Contacts of the strand formed by residues 265 - 271 (chain A) in PDB entry 2VXO
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A VAL* 3.5 5.4 - - + +
241A VAL* 4.2 19.7 - - + -
253A THR* 4.4 11.0 - - + +
256A LEU* 3.5 47.6 - - + +
257A ASN* 3.8 23.5 + - + +
260A LEU* 4.1 10.1 - - + -
261A ASN 4.1 9.0 - - - +
262A GLN 3.7 10.8 + - - +
263A GLU 3.4 0.8 - - - -
264A GLN* 1.3 82.9 - - - +
266A ILE* 1.3 64.4 + - - +
267A ALA* 3.9 2.6 + - + +
292A ILE* 5.4 4.8 - - + +
293A GLN 5.2 2.9 - - - +
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Residues in contact with ILE 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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238A LYS* 3.7 37.5 - - + +
239A VAL 2.8 19.0 + - - +
240A LEU* 3.4 14.8 - - + +
241A VAL* 2.9 29.8 + - - +
263A GLU 5.0 4.7 - - - +
264A GLN 4.2 2.7 - - - +
265A VAL* 1.3 75.7 - - - +
267A ALA* 1.3 61.4 + - - +
268A VAL* 4.1 8.1 - - + -
293A GLN 5.6 0.2 - - - -
295A LYS* 5.4 2.9 - - + -
355A MET* 3.8 32.8 - - + -
357A LEU* 4.7 15.9 - - + -
362A VAL* 6.3 0.2 - - + -
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Residues in contact with ALA 267 (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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241A VAL* 3.8 8.5 - - + -
243A LEU* 4.5 7.4 - - + -
253A THR* 3.8 28.0 - - + -
265A VAL* 3.9 3.6 + - + -
266A ILE* 1.3 73.1 - - - +
268A VAL* 1.3 62.9 + - - +
269A HIS 4.2 0.2 - - - -
292A ILE* 4.8 3.4 - - + -
293A GLN 3.9 18.0 + - - +
294A VAL* 3.6 16.4 - - + -
295A LYS* 2.8 27.7 + - - +
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Residues in contact with VAL 268 (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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240A LEU* 4.1 20.9 - - + -
241A VAL 3.0 12.9 + - - +
242A LEU* 3.6 10.2 - - + +
243A LEU* 3.0 26.2 + - - +
266A ILE* 4.1 9.0 - - + -
267A ALA* 1.3 77.2 - - - +
269A HIS* 1.3 61.4 + - - +
270A ILE* 3.8 15.5 + - + -
295A LYS* 3.3 10.8 - - + +
297A ILE* 4.0 23.8 - - + -
351A VAL* 4.3 12.1 - - + -
355A MET* 3.9 28.7 - - + -
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Residues in contact with HIS 269 (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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243A LEU* 2.8 27.6 + - + +
244A SER* 3.4 25.3 - - - -
245A GLY* 4.3 3.4 + - - -
267A ALA 4.2 0.6 - - - -
268A VAL* 1.3 73.4 - - - +
270A ILE* 1.3 71.4 + - - +
271A ASP* 3.7 26.4 + - + +
275A MET* 4.6 12.9 - - + +
280A SER* 4.3 17.5 - - - -
284A GLU* 4.7 10.1 - - + +
294A VAL* 4.0 19.0 - - + +
295A LYS 2.8 10.2 + - - +
296A VAL* 3.4 16.6 - - + -
297A ILE 2.8 26.3 + - - -
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Residues in contact with ILE 270 (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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242A LEU* 4.5 12.1 - - + -
243A LEU 4.3 1.6 + - - -
244A SER* 5.9 0.7 - - - -
268A VAL* 3.8 8.7 + - + +
269A HIS* 1.3 84.7 + - - +
271A ASP* 1.3 61.7 + - - +
272A ASN* 3.5 5.7 + - - +
275A MET* 5.9 0.5 - - - +
297A ILE* 3.8 20.9 - - + +
299A ALA* 3.9 13.7 - - + -
303A PHE* 3.9 29.4 - - + -
344A PHE* 4.0 31.3 - - + -
347A ILE* 4.0 17.0 - - + -
348A ALA* 3.9 29.6 - - + +
351A VAL* 5.0 2.2 - - + -
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Residues in contact with ASP 271 (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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269A HIS* 3.7 22.2 + - + +
270A ILE* 1.3 70.5 - - - +
272A ASN* 1.3 59.4 + - - +
273A GLY* 3.1 19.9 + - - -
275A MET* 3.6 20.4 - - - +
280A SER* 5.8 4.6 - - - -
296A VAL* 5.2 2.9 - - + -
297A ILE 3.0 15.8 + - - +
298A ASN* 4.7 14.1 - - - +
299A ALA* 3.2 22.9 + - - +
300A ALA* 3.3 12.8 + - - +
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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