Contacts of the helix formed by residues 285 - 295 (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 PHE 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B LEU* 3.5 35.4 - - + +
284B ALA* 1.3 76.2 - - + +
286B LEU* 1.3 58.3 + - - +
287B ALA 3.0 4.9 - - - -
288B GLU* 2.9 30.1 + - - +
312B ILE* 4.4 17.0 - - + -
314B ILE* 3.9 7.6 - - - +
388B LEU* 4.8 11.0 - - + +
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Residues in contact with LEU 286 (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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238B TRP* 4.2 14.0 - - + -
284B ALA 3.3 6.3 - - - +
285B PHE* 1.3 81.0 - - - +
287B ALA* 1.3 60.7 + - - +
288B GLU 3.1 0.4 - - - -
289B ALA* 3.1 16.5 + - + +
290B ASN* 3.2 20.2 + - - +
306B VAL* 4.0 32.8 - - + -
307B VAL 4.8 0.7 - - - +
308B THR* 4.1 26.0 - - + +
312B ILE* 3.8 30.9 - - + +
314B ILE* 5.4 0.7 - - + -
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Residues in contact with ALA 287 (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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284B ALA* 3.3 23.7 + - - +
285B PHE 3.0 0.6 - - - -
286B LEU* 1.3 79.1 - - - +
288B GLU* 1.3 61.4 + - - +
290B ASN* 3.4 12.2 + - - +
291B LEU* 3.0 23.9 + - - +
389B ILE 5.1 6.1 - - - +
390B GLU* 5.8 3.8 - - - -
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Residues in contact with GLU 288 (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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273B LYS* 2.8 35.6 + - - +
275B LEU* 4.2 7.8 - - - +
284B ALA 4.3 1.2 + - - +
285B PHE* 2.9 14.5 + - - +
287B ALA* 1.3 79.9 - - - +
289B ALA* 1.3 57.7 + - - +
291B LEU* 3.3 6.8 + - - +
292B MET* 3.0 36.6 + - - +
314B ILE* 3.7 17.2 - - + +
389B ILE* 4.0 25.5 + - + +
503B 242 2.8 45.8 + - + -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TRP* 3.3 27.4 - - + -
285B PHE 3.9 0.6 + - - -
286B LEU* 3.1 14.8 + - + +
288B GLU* 1.3 79.9 - - - +
290B ASN* 1.3 62.4 + - - +
292B MET* 3.3 7.8 + - - -
293B LYS* 3.0 19.9 + - - +
303B LEU* 3.4 17.7 - - + +
306B VAL* 3.7 18.8 - - + -
314B ILE* 3.9 8.2 - - + +
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Residues in contact with ASN 290 (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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238B TRP* 3.4 20.9 - - - -
286B LEU* 3.2 20.5 + - - +
287B ALA* 3.8 12.4 - - - +
288B GLU 3.3 0.4 - - - -
289B ALA* 1.3 75.3 - - - +
291B LEU* 1.3 58.5 + - - +
293B LYS* 3.2 6.1 + - - +
294B GLN* 2.9 49.2 + - - +
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Residues in contact with LEU 291 (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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287B ALA 3.0 14.4 + - - +
288B GLU* 3.4 7.6 - - - +
290B ASN* 1.3 76.7 - - - +
292B MET* 1.3 55.1 + - - +
294B GLN* 3.1 17.0 + - - +
295B LEU* 2.8 46.6 + - + +
360B TYR* 3.2 46.4 - - + +
389B ILE* 3.8 18.4 - - + -
391B ASP* 3.5 31.0 - - + +
503B 242 3.9 13.2 - - + -
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Residues in contact with MET 292 (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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288B GLU* 3.0 24.4 + - - +
289B ALA* 3.5 8.3 - - - +
290B ASN 3.3 0.2 - - - -
291B LEU* 1.3 76.8 - - - +
293B LYS* 1.3 62.5 + - - +
295B LEU* 3.1 7.6 + - - +
296B GLN* 3.0 21.5 + - - +
300B LEU* 5.5 0.3 - - - +
301B VAL* 4.1 17.0 - - + +
303B LEU* 4.2 20.4 + - + +
314B ILE* 3.9 14.6 - - + -
316B THR* 3.7 20.6 - - + -
503B 242 3.4 70.9 - - + +
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Residues in contact with LYS 293 (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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236B ASP* 4.3 18.8 + - - -
238B TRP* 5.4 4.7 - - + -
289B ALA 3.0 14.0 + - - +
290B ASN* 3.6 9.4 - - - +
292B MET* 1.3 75.4 - - - +
294B GLN* 1.3 66.8 + - + +
296B GLN* 2.6 54.9 + - - +
303B LEU* 4.2 16.7 - - + +
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Residues in contact with GLN 294 (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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290B ASN* 2.9 33.1 + - - +
291B LEU* 3.1 19.3 + - + +
293B LYS* 1.3 81.8 - - + +
295B LEU* 1.3 64.6 + - + +
296B GLN 3.3 1.1 + - - +
354B PHE* 4.5 8.5 - - - -
358B ARG* 4.6 9.6 + - - -
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Residues in contact with LEU 295 (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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291B LEU* 2.8 41.1 + - + +
292B MET 3.1 5.1 + - - +
294B GLN* 1.3 79.9 - - + +
296B GLN* 1.3 68.1 + - - +
297B HIS* 3.0 3.5 + - - +
300B LEU* 3.2 27.4 - - + +
354B PHE* 3.3 18.3 - - + -
355B ILE* 4.7 7.0 - - + -
358B ARG* 3.7 33.4 - - + -
360B TYR* 3.9 24.5 - - + -
503B 242 3.8 27.1 - - - -
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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