Contacts of the helix formed by residues 466 - 477 (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 PRO 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ILE* 4.7 19.5 - - + -
461A ARG* 5.0 0.2 - - - +
464A ASN 3.6 9.1 - - - +
465A CYS* 1.3 91.5 - - - +
467A GLU* 1.3 64.9 + - - +
468A GLU* 3.0 21.3 - - - +
469A LEU* 3.0 31.9 + - + +
470A TYR* 3.0 9.5 + - - +
497A PHE* 4.8 11.0 - - + -
498A PHE* 5.7 3.1 - - + -
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Residues in contact with GLU 467 (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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461A ARG* 3.2 34.8 + - - +
465A CYS 3.5 2.2 + - - -
466A PRO* 1.3 72.4 - - - +
468A GLU* 1.3 68.2 + - + +
470A TYR* 3.2 12.4 + - - +
471A GLN* 2.5 62.1 + - + +
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Residues in contact with GLU 468 (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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466A PRO* 3.0 26.4 - - - +
467A GLU* 1.3 89.3 + - + +
469A LEU* 1.3 61.0 + - - +
471A GLN* 3.4 15.2 + - - +
472A LEU* 3.4 11.1 + - - +
497A PHE* 3.8 21.4 - - + -
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Residues in contact with LEU 469 (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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338A ILE* 4.3 4.0 - - + -
342A LEU* 3.9 24.9 - - + -
430A LEU* 4.5 11.7 - - + -
434A VAL* 3.2 34.3 - - + -
465A CYS* 3.9 9.9 - - - -
466A PRO* 3.0 21.9 + - + +
468A GLU* 1.3 77.4 - - - +
470A TYR* 1.3 59.4 + - - +
472A LEU* 3.0 34.9 + - + +
473A MET* 3.1 14.4 + - + +
494A LEU* 4.3 23.6 - - + -
497A PHE* 3.7 17.4 - - + -
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Residues in contact with TYR 470 (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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458A ARG 4.8 0.5 + - - -
459A MET 2.7 30.3 + - - -
460A VAL* 3.9 2.9 - - - -
461A ARG* 3.5 56.1 + - + -
462A PRO* 4.6 0.2 - - + -
465A CYS* 3.9 2.2 - - - -
466A PRO 3.0 5.5 + - - +
467A GLU* 3.2 28.0 + - - +
469A LEU* 1.3 75.9 - - - +
471A GLN* 1.3 62.7 + - - +
473A MET* 3.2 24.3 + - - +
474A ARG* 3.0 64.0 + - + +
477A TRP* 4.3 12.1 - + - -
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Residues in contact with GLN 471 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A GLU* 2.5 46.2 + - + +
468A GLU* 3.8 7.9 - - - +
469A LEU 3.3 0.4 - - - -
470A TYR* 1.3 82.2 - - - +
472A LEU* 1.3 65.8 + - - +
474A ARG* 3.2 15.9 + - - +
475A LEU* 3.0 29.3 + - + +
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Residues in contact with LEU 472 (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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430A LEU* 4.3 12.6 - - + -
468A GLU 3.4 7.0 + - - +
469A LEU* 3.0 20.8 + - + +
471A GLN* 1.3 78.2 - - - +
473A MET* 1.3 60.6 + - - +
475A LEU* 3.3 15.9 + - + +
476A CYS* 3.2 21.1 + - - -
489A TYR* 4.3 16.8 - - + -
490A LEU* 3.5 31.9 - - + -
493A VAL* 4.2 25.6 - - + -
494A LEU* 3.9 32.8 - - + -
497A PHE* 5.5 1.8 - - + -
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Residues in contact with MET 473 (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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427A GLY* 4.2 6.5 - - - +
430A LEU* 3.7 47.6 - - + +
431A THR* 3.7 22.0 - - + +
434A VAL* 4.1 8.7 - - + -
462A PRO* 4.8 3.6 - - + -
465A CYS* 3.9 21.5 - - - -
469A LEU* 3.5 12.6 - - + +
470A TYR* 3.3 31.2 - - - +
472A LEU* 1.3 77.7 - - - +
474A ARG* 1.3 58.4 + - - +
476A CYS* 2.9 27.6 + - - +
477A TRP* 3.0 35.7 + - + -
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Residues in contact with ARG 474 (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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458A ARG* 3.8 31.6 - - - +
470A TYR* 3.0 58.7 + - + +
471A GLN* 3.2 22.2 + - - +
473A MET* 1.3 78.9 - - - +
475A LEU* 1.3 61.1 + - + +
477A TRP* 3.3 30.3 + - - -
478A LYS* 3.5 16.3 + - - +
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Residues in contact with LEU 475 (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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471A GLN* 3.0 21.2 + - + +
472A LEU* 3.4 24.5 - - + +
473A MET 3.1 0.2 - - - -
474A ARG* 1.3 77.9 - - + +
476A CYS* 1.3 62.7 + - - +
478A LYS* 3.4 22.3 + - + +
483A ASP 4.6 2.2 - - - +
484A ARG* 3.3 15.2 - - - +
485A PRO* 3.4 21.7 - - + +
489A TYR* 4.4 20.0 - - + +
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Residues in contact with CYS 476 (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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423A VAL* 3.5 31.9 - - - +
424A TRP* 3.4 15.6 - - - -
426A PHE* 4.5 3.1 - - - -
427A GLY* 3.8 22.4 - - - -
430A LEU* 4.9 2.0 - - - -
472A LEU 3.2 16.8 + - - -
473A MET* 2.9 10.5 + - - +
475A LEU* 1.3 81.6 - - - +
477A TRP* 1.3 56.5 + - - +
478A LYS 3.3 0.4 - - - -
484A ARG* 2.9 23.6 + - - +
485A PRO* 4.2 1.8 - - - -
490A LEU* 3.9 27.8 - - - -
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Residues in contact with TRP 477 (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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424A TRP* 3.2 40.4 - + + -
427A GLY* 3.4 22.4 - - - -
428A ILE* 3.2 38.9 - - + +
431A THR* 3.8 19.3 - - + -
441A TYR* 5.7 1.6 - - - -
458A ARG* 2.8 46.7 + - + +
459A MET* 4.0 34.3 - - + -
460A VAL 6.0 0.2 - - - -
470A TYR* 4.3 3.8 - + - -
473A MET* 3.0 30.3 + - + +
474A ARG* 3.3 32.7 + - - +
475A LEU 3.2 0.6 - - - -
476A CYS* 1.3 81.2 - - + +
478A LYS* 1.3 66.0 + - - -
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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