Contacts of the helix formed by residues 504 - 518 (chain B) in PDB entry 1OPL
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 SER 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374B GLU* 3.5 19.7 - - - -
438B LYS* 3.7 14.4 - - - +
441B VAL* 4.7 0.9 - - - -
503B PRO* 1.3 76.3 - - - +
505B PHE* 1.3 60.2 + - - +
506B ALA* 3.5 6.5 + - - +
507B GLU* 3.0 37.4 + - - +
508B ILE* 3.0 27.4 + - - +
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Residues in contact with PHE 505 (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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367B SER* 4.4 6.3 - - - +
370B MET* 3.4 52.9 - - + -
371B GLU* 3.6 24.0 - - - +
374B GLU* 2.8 21.0 + - - +
383B LEU* 4.4 0.2 - - + -
437B ILE* 3.8 19.7 - - + -
440B ASP* 3.5 24.7 - - + -
441B VAL* 3.6 20.0 - - + -
444B PHE* 3.6 28.7 - + + -
504B SER* 1.3 69.7 - - - +
506B ALA* 1.3 66.6 + - - +
508B ILE* 3.6 17.9 - - + +
509B HIS* 2.8 26.7 + - - +
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Residues in contact with ALA 506 (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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371B GLU* 3.7 30.2 - - + +
374B GLU* 3.1 12.5 + - - +
504B SER* 3.2 8.2 - - - +
505B PHE* 1.3 77.7 - - - +
507B GLU* 1.3 62.1 + - + +
509B HIS* 3.5 1.4 + - - +
510B GLN* 3.2 24.8 + - - +
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Residues in contact with GLU 507 (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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490B LEU* 5.5 0.4 - - - +
502B ARG 4.9 0.2 - - - +
503B PRO* 3.3 18.4 - - + +
504B SER* 3.0 36.8 + - - +
506B ALA* 1.3 76.5 - - + +
508B ILE* 1.3 65.2 + - - +
510B GLN* 3.8 6.8 + - - +
511B ALA* 3.4 18.4 + - - +
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Residues in contact with ILE 508 (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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367B SER* 3.9 9.0 - - - -
441B VAL* 3.9 16.2 - - + -
444B PHE* 3.8 13.2 - - + -
490B LEU* 4.3 13.7 - - + -
494B CYS* 3.9 22.9 - - - -
503B PRO* 3.8 15.9 - - + -
504B SER 3.0 18.6 + - - +
505B PHE* 3.2 27.3 + - + +
507B GLU* 1.3 74.6 - - - +
509B HIS* 1.3 67.4 + - - +
511B ALA* 2.9 11.2 - - - +
512B PHE* 2.9 44.5 + - + -
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Residues in contact with HIS 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR* 3.6 18.4 - - + +
367B SER* 3.3 31.2 - - - +
368B SER* 3.8 21.7 + - - -
371B GLU* 3.5 23.1 + - - +
505B PHE 2.8 16.1 + - - +
506B ALA 3.9 1.5 + - - +
508B ILE* 1.3 72.8 - - - +
510B GLN* 1.3 55.5 + - - +
511B ALA 2.5 7.1 + - - -
512B PHE 2.3 25.4 + - - +
513B GLU* 2.5 55.9 + - + +
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Residues in contact with GLN 510 (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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506B ALA 3.2 15.3 + - - +
507B GLU* 3.9 8.1 - - - +
509B HIS* 1.3 82.7 + - - +
511B ALA* 1.3 60.3 + - - +
513B GLU* 4.2 5.8 - - - +
514B THR* 2.7 46.8 + - - -
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Residues in contact with ALA 511 (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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490B LEU* 4.2 22.4 - - + -
507B GLU 3.4 10.5 + - - +
508B ILE* 2.9 15.8 + - - +
509B HIS 2.5 1.0 + - - -
510B GLN* 1.3 86.0 - - - +
512B PHE* 1.3 54.6 + - - +
514B THR* 3.3 4.4 + - - -
515B MET* 2.8 36.3 + - + +
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Residues in contact with PHE 512 (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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360B LEU* 3.5 20.4 - - + +
363B ALA* 4.0 16.2 - - + -
364B THR* 3.4 27.6 + - + +
367B SER* 3.9 9.6 - - - +
444B PHE* 3.7 13.5 - + - -
448B LEU* 3.7 30.3 - - + -
487B VAL* 5.2 6.3 - - + -
490B LEU* 3.4 26.2 - - + -
508B ILE* 2.9 42.4 + - + -
509B HIS 2.3 16.8 + - - +
511B ALA* 1.3 66.8 - - - +
513B GLU* 1.3 59.8 + - - +
515B MET* 3.4 18.1 - - + +
516B PHE* 2.8 33.4 + - - +
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Residues in contact with GLU 513 (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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364B THR* 3.3 12.1 - - - +
509B HIS* 2.5 49.9 + - + +
510B GLN* 4.5 7.6 - - - +
512B PHE* 1.3 73.8 - - - +
514B THR* 1.3 63.3 + - - +
516B PHE* 3.3 6.3 + - - +
517B GLN* 3.0 49.6 + - + +
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Residues in contact with THR 514 (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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510B GLN* 2.7 37.2 + - - -
511B ALA* 3.3 4.6 + - - -
512B PHE 3.1 0.4 - - - -
513B GLU* 1.3 74.5 - - - +
515B MET* 1.3 69.8 + - + +
516B PHE 3.0 1.9 + - - -
517B GLN* 3.0 6.0 + - - +
518B GLU* 2.8 53.4 + - + +
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Residues in contact with MET 515 (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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360B LEU* 3.0 21.6 - - + +
486B LYS* 4.6 23.1 - - + -
487B VAL* 4.2 21.3 - - + -
490B LEU* 3.4 32.5 - - + -
511B ALA* 2.8 26.5 + - + +
512B PHE* 3.4 27.6 - - + +
514B THR* 1.3 74.0 - - + +
516B PHE* 1.3 62.6 + - - +
518B GLU* 3.5 29.1 + - - +
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Residues in contact with PHE 516 (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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357B VAL* 3.6 23.4 - - + +
360B LEU* 3.0 21.5 - - + +
361B TYR* 3.0 66.2 - + + -
364B THR* 3.8 9.2 - - + +
512B PHE 2.8 19.7 + - - +
513B GLU* 3.5 9.6 - - - +
515B MET* 1.3 78.7 - - - +
517B GLN* 1.3 86.6 + - - +
518B GLU 4.2 2.8 - - - -
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Residues in contact with GLN 517 (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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513B GLU* 3.0 40.5 + - + +
514B THR* 3.8 4.3 - - - +
516B PHE* 1.3 95.0 - - - +
518B GLU* 1.3 68.2 + - + +
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Residues in contact with GLU 518 (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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486B LYS* 6.1 0.7 - - - +
514B THR* 2.8 40.2 + - + +
515B MET* 3.8 26.4 - - - +
516B PHE 3.3 3.1 - - - -
517B GLN* 1.3 84.1 - - + +
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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