Contacts of the helix formed by residues 504 - 514 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A GLU* 3.5 19.1 - - - -
438A LYS* 3.7 14.1 - - - +
441A VAL* 4.7 1.1 - - - -
503A PRO* 1.3 75.7 - - - +
505A PHE* 1.3 60.1 + - - +
506A ALA* 3.5 6.6 + - - +
507A GLU* 3.0 37.7 + - - +
508A ILE* 3.0 25.9 + - - +
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Residues in contact with PHE 505 (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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367A SER* 4.4 6.3 - - - +
370A MET* 3.4 51.4 - - + -
371A GLU* 3.6 23.6 - - - +
374A GLU* 2.8 21.0 + - - +
383A LEU* 4.4 0.2 - - + -
437A ILE* 3.8 19.5 - - + -
440A ASP* 3.5 24.2 - - + -
441A VAL* 3.6 20.4 - - + -
444A PHE* 3.6 29.2 - + + -
504A SER* 1.3 68.8 - - - +
506A ALA* 1.3 67.2 + - - +
508A ILE* 3.6 17.1 - - + +
509A HIS* 2.8 26.7 + - - +
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Residues in contact with ALA 506 (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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371A GLU* 3.7 29.5 - - + +
374A GLU* 3.1 13.1 + - - +
504A SER* 3.2 8.0 - - - +
505A PHE* 1.3 77.6 - - - +
507A GLU* 1.3 57.8 - - + +
509A HIS* 3.5 2.1 + - - +
510A GLN* 3.1 29.2 + - - +
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Residues in contact with GLU 507 (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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502A ARG 4.9 0.2 - - - +
503A PRO* 3.3 17.4 - - + +
504A SER* 3.0 37.9 + - - +
506A ALA* 1.3 76.6 - - + +
508A ILE* 1.3 59.7 + - - +
510A GLN* 3.8 5.8 - - - +
511A ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 508 (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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367A SER* 3.9 8.7 - - - -
441A VAL* 3.9 15.5 - - + -
444A PHE* 3.8 15.5 - - + -
490A LEU* 4.0 17.0 - - + -
494A CYS* 3.9 22.0 - - - -
503A PRO* 3.8 16.4 - - + -
504A SER 3.0 17.7 + - - +
505A PHE* 3.2 28.7 + - + +
507A GLU* 1.3 74.9 - - - +
509A HIS* 1.3 67.4 + - - +
511A ALA* 3.1 8.9 + - - +
512A PHE* 3.1 44.1 + - + -
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Residues in contact with HIS 509 (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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364A THR* 3.6 29.0 - - + +
367A SER* 3.3 31.4 - - - +
368A SER* 3.8 21.0 + - - -
371A GLU* 3.5 23.1 + - - +
505A PHE 2.8 17.1 + - - +
506A ALA 3.9 1.6 - - - +
508A ILE* 1.3 74.9 - - - +
510A GLN* 1.3 68.7 + - - +
512A PHE* 3.1 13.8 + - - +
513A GLU* 3.2 36.5 + - + +
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Residues in contact with GLN 510 (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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175A SER* 5.9 6.8 - - - -
506A ALA 3.1 18.8 + - - +
507A GLU* 3.9 6.1 - - - +
509A HIS* 1.3 81.5 + - - +
511A ALA* 1.3 62.6 + - - +
513A GLU* 3.3 10.6 + - - +
514A THR* 3.1 51.4 + - + +
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Residues in contact with ALA 511 (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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490A LEU* 4.5 19.3 - - + -
507A GLU 2.9 19.6 + - - +
508A ILE* 3.1 8.7 + - - +
510A GLN* 1.3 74.5 - - - +
512A PHE* 1.3 65.7 + - - +
514A THR* 3.3 8.0 + - - -
515A MET* 3.1 31.5 + - + +
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Residues in contact with PHE 512 (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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154A ASN* 3.1 18.9 + - - -
360A LEU* 3.6 18.0 - - + +
363A ALA* 4.0 18.6 - - + -
364A THR* 3.6 24.2 - - + +
367A SER* 3.7 14.8 - - - -
444A PHE* 3.7 29.2 - + - -
448A LEU* 4.1 10.1 - - + -
487A VAL* 5.3 2.5 - - + -
490A LEU* 3.5 22.4 - - + -
508A ILE* 3.1 30.8 + - + -
509A HIS 3.1 5.4 + - - +
511A ALA* 1.3 75.5 - - - +
513A GLU* 1.3 64.5 + - - +
514A THR 3.2 0.9 + - - -
515A MET* 3.2 25.8 + - + +
538A MYR 4.2 18.4 - - + -
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Residues in contact with GLU 513 (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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152A SER* 3.0 38.8 + - - -
153A ARG* 5.3 9.5 + - - +
154A ASN* 4.3 16.3 + - - +
174A GLU* 3.8 11.3 - - + +
364A THR* 4.1 18.2 - - + +
509A HIS* 3.2 39.4 + - + +
510A GLN* 3.7 14.8 - - - +
511A ALA 3.3 0.2 - - - -
512A PHE* 1.3 76.1 - - - +
514A THR* 1.3 63.5 + - + +
515A MET 3.5 0.7 + - - -
516A PHE 5.3 0.7 + - - -
517A GLN* 5.1 2.4 - - - +
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Residues in contact with THR 514 (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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510A GLN* 3.1 42.2 + - - +
511A ALA* 3.5 8.1 + - - -
512A PHE 3.2 0.2 - - - -
513A GLU* 1.3 81.9 - - + +
515A MET* 1.3 62.1 + - - +
516A PHE 3.6 1.8 - - - -
517A GLN* 3.0 40.8 + - - +
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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