Contacts of the helix formed by residues 484 - 495 (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 PRO 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A GLY 3.3 8.3 - - - +
483A CYS* 1.3 89.3 - - - +
485A GLU* 1.3 65.9 + - - +
486A LYS* 4.6 3.4 - - + +
487A VAL* 3.0 35.4 + - + +
488A TYR* 3.2 9.7 + - - +
516A PHE* 3.9 18.8 - - + -
521A ILE* 4.3 10.1 - - + -
524A GLU* 4.0 25.8 - - + +
525A VAL* 4.3 5.4 - - + -
528A GLU* 3.9 10.5 - - + +
538A MYR 4.0 16.8 - - + -
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Residues in contact with GLU 485 (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* 3.5 25.7 + - - +
483A CYS 3.5 2.4 + - - -
484A PRO* 1.3 72.5 - - - +
486A LYS* 1.3 60.2 + - + +
488A TYR* 3.2 11.3 + - - +
489A GLU* 2.9 54.2 + - - +
524A GLU* 5.7 1.4 + - - +
528A GLU* 3.5 15.8 + - - +
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Residues in contact with LYS 486 (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* 3.3 1.6 - - + +
485A GLU* 1.3 79.8 - - + +
487A VAL* 1.3 61.6 + - + +
489A GLU* 3.5 14.4 + - - +
490A LEU* 3.2 20.6 + - - +
515A MET* 3.5 51.4 - - + +
516A PHE* 5.4 7.2 - - + -
518A GLU* 5.6 5.8 - - - -
524A GLU* 6.5 0.4 - - + -
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Residues in contact with VAL 487 (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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448A LEU* 3.9 21.2 - - + +
452A ALA* 5.3 0.2 - - + -
483A CYS* 3.6 19.1 - - - -
484A PRO* 3.0 31.8 + - + +
486A LYS* 1.3 77.3 - - - +
488A TYR* 1.3 64.0 + - - +
490A LEU* 3.1 9.7 + - - +
491A MET* 3.1 30.6 + - + +
512A PHE* 5.3 2.5 - - + -
515A MET* 3.7 22.2 - - - -
516A PHE* 4.0 4.7 - - + -
538A MYR 4.1 23.1 - - + -
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Residues in contact with TYR 488 (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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449A TRP* 5.5 0.2 - + - -
476A ARG 4.6 0.3 + - - -
477A MET 2.6 30.3 + - - -
478A GLU* 3.7 11.0 + - - -
479A ARG* 3.4 60.1 - - + -
480A PRO* 4.3 0.7 - - + -
483A CYS* 4.0 2.4 - - - -
484A PRO 3.2 4.5 + - - +
485A GLU* 3.2 15.9 + - - +
487A VAL* 1.3 78.4 - - - +
489A GLU* 1.3 61.5 + - + +
491A MET* 3.0 29.4 + - - +
492A ARG* 2.9 69.7 + - + +
495A TRP* 4.4 2.7 - + - -
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Residues in contact with GLU 489 (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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485A GLU* 2.9 46.8 + - + +
486A LYS* 3.8 12.2 + - - +
487A VAL 3.3 0.2 - - - -
488A TYR* 1.3 77.7 - - + +
490A LEU* 1.3 57.4 + - - +
492A ARG* 3.2 10.6 + - + +
493A ALA* 2.9 27.6 + - - +
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Residues in contact with LEU 490 (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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444A PHE* 5.2 0.7 - - + -
448A LEU* 4.4 6.1 - - + -
486A LYS 3.2 12.1 + - - +
487A VAL 3.1 10.7 + - - +
489A GLU* 1.3 74.9 - - - +
491A MET* 1.3 65.5 + - - +
493A ALA* 3.1 12.4 + - + +
494A CYS* 3.0 32.9 + - - -
503A PRO* 4.7 2.9 - - + -
508A ILE* 4.0 36.3 - - + +
511A ALA* 4.5 9.6 - - + -
512A PHE* 3.5 44.0 - - + -
515A MET* 4.1 16.2 - - + -
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Residues in contact with MET 491 (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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445A GLY* 3.9 13.5 - - - +
448A LEU* 3.6 25.1 - - + +
449A TRP* 3.9 32.1 - - - -
452A ALA* 4.1 5.8 - - + -
480A PRO* 4.2 4.9 - - + -
483A CYS* 3.9 28.3 - - - -
487A VAL* 3.1 19.7 + - + +
488A TYR* 3.0 24.8 + - + +
490A LEU* 1.3 77.0 - - - +
492A ARG* 1.3 61.7 + - - +
494A CYS* 3.1 9.3 + - - +
495A TRP* 3.1 53.3 + - + -
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Residues in contact with ARG 492 (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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474A ASP* 4.2 22.4 + - - -
476A ARG* 3.6 31.6 + - - +
488A TYR* 2.9 59.5 + - + +
489A GLU* 3.6 10.5 - - - +
491A MET* 1.3 75.1 - - - +
493A ALA* 1.3 64.0 + - - +
495A TRP* 3.3 27.9 + - - +
496A GLN* 3.0 27.1 + - - +
466B GLN* 5.6 6.3 - - - +
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Residues in contact with ALA 493 (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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489A GLU 2.9 13.4 + - - +
490A LEU* 3.1 15.0 + - + +
492A ARG* 1.3 76.5 - - - +
494A CYS* 1.3 62.0 + - - +
496A GLN* 3.2 26.3 + - - +
501A ASP 5.8 0.2 - - - +
502A ARG* 3.6 2.8 - - - -
503A PRO* 3.3 31.4 - - + +
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Residues in contact with CYS 494 (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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441A VAL* 3.5 30.1 - - - +
442A TRP* 3.5 10.7 - - - -
444A PHE* 4.2 8.7 - - - -
445A GLY* 3.8 20.4 - - - -
448A LEU* 5.8 1.1 - - - -
490A LEU* 3.0 24.9 + - - -
491A MET 3.4 8.5 - - - +
493A ALA* 1.3 79.1 - - - +
495A TRP* 1.3 57.6 + - + +
496A GLN 3.3 0.4 - - - -
502A ARG* 3.1 24.4 + - - -
503A PRO* 4.6 1.1 - - - -
508A ILE* 3.9 26.5 - - - -
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Residues in contact with TRP 495 (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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442A TRP* 3.2 41.5 + + + -
445A GLY* 3.4 24.2 - - - -
446A VAL* 3.4 25.2 - - + +
449A TRP* 4.2 6.5 - + + -
459A TYR* 5.3 4.3 - - - -
476A ARG* 2.9 46.1 + - + +
477A MET* 3.8 53.2 - - + -
488A TYR* 4.4 2.9 - + - -
491A MET* 3.1 41.9 + - + +
492A ARG* 3.3 26.9 + - - +
493A ALA 3.2 0.6 - - - -
494A CYS* 1.3 79.4 - - - +
496A GLN* 1.3 66.7 + - - +
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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