Contacts of the helix formed by residues 460 - 471 (chain B) in PDB entry 4OSV
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 460 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B CYS* 4.0 1.6 - - - -
458B GLY 5.2 2.5 - - - +
459B LEU* 1.3 75.8 - - - +
461B PRO* 1.3 70.6 - - - +
462B GLN* 3.5 19.3 + - - +
463B GLN* 2.8 45.1 + - - +
464B VAL* 2.9 20.8 + - - +
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Residues in contact with PRO 461 (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 HIS 6.1 1.3 - - - +
424B GLY 4.9 12.6 - - - +
425B LEU* 4.9 4.0 - - + -
429B GLN* 4.6 8.1 - - - +
450B LEU* 4.3 11.4 - - + -
454B CYS* 3.7 23.7 - - + -
459B LEU 4.3 0.4 - - - +
460B THR* 1.3 87.1 - - - +
462B GLN* 1.3 64.7 + - - +
464B VAL* 3.1 3.0 + - - +
465B VAL* 2.8 36.5 + - - +
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Residues in contact with GLN 462 (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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429B GLN* 4.2 19.1 - - - +
460B THR* 3.5 20.3 - - - +
461B PRO* 1.3 89.2 - - - +
463B GLN* 1.3 56.8 + - + +
465B VAL* 3.4 3.5 + - - +
466B ALA* 2.9 28.3 + - - +
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Residues in contact with GLN 463 (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 GLY 4.5 1.2 - - - +
459B LEU* 3.4 16.9 - - + +
460B THR* 2.8 50.4 + - - +
462B GLN* 1.3 74.5 - - + +
464B VAL* 1.3 65.3 + - - +
466B ALA* 3.3 7.0 + - - +
467B ILE* 3.1 30.5 + - - +
495B PRO 4.7 0.4 + - - -
496B GLN* 3.2 34.5 + - - +
499B VAL* 3.9 36.6 - - + +
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Residues in contact with VAL 464 (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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446B VAL* 4.1 20.4 - - + -
450B LEU* 4.0 21.1 - - + -
453B LEU* 3.9 35.2 - - + -
454B CYS* 3.9 13.5 - - - -
459B LEU* 4.1 11.0 - - + -
460B THR 2.9 16.9 + - - +
461B PRO 3.5 6.7 - - - +
463B GLN* 1.3 76.6 - - - +
465B VAL* 1.3 63.2 + - - +
467B ILE* 3.5 5.8 + - - +
468B ALA* 3.0 21.1 + - - +
477B LEU* 3.8 19.2 - - + +
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Residues in contact with VAL 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 3.9 18.8 - - + -
429B GLN* 3.8 45.1 - - + +
432B ALA* 5.0 3.6 - - + -
433B ILE* 3.9 17.9 - - + -
461B PRO 2.8 20.0 + - - +
462B GLN* 3.8 4.3 - - - +
464B VAL* 1.3 78.9 - - + +
466B ALA* 1.3 52.5 + - - +
468B ALA* 3.1 6.6 + - - -
469B SER* 2.6 53.3 + - - +
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Residues in contact with ALA 466 (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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462B GLN 2.9 18.0 + - - +
463B GLN* 3.3 9.1 + - - +
465B VAL* 1.3 76.8 - - - +
467B ILE* 1.3 55.4 + - - +
469B SER* 4.8 0.7 - - - -
470B ASN* 2.8 58.3 + - - +
499B VAL* 5.1 3.8 - - + -
503B SER* 3.8 7.9 - - - +
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Residues in contact with ILE 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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459B LEU* 4.3 13.9 - - + -
463B GLN 3.1 14.4 + - - +
464B VAL* 3.7 6.1 - - - +
466B ALA* 1.3 76.0 - - - +
468B ALA* 1.3 61.4 + - - +
471B GLY 3.9 0.5 + - - -
472B GLY 3.3 9.5 + - - -
473B GLY 2.9 20.7 + - - +
476B ALA* 3.6 29.4 - - + -
477B LEU* 3.8 23.3 - - + +
480B VAL* 3.9 25.1 - - + -
499B VAL* 4.3 20.4 - - + -
502B ALA* 4.0 11.9 - - + +
503B SER* 3.6 18.4 + - - +
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Residues in contact with ALA 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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433B ILE* 4.0 20.8 - - + +
436B ASN* 4.6 3.5 + - - +
442B ALA* 3.8 17.2 - - + +
446B VAL* 3.6 27.1 - - + -
464B VAL 3.0 17.7 + - - +
465B VAL 3.1 4.0 + - - +
467B ILE* 1.3 77.8 - - - +
469B SER* 1.3 59.8 + - - +
471B GLY* 4.8 0.5 + - - -
473B GLY* 3.8 16.6 + - - -
477B LEU* 4.0 7.9 - - + -
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Residues in contact with SER 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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432B ALA* 4.0 21.1 - - - +
433B ILE* 3.3 21.9 + - - +
436B ASN* 3.1 28.9 + - - +
465B VAL* 2.6 33.3 + - - +
466B ALA* 4.9 0.4 - - - -
468B ALA* 1.3 73.4 - - - +
470B ASN* 1.3 71.5 + - - +
471B GLY* 3.3 4.1 + - - -
505B MET* 5.7 1.2 - - - +
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Residues in contact with ASN 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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466B ALA* 2.8 47.1 + - - +
469B SER* 1.3 81.5 - - - +
471B GLY* 1.3 55.6 + - - +
503B SER* 2.9 26.7 - - - +
504B ASN* 4.2 3.1 - - - +
505B MET* 4.0 17.7 + - - +
-11H G 5.0 11.5 + - - +
-10H A 4.0 20.7 + - - -
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Residues in contact with GLY 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 ILE 3.9 0.8 + - - -
468B ALA 4.8 0.9 + - - -
469B SER 3.3 5.1 - - - -
470B ASN* 1.3 79.9 - - - +
472B GLY* 1.3 66.9 + - - +
473B GLY* 3.2 4.4 + - - -
503B SER 2.8 1.5 + - - -
504B ASN 3.2 7.4 - - - +
505B MET* 3.7 30.2 - - - -
506B GLY 4.3 2.6 + - - -
5G T 5.8 0.5 - - - +
6G T 4.3 15.0 + - - +
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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