Contacts of the strand formed by residues 268 - 275 (chain A) in PDB entry 2OFV
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 THR 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A TYR* 3.3 4.1 - - - -
264A TYR* 2.8 53.8 + - + -
265A ASN* 5.8 0.3 - - - +
266A GLY 3.9 0.4 - - - -
267A HIS* 1.3 91.9 + - - +
269A LYS* 1.3 70.7 + - - +
270A VAL* 3.5 11.0 + - + +
304A TYR* 5.3 7.9 - - + -
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Residues in contact with LYS 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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261A MET* 3.7 34.6 - - - +
262A GLY 3.5 8.5 - - - +
263A TYR* 3.7 34.3 + - + +
267A HIS 3.9 2.2 + - - -
268A THR* 1.3 77.6 - - - +
270A VAL* 1.3 67.0 + - - +
304A TYR* 4.9 3.6 - - - -
318A TYR* 3.7 26.3 + - + +
320A GLU* 2.7 35.5 + - - +
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Residues in contact with VAL 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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245A LEU* 4.3 6.7 - - + -
261A MET* 3.6 3.6 - - - +
262A GLY 2.8 44.6 + - - +
263A TYR 4.3 2.5 - - - +
264A TYR* 4.3 15.3 - - + +
268A THR* 3.8 17.5 - - + +
269A LYS* 1.3 80.5 - - - +
271A ALA* 1.3 60.0 + - - +
272A VAL* 3.8 20.4 - - + -
304A TYR* 4.0 17.5 - - + -
315A ILE* 3.7 14.1 - - + -
316A THR 3.5 14.4 - - - +
318A TYR* 3.7 11.7 - - - +
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Residues in contact with ALA 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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251A LEU* 5.2 0.7 - - + -
259A VAL* 5.6 0.2 - - + -
260A TRP 3.3 8.5 - - - +
270A VAL* 1.3 73.5 - - - +
272A VAL* 1.3 65.0 + - - +
315A ILE* 3.5 2.6 - - - +
316A THR* 3.0 30.0 + - - +
317A GLU 3.6 6.1 - - - +
318A TYR* 3.9 9.3 - - + +
503A 242 3.4 53.2 - - + +
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Residues in contact with VAL 272 (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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245A LEU* 4.7 6.3 - - + -
247A LEU* 4.3 23.3 - - + -
258A GLU 3.9 0.3 - - - +
259A VAL* 3.3 2.3 - - - -
260A TRP* 2.7 46.8 + - + +
262A GLY* 5.0 4.0 - - - +
270A VAL* 3.8 21.1 - - + +
271A ALA* 1.3 81.4 - - - +
273A LYS* 1.3 66.2 + - - +
274A SER* 3.9 2.0 + - - +
313A TYR* 3.8 43.5 - - + -
314A ILE 3.6 5.6 - - - +
315A ILE* 4.4 11.2 - - + -
503A 242 3.6 3.1 - - - +
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Residues in contact with LYS 273 (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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258A GLU 3.3 10.8 - - - +
259A VAL* 4.4 4.5 - - + +
272A VAL* 1.3 75.3 - - - +
274A SER* 1.3 60.5 + - - +
275A LEU* 3.8 24.4 + - + +
288A GLU* 2.8 31.5 + - - +
312A ILE 3.5 1.2 - - - +
313A TYR* 3.4 4.2 - - - -
314A ILE* 3.0 33.3 + - + +
382A ASP* 2.8 28.2 + - - -
383A PHE* 3.9 13.8 - - - +
385A LEU* 3.8 28.1 - - + +
503A 242 3.5 29.0 + - + +
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Residues in contact with SER 274 (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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247A LEU* 5.5 2.9 - - - -
257A GLY* 3.1 6.2 - - - -
258A GLU* 2.9 47.6 + - - +
260A TRP* 4.9 8.1 - - - -
272A VAL* 3.9 3.6 + - - -
273A LYS* 1.3 73.8 - - - +
275A LEU* 1.3 61.3 + - - +
276A LYS 3.9 0.2 - - - -
311A PRO* 3.8 12.5 - - - +
312A ILE 3.5 4.7 - - - -
313A TYR* 3.2 28.5 + - - -
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Residues in contact with LEU 275 (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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256A PHE* 3.5 15.5 - - + +
273A LYS* 3.9 29.2 - - + +
274A SER* 1.3 74.6 + - - +
276A LYS* 1.3 67.8 + - - +
277A GLN* 3.1 5.0 + - - +
286A LEU 4.7 9.0 - - - +
288A GLU* 4.2 11.0 - - - +
310A GLU* 5.5 0.2 - - - +
311A PRO* 3.8 6.9 - - - +
312A ILE* 2.9 66.3 + - + +
314A ILE* 4.2 18.2 - - + -
385A LEU* 5.1 3.6 - - + -
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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