Contacts of the helix formed by residues 466 - 477 (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 PRO 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B ILE* 3.2 34.5 - - + -
434B VAL* 5.5 0.9 - - + -
464B ASN 3.4 8.5 - - - +
465B CYS* 1.3 87.1 - - + +
467B GLU* 1.3 54.8 + - - +
468B GLU* 2.6 7.4 + - + +
469B LEU* 2.3 49.1 + - + +
470B TYR 3.0 6.4 + - - -
497B PHE* 4.3 10.5 - - + -
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Residues in contact with GLU 467 (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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461B ARG* 5.0 4.3 - - - +
465B CYS 3.3 5.4 + - - -
466B PRO* 1.3 70.0 - - - +
468B GLU* 1.3 56.3 + - - +
469B LEU 3.2 0.2 - - - -
470B TYR* 3.2 17.6 + - - +
471B GLN* 2.8 60.2 + - + +
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Residues in contact with GLU 468 (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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466B PRO* 2.6 8.5 + - + -
467B GLU* 1.3 77.8 - - - +
469B LEU* 1.3 57.5 + - - +
470B TYR 3.2 0.8 + - - -
471B GLN* 3.8 6.9 + - - +
472B LEU* 3.5 18.0 + - - +
493B VAL* 5.8 2.1 - - - +
497B PHE* 4.2 20.9 - - + -
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Residues in contact with LEU 469 (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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338B ILE* 5.4 1.3 - - + -
342B LEU* 3.6 28.7 - - + -
430B LEU* 4.5 15.0 - - + -
434B VAL* 3.5 31.4 - - + -
465B CYS* 3.7 11.9 - - - -
466B PRO* 2.3 38.4 + - + +
468B GLU* 1.3 69.2 - - - +
470B TYR* 1.3 56.9 + - - -
472B LEU* 3.9 6.9 - - + +
473B MET* 2.9 30.9 + - + +
494B LEU* 4.1 17.5 - - + -
497B PHE* 4.0 26.6 - - + -
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Residues in contact with TYR 470 (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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459B MET 2.5 29.9 + - - -
460B VAL* 3.9 3.1 - - - -
461B ARG* 3.4 39.5 + - + -
462B PRO* 4.6 0.9 - - + -
465B CYS* 4.4 4.3 - - - +
466B PRO 3.0 2.7 + - - +
467B GLU* 3.5 24.7 - - - +
468B GLU 3.2 0.2 - - - -
469B LEU* 1.3 78.5 - - - +
471B GLN* 1.3 81.1 + - - +
472B LEU 2.9 4.5 - - - -
473B MET* 2.7 35.6 + - - +
474B ARG* 2.8 58.0 + - + +
477B TRP* 4.3 8.1 - + - -
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Residues in contact with GLN 471 (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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467B GLU* 2.8 48.4 + - + +
468B GLU* 3.8 8.3 + - - +
470B TYR* 1.3 97.4 - - - +
472B LEU* 1.3 60.4 + - - +
474B ARG* 3.8 14.6 - - - +
475B LEU* 3.3 28.7 + - + +
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Residues in contact with LEU 472 (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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430B LEU* 4.8 7.6 - - + -
468B GLU 3.5 14.2 + - - +
469B LEU* 4.0 17.7 - - + +
470B TYR 2.9 1.0 - - - -
471B GLN* 1.3 77.5 - - - +
473B MET* 1.3 65.0 + - - +
475B LEU* 2.9 21.7 + - - +
476B CYS* 2.9 17.2 + - - -
490B LEU* 4.9 13.9 - - + +
493B VAL* 5.6 10.5 - - + -
494B LEU* 5.7 3.4 - - + -
497B PHE* 6.4 0.4 - - + -
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Residues in contact with MET 473 (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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427B GLY* 4.2 4.0 - - - +
430B LEU* 3.6 46.2 - - + +
431B THR* 3.7 22.2 - - + +
434B VAL* 4.4 5.8 - - + -
462B PRO* 4.6 4.0 - - + -
465B CYS* 3.8 18.8 - - - -
469B LEU* 2.9 33.0 - - + +
470B TYR* 2.7 23.4 + - + +
472B LEU* 1.3 76.5 - - - +
474B ARG* 1.3 56.1 + - - +
476B CYS* 3.1 12.2 + - - +
477B TRP* 2.9 54.7 + - + -
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Residues in contact with ARG 474 (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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458B ARG* 3.6 33.7 + - - +
459B MET 4.3 0.2 + - - -
470B TYR* 2.8 73.0 + - + +
471B GLN* 3.9 17.5 - - - +
473B MET* 1.3 72.6 - - - +
475B LEU* 1.3 66.2 + - + +
477B TRP* 3.1 35.7 + - - +
478B LYS* 3.3 3.6 + - - +
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Residues in contact with LEU 475 (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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471B GLN* 3.3 15.0 + - + +
472B LEU* 2.9 13.5 + - - +
474B ARG* 1.3 79.4 - - + +
476B CYS* 1.3 61.6 + - - +
477B TRP 3.4 0.2 + - - -
478B LYS* 3.5 8.2 + - - +
483B ASP 4.7 6.0 - - - +
484B ARG* 3.1 18.5 - - - +
485B PRO* 3.4 23.9 - - + +
489B TYR* 4.6 22.2 - - + +
490B LEU* 6.3 0.2 - - + -
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Residues in contact with CYS 476 (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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423B VAL* 3.6 19.3 - - - +
424B TRP* 3.6 10.1 - - - +
426B PHE* 4.7 3.1 - - - -
427B GLY* 3.5 31.9 - - - -
430B LEU* 4.8 3.4 - - - -
472B LEU 2.9 20.5 + - - -
473B MET* 3.1 9.6 - - - +
474B ARG 3.1 0.2 - - - -
475B LEU* 1.3 79.3 - - - +
477B TRP* 1.3 58.9 + - + +
484B ARG* 2.8 31.0 + - - +
485B PRO* 4.6 1.1 - - - -
490B LEU* 4.1 29.8 - - - -
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Residues in contact with TRP 477 (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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424B TRP* 3.5 40.0 + + + -
427B GLY 3.3 20.7 - - - -
428B ILE* 3.3 37.1 - - + +
431B THR* 3.8 19.7 - - + -
441B TYR* 5.5 1.6 - - - -
458B ARG* 2.7 56.1 + - - +
459B MET* 3.6 42.4 - - + -
462B PRO* 6.3 0.4 - - + -
470B TYR* 4.3 4.0 - + - -
473B MET* 2.9 37.5 + - + +
474B ARG* 3.1 25.7 + - - +
476B CYS* 1.3 79.3 - - + +
478B LYS* 1.3 58.7 + - - -
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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