Contacts of the strand formed by residues 268 - 275 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TRP* 4.0 28.7 - - + +
235A GLU* 3.3 12.5 - - - +
236A ASP* 3.0 35.0 + - - +
293A LYS* 4.7 0.2 - - - +
263B TYR* 3.1 3.5 - - - -
264B TYR* 2.7 46.6 + - - -
266B GLY 3.8 0.6 - - - -
267B HIS* 1.3 79.8 - - - +
269B LYS* 1.3 64.9 + - - +
270B VAL* 3.6 19.6 + - + +
304B TYR* 5.2 2.0 - - + -
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Residues in contact with LYS 269 (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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236A ASP* 5.6 1.2 + - - -
293A LYS* 4.4 12.0 - - - +
296A GLN* 6.3 2.2 - - - +
261B MET* 3.5 31.1 - - + +
262B GLY 3.4 7.9 - - - +
263B TYR* 3.4 36.5 + - + +
267B HIS 3.8 3.0 + - - -
268B THR* 1.3 75.6 - - - +
270B VAL* 1.3 68.1 + - - +
304B TYR* 4.9 3.3 - - - -
318B TYR* 3.6 31.5 + - + +
320B GLU* 2.5 36.5 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP* 4.1 11.9 - - + -
245B LEU* 4.4 10.3 - - + -
261B MET* 3.5 4.9 - - - +
262B GLY 2.8 42.3 + - - +
263B TYR 4.3 2.0 - - - +
264B TYR* 4.3 1.6 - - + +
268B THR* 3.7 22.4 - - + +
269B LYS* 1.3 81.7 - - - +
271B ALA* 1.3 59.9 + - - +
272B VAL* 3.8 15.9 - - + -
304B TYR* 4.2 5.8 - - + -
315B ILE* 3.6 26.2 - - + -
316B THR 3.4 12.3 - - - +
318B TYR* 3.9 12.4 - - - -
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 5.3 0.7 - - + -
259B VAL* 5.3 0.4 - - + -
260B TRP 3.3 7.4 - - - +
270B VAL* 1.3 75.3 - - - +
272B VAL* 1.3 62.5 + - - +
315B ILE* 3.3 5.2 - - - +
316B THR* 2.9 49.0 + - - +
317B GLU 3.8 1.7 + - - +
318B TYR* 4.1 7.4 - - + -
503B 242 3.4 41.4 - - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.9 5.2 - - + -
247B LEU* 4.3 26.7 - - + -
258B GLU 3.7 0.5 - - - +
259B VAL* 3.3 3.1 - - - +
260B TRP* 2.6 44.7 + - + +
262B GLY* 4.8 5.2 - - - +
270B VAL* 3.8 20.6 - - + +
271B ALA* 1.3 81.1 - - - +
273B LYS* 1.3 65.4 + - - +
274B SER 3.9 0.8 + - - +
313B TYR* 3.7 43.7 - - + -
314B ILE 3.5 4.0 - - - +
315B ILE* 4.4 10.1 - - + -
503B 242 3.7 3.8 - - - +
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Residues in contact with LYS 273 (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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258B GLU 3.3 11.7 - - - +
259B VAL* 4.3 5.4 - - + +
272B VAL* 1.3 74.4 - - - +
274B SER* 1.3 59.0 + - - +
275B LEU* 3.7 27.4 - - + +
288B GLU* 2.8 36.9 + - - +
312B ILE 3.4 1.6 - - - +
313B TYR* 3.1 7.6 - - - +
314B ILE* 2.8 36.4 + - + +
382B ASP* 2.8 26.3 + - - -
383B PHE* 3.8 14.9 - - - +
385B LEU* 3.7 19.0 - - + +
389B ILE* 5.4 2.0 - - - +
503B 242 3.6 31.1 - - + -
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Residues in contact with SER 274 (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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247B LEU* 5.2 3.5 - - - +
257B GLY* 3.2 4.2 - - - -
258B GLU* 2.9 49.5 + - - +
260B TRP* 4.2 8.2 + - - -
272B VAL* 3.9 1.9 + - - -
273B LYS* 1.3 72.1 - - - +
275B LEU* 1.3 64.0 + - - +
311B PRO* 5.1 6.1 - - - -
312B ILE 3.5 4.5 - - - -
313B TYR* 3.5 26.2 - - - -
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Residues in contact with LEU 275 (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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256B PHE* 3.4 20.9 - - + +
273B LYS* 3.7 29.8 - - + +
274B SER* 1.3 75.5 - - - +
276B LYS* 1.3 64.8 + - - +
277B GLN* 3.4 2.9 + - - -
285B PHE* 3.5 33.9 - - + -
288B GLU* 4.2 9.2 - - - +
310B GLU* 5.3 0.7 - - - +
311B PRO* 3.6 15.1 - - - +
312B ILE* 3.0 23.2 + - + +
314B ILE* 4.1 27.6 - - + -
385B LEU* 4.1 10.3 - - + -
388B LEU* 6.4 0.4 - - + -
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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