Contacts of the helix formed by residues 486 - 496 (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 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B GLU* 3.6 23.1 - - - +
420B LYS* 3.8 15.8 - - - +
423B VAL* 5.1 0.7 - - - -
485B PRO* 1.3 73.7 - - - +
487B PHE* 1.3 61.1 + - - +
488B ASP* 3.9 10.0 + - - +
489B TYR* 2.9 40.3 + - - +
490B LEU* 3.3 4.5 + - - +
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Residues in contact with PHE 487 (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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349B ALA* 3.9 9.6 - - - +
352B MET* 3.6 37.7 - - + -
353B ALA* 3.8 18.2 - - - +
356B GLU* 3.1 11.7 + - - +
419B ILE* 3.4 39.9 - - + -
422B ASP* 3.6 10.8 - - + -
423B VAL* 3.6 34.1 - - + -
426B PHE* 3.6 31.4 - + + -
485B PRO 3.7 1.4 + - - -
486B THR* 1.3 68.5 - - - +
488B ASP* 1.3 56.3 + - - +
490B LEU* 3.0 17.1 + - + +
491B ARG* 2.8 36.9 + - - +
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Residues in contact with ASP 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA* 4.3 12.8 - - + +
356B GLU* 3.7 6.4 + - - +
486B THR* 3.1 12.9 + - - +
487B PHE* 1.3 78.1 - - - +
489B TYR* 1.3 63.9 + - - +
491B ARG* 3.6 5.8 - - - +
492B SER* 3.4 18.4 + - - -
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Residues in contact with TYR 489 (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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475B LEU* 4.6 17.7 - - + +
485B PRO* 3.4 26.5 - - + -
486B THR* 2.9 24.5 + - - +
488B ASP* 1.3 82.9 + - - +
490B LEU* 1.3 66.2 + - + +
491B ARG 3.2 0.2 - - - -
492B SER* 3.3 8.0 + - - -
493B VAL* 3.3 43.9 + - + +
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Residues in contact with LEU 490 (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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349B ALA* 4.2 2.7 - - + -
423B VAL* 4.2 20.4 - - + -
426B PHE* 3.7 36.1 - - + -
430B LEU* 5.6 2.0 - - + -
472B LEU* 4.9 15.3 - - + +
475B LEU* 6.3 0.2 - - + -
476B CYS* 4.1 17.7 - - - -
485B PRO* 4.3 16.4 - - + +
486B THR 3.3 4.9 + - - +
487B PHE* 3.0 29.7 + - + +
489B TYR* 1.3 80.4 - - + +
491B ARG* 1.3 64.2 + - - +
493B VAL* 4.0 5.7 - - + +
494B LEU* 2.9 36.7 + - + +
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Residues in contact with ARG 491 (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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346B ALA 4.8 2.2 - - - +
349B ALA* 3.7 27.3 - - + +
350B GLU* 4.4 8.7 - - + +
353B ALA* 5.1 2.2 - - + -
487B PHE 2.8 16.0 + - - +
488B ASP* 3.6 9.9 - - - +
490B LEU* 1.3 79.0 - - - +
492B SER* 1.3 60.0 + - - +
494B LEU* 3.9 1.3 - - - +
495B GLU* 2.8 41.5 + - - +
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Residues in contact with SER 492 (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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488B ASP 3.4 8.9 + - - -
489B TYR* 3.3 13.6 + - - -
490B LEU 3.3 0.6 - - - -
491B ARG* 1.3 79.6 - - - +
493B VAL* 1.3 56.1 + - - +
495B GLU* 3.3 8.2 + - - +
496B ASP* 2.8 52.5 + - - +
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Residues in contact with VAL 493 (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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468B GLU 5.8 2.5 - - - +
472B LEU* 5.6 9.4 - - + -
489B TYR* 3.3 45.1 + - + +
490B LEU* 4.1 7.0 - - + +
492B SER* 1.3 79.0 - - - +
494B LEU* 1.3 67.0 + - + +
496B ASP* 3.7 4.3 - - - +
497B PHE* 3.3 38.3 + - + -
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Residues in contact with LEU 494 (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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342B LEU* 4.0 21.2 - - + +
343B ASP* 5.3 0.9 - - - -
345B ALA* 3.4 41.5 - - + +
346B ALA* 3.6 17.8 - - + +
349B ALA* 4.0 2.5 - - + -
426B PHE* 3.6 22.9 - - + -
430B LEU* 4.4 7.2 - - + -
469B LEU* 4.1 25.6 - - + -
472B LEU* 5.7 4.0 - - + -
490B LEU* 2.9 30.0 + - + +
491B ARG 3.9 0.4 - - - +
492B SER 3.2 0.2 - - - -
493B VAL* 1.3 83.3 - - + +
495B GLU* 1.3 63.5 + - - +
497B PHE* 3.7 16.2 - - + +
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Residues in contact with GLU 495 (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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343B ASP* 6.0 0.7 - - - +
346B ALA* 3.4 25.4 - - + +
350B GLU* 4.9 10.4 - - - +
491B ARG* 2.8 34.3 + - - +
492B SER* 3.8 6.4 - - - +
494B LEU* 1.3 76.5 - - - +
496B ASP* 1.3 60.5 + - - +
497B PHE* 2.7 17.6 + - - +
498B PHE 4.6 1.6 + - - -
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Residues in contact with ASP 496 (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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492B SER* 2.8 36.0 + - - +
493B VAL* 3.7 6.2 - - - +
495B GLU* 1.3 74.5 - - - +
497B PHE* 1.3 61.4 + - - +
498B PHE 3.8 1.1 - - - -
499B THR* 4.0 20.2 - - - -
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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