Contacts of the strand formed by residues 261 - 266 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ASN 2.8 13.2 + - - +
218A ILE* 3.2 16.8 - - + +
219A VAL 2.8 25.8 + - - +
259A LYS* 4.3 10.0 - - - +
260A ARG* 1.3 74.0 - - - +
262A VAL* 1.3 64.8 + - - +
263A ILE* 4.1 10.1 - - + -
273A TYR* 4.9 2.5 - - + -
274A THR 3.2 24.0 - - - +
275A ASP* 4.1 11.7 - - + +
308A PHE* 3.7 33.7 - - + -
312A TYR* 4.8 11.2 - - + +
318A MET* 3.8 28.5 - - + -
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A VAL* 3.4 11.7 - - + +
244A ALA* 4.1 19.2 - - + +
247A ILE* 3.7 21.5 - - + -
248A ALA* 3.6 37.7 - - + +
260A ARG* 4.4 6.1 - - + -
261A LEU* 1.3 79.4 - - - +
263A ILE* 1.3 65.3 + - - +
264A ILE* 4.0 24.5 - - + -
273A TYR* 3.2 6.9 - - - +
274A THR* 2.9 35.5 + - + +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.8 2.7 - - + -
219A VAL 2.9 12.7 + - - +
220A PHE* 3.5 22.1 - - + +
221A GLY 3.0 25.5 + - - +
261A LEU* 4.1 12.3 - - + -
262A VAL* 1.3 78.9 - - - +
264A ILE* 1.3 66.6 + - - +
265A THR* 4.7 1.0 - - + +
271A LEU* 4.3 13.0 - - + -
272A LEU 3.4 8.3 - - - +
273A TYR* 4.2 9.6 - - + -
304A PHE* 3.8 28.5 - - + -
308A PHE* 3.7 43.3 - - + -
318A MET* 4.0 6.5 - - + -
322A LEU* 4.2 1.6 - - + -
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.8 7.9 - - + -
219A VAL* 6.0 0.4 - - + -
220A PHE 4.8 0.7 - - - -
221A GLY* 3.3 17.9 - - - +
222A ASN 3.8 17.0 - - - +
223A GLU* 4.2 0.9 - - - +
226A ALA* 4.1 13.0 - - + -
240A VAL* 4.1 24.0 - - + +
243A THR* 5.5 0.9 - - + -
244A ALA* 4.3 19.1 - - + -
247A ILE* 5.4 3.8 - - + -
262A VAL* 4.0 22.0 - - + -
263A ILE* 1.3 81.5 - - - +
265A THR* 1.3 71.7 + - - +
266A ARG* 4.0 4.4 - - + +
271A LEU* 3.4 1.8 - - - -
272A LEU* 2.8 46.7 + - + +
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 6.3 0.2 - - + -
221A GLY 2.8 18.9 + - - +
222A ASN* 3.3 15.0 - - - +
223A GLU 3.0 25.1 + - - -
263A ILE* 4.0 2.0 - - + +
264A ILE* 1.3 74.7 - - - +
266A ARG* 1.3 62.7 + - - +
267A GLY 3.8 4.0 - - - -
271A LEU* 3.9 11.4 - - + -
301A GLY* 5.8 5.1 - - - -
304A PHE* 3.7 50.5 - - + -
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.2 45.3 + - + +
240A VAL* 4.7 3.5 - - - +
241A HIS* 6.3 0.7 - - - -
264A ILE* 4.0 9.6 - - + +
265A THR* 1.3 81.3 - - - +
267A GLY* 1.3 66.6 + - - +
268A LYS 3.3 0.5 + - - -
269A ASN* 3.1 55.5 + - - +
270A PRO* 2.8 48.7 + - - +
271A LEU* 4.4 2.0 - - - +
272A LEU* 3.9 29.9 - - - +
283A GLN* 5.2 3.2 + - - -
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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