Contacts of the helix formed by residues 474 - 487 (chain B) in PDB entry 4OL0
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 HIS 474 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B HIS 3.3 21.8 + - - -
387B GLU* 4.1 4.2 - - - +
388B GLY 3.8 28.9 - - - -
434B TRP* 3.5 61.7 - + + -
472B THR 3.7 1.4 + - - -
473B VAL* 1.3 78.4 - - - +
475B THR* 1.3 79.3 + - - +
476B ALA* 3.2 13.6 + - + +
477B VAL* 3.0 18.5 + - + +
478B ARG* 3.2 9.7 + - - +
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Residues in contact with THR 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLY* 3.4 30.3 + - - -
389B VAL* 4.2 10.5 - - - -
473B VAL 3.4 3.5 + - - +
474B HIS* 1.3 75.9 + - - +
476B ALA* 1.3 59.0 + - - +
478B ARG* 3.4 23.0 + - - +
479B TYR* 2.8 29.6 + - - +
512B GLU* 5.8 1.8 - - - +
514B PRO* 5.4 9.4 - - + -
515B LEU* 3.7 10.4 - - + +
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 4.4 1.3 - - + -
388B GLY 3.9 8.1 - - - +
389B VAL* 4.2 0.7 - - - +
390B PRO* 3.8 28.9 - - + +
434B TRP* 3.5 30.1 - - + -
438B GLU* 3.9 7.6 - - + -
474B HIS* 3.2 6.7 + - - +
475B THR* 1.3 77.2 + - - +
477B VAL* 1.3 60.7 + - - +
479B TYR* 3.3 1.8 + - - +
480B THR* 2.9 35.2 + - - -
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B TRP* 3.6 47.1 - - + +
437B THR* 3.7 23.8 - - + -
438B GLU* 4.2 9.4 - - + +
441B LEU* 3.7 11.0 - - + +
469B LEU* 5.0 7.2 - - + -
473B VAL* 3.5 19.5 - - + -
474B HIS* 3.0 14.5 + - + +
476B ALA* 1.3 77.4 - - - +
478B ARG* 1.3 57.0 + - - +
480B THR 3.8 0.2 - - - -
481B SER* 2.8 31.5 + - - -
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Residues in contact with ARG 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B LEU* 4.1 16.8 - - + -
470B PRO 4.8 1.1 + - - +
471B GLU* 3.0 48.4 + - - +
473B VAL* 4.2 10.0 + - - +
474B HIS 3.2 7.2 + - - +
475B THR* 3.7 23.1 - - - +
477B VAL* 1.3 77.2 - - - +
479B TYR* 1.3 59.9 - - - +
481B SER* 2.6 20.3 + - - -
482B ILE* 2.8 25.1 + - + +
505B TYR* 3.6 24.9 - - + +
508B LYS* 6.0 3.4 - - - +
509B GLY* 5.9 1.4 - - - -
512B GLU* 2.8 41.6 + - - -
515B LEU* 4.0 15.9 - - + +
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Residues in contact with TYR 479 (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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389B VAL* 3.9 16.2 - - + -
390B PRO* 3.9 30.8 + - + -
392B GLU* 4.8 14.1 + - + +
400B ARG* 6.1 1.3 - - - -
475B THR 2.8 19.0 + - - +
476B ALA* 3.4 5.6 - - - +
478B ARG* 1.3 74.5 - - - +
480B THR* 1.3 68.8 + - - +
482B ILE* 3.0 9.8 + - - +
483B GLU* 2.9 48.0 + - - +
514B PRO 3.7 23.3 - - - -
515B LEU* 3.8 12.7 - - + +
517B SER* 4.0 16.4 + - - -
518B ALA* 3.6 25.4 - - + +
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Residues in contact with THR 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PRO* 4.4 1.7 - - - +
400B ARG* 4.6 1.6 + - - -
438B GLU* 2.4 29.6 + - - +
441B LEU* 3.4 11.9 - - + +
442B PHE* 3.2 45.7 - - + +
445B ALA* 4.7 1.5 - - + +
476B ALA 2.9 17.4 + - - -
477B VAL 4.0 2.5 - - - -
479B TYR* 1.3 82.7 - - - +
481B SER* 1.3 57.4 + - - +
483B GLU* 3.2 12.0 + - - +
484B LEU* 2.9 26.4 + - - +
