Contacts of the helix formed by residues 520 - 531 (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 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG* 5.9 0.4 - - - +
157A GLU* 3.9 26.2 - - - -
189A ARG* 3.8 8.7 + - - +
190A VAL 6.2 0.4 - - - -
516A PHE* 4.1 4.7 - - - -
519A SER* 1.3 78.3 - - - +
521A ILE* 1.3 64.8 + - - +
522A SER* 3.4 13.0 + - - -
523A ASP* 2.9 40.8 + - - +
524A GLU* 3.0 14.7 + - - +
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Residues in contact with ILE 521 (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* 5.7 0.9 + - - +
157A GLU* 4.8 2.8 + - - +
356A ALA* 3.7 22.7 - - + +
357A VAL* 3.3 39.0 - - + +
360A LEU* 4.1 13.7 - - + -
484A PRO* 4.3 3.8 - - + -
516A PHE* 3.7 49.1 - - + +
520A SER* 1.3 73.7 - - - +
522A SER* 1.3 67.1 + - - +
524A GLU* 3.1 1.0 + - - +
525A VAL* 2.9 34.4 + - + +
538A MYR 3.6 32.3 - - + -
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Residues in contact with SER 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 4.9 0.3 + - - -
189A ARG* 5.2 5.6 - - - -
355A ASN* 5.2 4.2 + - - -
356A ALA* 5.3 2.7 - - - -
357A VAL* 3.7 20.8 - - - +
520A SER* 3.4 12.2 + - - -
521A ILE* 1.3 82.4 - - - +
523A ASP* 1.3 61.3 + - - +
525A VAL* 3.4 6.9 + - - +
526A GLU* 3.0 31.6 + - - +
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Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 2.6 43.4 + - - -
519A SER* 3.9 15.6 - - - -
520A SER* 2.9 32.5 + - - +
522A SER* 1.3 77.6 - - - +
524A GLU* 1.3 62.5 + - - +
526A GLU* 3.1 24.1 - - - +
527A LYS* 3.1 13.9 + - + +
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Residues in contact with GLU 524 (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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484A PRO* 4.0 20.2 - - + +
485A GLU* 5.7 1.0 + - - +
486A LYS* 6.5 0.4 - - + -
516A PHE* 3.8 20.9 - - + -
519A SER* 3.1 21.1 + - - +
520A SER 3.0 16.0 + - - +
521A ILE 3.1 6.9 + - - +
523A ASP* 1.3 73.0 - - - +
525A VAL* 1.3 66.2 + - - +
527A LYS* 2.9 41.7 + - - +
528A GLU* 3.0 32.9 + - - +
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Residues in contact with VAL 525 (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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356A ALA* 3.8 25.8 - - + -
482A GLY 3.8 24.2 - - - +
484A PRO* 4.3 4.7 - - + -
521A ILE* 2.9 27.9 + - + +
522A SER* 3.7 6.1 - - - +
523A ASP 3.3 0.2 - - - -
524A GLU* 1.3 74.6 - - - +
526A GLU* 1.3 61.8 + - - +
528A GLU* 3.3 2.9 + - - +
529A LEU* 3.0 42.6 + - + +
538A MYR 3.8 26.7 - - + -
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Residues in contact with GLU 526 (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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522A SER* 3.0 25.3 - - - +
523A ASP* 3.1 15.9 - - - +
525A VAL* 1.3 81.2 - - - +
527A LYS* 1.3 58.9 + - + +
529A LEU* 3.0 8.5 + - - +
530A GLY* 2.7 35.0 + - - -
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Residues in contact with LYS 527 (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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523A ASP* 3.1 13.8 + - + +
524A GLU* 2.9 40.5 + - - +
526A GLU* 1.3 78.9 - - + +
528A GLU* 1.3 67.6 + - + +
530A GLY* 5.3 0.4 - - - -
531A LYS* 3.3 31.5 + - - +
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Residues in contact with GLU 528 (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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479A ARG* 3.2 30.2 + - - +
482A GLY* 3.8 19.5 + - - +
483A CYS 3.5 21.1 - - - +
484A PRO* 3.9 8.0 - - + +
485A GLU* 3.5 23.4 + - - +
524A GLU* 3.0 22.4 + - - +
525A VAL 3.4 8.7 - - - +
527A LYS* 1.3 80.8 - - - +
529A LEU* 1.3 65.2 + - - +
531A LYS* 3.8 22.6 + - - +
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Residues in contact with LEU 529 (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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481A GLU* 4.2 11.2 - - + +
482A GLY* 3.9 22.0 - - - +
525A VAL* 3.0 27.1 + - + +
526A GLU* 3.8 7.6 - - - +
528A GLU* 1.3 75.7 - - - +
530A GLY* 1.3 71.2 + - - +
531A LYS 2.7 11.8 + - - -
538A MYR 3.3 47.6 - - + +
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Residues in contact with GLY 530 (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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526A GLU 2.7 20.2 + - - -
527A LYS* 4.3 0.9 - - - -
529A LEU* 1.3 72.1 - - - +
531A LYS* 1.3 60.8 + - - +
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Residues in contact with LYS 531 (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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479A ARG* 6.3 0.4 - - - +
527A LYS* 3.3 24.9 + - - +
528A GLU* 3.8 21.7 + - - +
529A LEU 2.7 11.2 + - - -
530A GLY* 1.3 80.1 - - - +
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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