Contacts of the strand formed by residues 261 - 266 (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 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B ASN 2.8 13.9 + - - +
218B ILE* 3.3 16.4 - - + +
219B VAL 2.8 26.0 + - - +
259B LYS* 3.9 1.6 + - + +
260B ARG* 1.3 74.5 - - - +
262B VAL* 1.3 67.3 + - - +
263B ILE* 4.1 10.8 - - + -
273B TYR* 4.9 1.6 - - + -
274B THR 3.3 20.2 - - - +
275B ASP* 4.1 9.0 - - + +
308B PHE* 3.5 36.3 - - + -
312B TYR* 4.8 11.9 - - + +
318B MET* 3.6 30.7 - - + -
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Residues in contact with VAL 262 (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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219B VAL* 3.4 11.4 - - + +
244B ALA* 4.1 24.2 - - + +
247B ILE* 3.7 22.7 - - + -
248B ALA* 3.6 35.0 - - + +
260B ARG* 4.3 5.8 - - + -
261B LEU* 1.3 78.7 - - - +
263B ILE* 1.3 65.1 + - - +
264B ILE* 4.1 22.4 - - + +
272B LEU 4.6 0.2 - - - -
273B TYR* 3.2 5.9 - - - +
274B THR* 2.9 38.9 + - + +
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Residues in contact with ILE 263 (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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218B ILE* 4.7 3.1 - - + -
219B VAL 2.9 9.3 + - - +
220B PHE* 3.5 26.9 - - + +
221B GLY 2.9 25.8 + - - +
261B LEU* 4.1 10.3 - - + -
262B VAL* 1.3 79.3 - - - +
264B ILE* 1.3 68.9 + - - +
265B THR* 4.1 2.0 - - + +
271B LEU* 4.2 12.1 - - + -
272B LEU 3.5 9.0 - - - +
273B TYR* 4.1 1.1 - - + -
304B PHE* 4.0 26.9 - - + -
308B PHE* 3.7 37.9 - - + -
318B MET* 4.0 17.9 - - + -
322B LEU* 4.1 1.3 - - + -
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Residues in contact with ILE 264 (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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196B LEU* 4.9 7.6 - - + -
219B VAL* 6.0 0.7 - - + -
220B PHE 4.8 0.4 - - - -
221B GLY* 3.3 18.8 - - - +
222B ASN 3.7 17.7 - - - +
223B GLU* 4.0 1.6 - - - +
226B ALA* 4.0 21.8 - - + -
240B VAL* 4.1 15.0 - - + -
243B THR* 5.6 0.2 - - + -
244B ALA* 4.2 25.4 - - + -
247B ILE* 5.4 3.4 - - + -
262B VAL* 4.1 14.1 - - + -
263B ILE* 1.3 81.2 - - - +
265B THR* 1.3 74.1 + - - +
266B ARG* 3.9 4.8 - - + +
271B LEU* 3.4 2.2 - - - -
272B LEU* 2.8 46.4 + - + +
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Residues in contact with THR 265 (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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221B GLY 3.0 15.6 + - - +
222B ASN* 3.4 3.8 - - - +
223B GLU 3.0 25.8 + - - -
263B ILE* 4.1 2.7 - - + -
264B ILE* 1.3 75.7 - - - +
266B ARG* 1.3 63.0 + - - +
267B GLY 3.7 0.9 - - - -
271B LEU* 3.8 9.6 - - + -
294B ILE* 4.2 15.3 - - + +
295B ILE* 3.1 26.9 + - - +
301B GLY* 6.2 0.3 - - - -
304B PHE* 3.9 43.3 - - + -
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Residues in contact with ARG 266 (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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223B GLU* 2.9 48.6 + - + +
227B GLU* 4.9 1.0 + - - -
240B VAL* 3.6 23.9 - - - +
241B HIS* 4.0 25.7 + - - -
264B ILE* 3.9 12.1 + - + +
265B THR* 1.3 78.1 - - - +
267B GLY* 1.3 65.5 + - - +
268B LYS 3.4 0.3 + - - -
269B ASN* 3.1 34.1 + - + +
270B PRO 3.7 23.3 - - - +
271B LEU* 4.3 2.4 - - - +
272B LEU* 4.1 19.7 - - - +
293B GLN* 5.0 0.3 + - - -
294B ILE* 6.1 0.2 - - - +
295B ILE* 3.8 4.9 - - - -
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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