.2 - - + -
178B MET* 3.8 19.1 - - + -
192B PHE* 4.1 9.2 - + + -
193B CYS* 1.3 74.1 - - - +
195B ASN* 1.3 67.8 + - - +
196B LEU* 4.2 19.5 - - + -
209B VAL* 4.1 15.3 - - + -
212B MET* 3.7 27.4 - - + -
213B ILE* 4.3 11.9 - - + -
216B SER* 3.2 27.8 - - - +
218B ILE 2.8 7.2 + - - +
219B VAL* 3.3 7.4 - - + +
220B PHE* 2.8 30.0 + - - +
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Residues in contact with ASN 195 (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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165B TYR* 3.0 31.4 + - + +
166B ILE 3.6 3.6 + - - -
167B ALA* 4.2 6.7 - - + -
168B GLY* 2.8 30.0 + - - -
194B PHE* 1.3 83.8 - - - +
196B LEU* 1.3 63.4 + - - +
197B SER* 2.9 34.3 + - - +
220B PHE* 3.5 24.7 - - + +
221B GLY* 4.7 0.9 - - - -
225B GLU* 4.1 6.2 - - - +
301B GLY 4.8 7.7 + - - -
302B ASP* 5.0 5.3 + - - -
305B ALA* 4.6 4.8 - - - +
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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