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Residues in contact with SER 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU* 4.1 16.3 - - - +
466B VAL* 4.3 18.5 - - - +
469B LEU* 4.4 5.5 - - - +
477B VAL* 2.8 17.6 + - - -
478B ARG* 2.6 23.5 + - - -
480B THR* 1.3 73.8 - - - +
482B ILE* 1.3 57.8 + - - +
484B LEU* 3.2 8.7 + - - +
485B VAL* 2.8 35.2 + - - +
505B TYR* 2.7 22.9 + - - -
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Residues in contact with ILE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ARG* 2.8 20.9 + - + +
479B TYR* 3.3 8.3 - - - +
481B SER* 1.3 76.7 + - - +
483B GLU* 1.3 63.0 + - - +
485B VAL* 3.2 8.1 + - - +
486B GLY* 2.9 20.8 + - - -
505B TYR* 3.9 23.3 - - + +
506B LEU* 4.0 11.4 - - + +
509B GLY* 4.5 13.0 - - - -
515B LEU* 3.9 40.6 - - + +
518B ALA* 3.7 10.8 - - + +
519B ALA* 3.5 32.3 - - + +
522B ALA* 3.9 2.1 - - + +
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Residues in contact with GLU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLU* 5.5 3.1 - - - +
442B PHE* 4.7 17.2 - - - -
445B ALA* 4.5 9.5 - - + +
479B TYR* 2.9 46.6 + - + +
480B THR* 3.4 14.1 + - - +
482B ILE* 1.3 77.2 - - - +
484B LEU* 1.3 56.6 + - - +
486B GLY* 3.0 4.5 + - - -
487B GLU* 2.8 34.7 + - + +
518B ALA* 4.5 13.1 - - + +
521B LYS* 6.4 1.8 - - + -
522B ALA* 5.6 0.9 - - - -
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B PHE* 4.5 3.6 - - + -
441B LEU* 3.6 31.4 - - + +
444B MET* 3.8 15.3 - - + +
445B ALA* 3.6 36.7 - - + +
448B ALA* 4.2 6.5 - - + -
462B VAL* 4.0 23.1 - - + -
466B VAL* 4.2 11.2 - - + -
480B THR 2.9 16.3 + - - +
481B SER* 3.4 8.7 - - - +
483B GLU* 1.3 73.1 - - - +
485B VAL* 1.3 58.4 + - - +
487B GLU* 2.9 19.0 + - - +
488B MET* 3.1 34.2 + - - +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 4.2 19.1 - - + +
466B VAL* 3.7 33.7 - - + +
467B VAL* 4.4 2.7 - - + -
481B SER 2.8 20.7 + - - +
482B ILE* 3.5 9.4 - - - +
484B LEU* 1.3 72.0 - - - +
486B GLY* 1.3 62.0 + - - +
488B MET* 3.1 19.1 + - - +
489B SER* 3.9 2.3 + - - -
492B VAL* 4.9 1.4 - - + +
502B VAL* 3.7 31.2 - - + -
505B TYR* 4.1 13.5 - - + -
506B LEU* 4.0 15.9 - - + -
526B ILE* 4.9 3.9 - - + +
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Residues in contact with GLY 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ILE 2.9 10.9 + - - -
483B GLU* 3.0 5.3 + - - -
485B VAL* 1.3 77.4 - - - +
487B GLU* 1.3 53.7 + - - +
488B MET 3.2 0.2 - - - -
489B SER* 2.8 12.1 + - - -
522B ALA* 3.5 32.5 - - - +
525B ASN* 2.6 31.0 + - - -
526B ILE* 5.3 0.9 - - - -
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Residues in contact with GLU 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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408B LYS* 5.4 6.6 + - - -
445B ALA* 3.3 30.2 - - + +
448B ALA* 3.7 14.6 - - + +
449B LYS* 3.3 52.0 + - - +
483B GLU* 2.8 19.4 + - + +
484B LEU* 2.9 11.8 + - - +
486B GLY* 1.3 74.8 - - - +
488B MET* 1.3 57.2 + - - +
489B SER 3.5 2.6 + - - -
490B GLU* 5.3 0.5 + - - +
525B ASN* 4.2 7.9 + - - +
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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
------------------------------------------------------------
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