Contacts of the helix formed by residues 484 - 495 (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 PRO 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B ALA* 6.2 3.6 - - + -
482B GLY 3.4 9.0 - - - +
483B CYS* 1.3 90.8 - - - +
485B GLU* 1.3 65.4 + - - +
486B LYS* 3.3 4.7 - - + +
487B VAL* 3.0 36.7 + - + +
488B TYR* 3.2 10.0 + - - +
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Residues in contact with GLU 485 (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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479B ARG* 3.5 26.5 + - - +
483B CYS 3.5 2.0 + - - -
484B PRO* 1.3 71.9 - - - +
486B LYS* 1.3 59.6 + - + +
488B TYR* 3.2 11.7 + - - +
489B GLU* 2.9 54.6 + - - +
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Residues in contact with LYS 486 (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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484B PRO* 3.3 3.9 - - + +
485B GLU* 1.3 78.5 - - + +
487B VAL* 1.3 63.3 + - + +
489B GLU* 3.8 14.8 + - - +
490B LEU* 3.2 23.9 + - - +
515B MET* 4.6 20.0 - - + +
518B GLU* 6.1 0.4 - - - +
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Residues in contact with VAL 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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360B LEU* 5.8 3.8 - - + -
448B LEU* 3.9 20.8 - - + +
452B ALA* 5.3 2.9 - - + -
483B CYS* 3.6 18.8 - - - -
484B PRO* 3.0 31.6 + - + +
486B LYS* 1.3 77.3 - - + +
488B TYR* 1.3 63.6 + - - +
490B LEU* 3.1 11.2 + - - +
491B MET* 3.1 30.6 + - + +
512B PHE* 5.2 4.9 - - + -
515B MET* 4.2 20.9 - - + -
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Residues in contact with TYR 488 (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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476B ARG 4.6 0.3 + - - -
477B MET 2.6 30.8 + - - -
478B GLU* 3.7 10.7 + - - -
479B ARG* 3.4 58.1 - - + -
480B PRO* 4.3 0.7 - - + -
483B CYS* 4.0 1.8 - - - -
484B PRO 3.2 4.1 + - - +
485B GLU* 3.6 16.2 - - - +
487B VAL* 1.3 77.7 - - - +
489B GLU* 1.3 61.1 + - + +
491B MET* 3.0 30.0 + - - +
492B ARG* 2.9 70.0 + - + +
495B TRP* 4.4 3.1 - + - -
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Residues in contact with GLU 489 (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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485B GLU* 2.9 46.6 + - + +
486B LYS* 3.8 12.8 + - - +
488B TYR* 1.3 77.4 - - + +
490B LEU* 1.3 57.6 + - - +
492B ARG* 3.2 9.9 + - - +
493B ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 490 (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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448B LEU* 4.4 5.2 - - + -
486B LYS 3.2 12.1 + - - +
487B VAL* 3.1 11.7 + - - +
489B GLU* 1.3 75.3 - - - +
491B MET* 1.3 64.5 + - - +
493B ALA* 3.1 11.4 + - + +
494B CYS* 3.0 30.3 + - - -
503B PRO* 5.2 2.9 - - + -
507B GLU 5.5 0.4 - - - +
508B ILE* 4.3 31.6 - - + -
511B ALA* 4.2 11.0 - - + -
512B PHE* 3.4 35.9 - - + -
515B MET* 3.4 23.3 - - + -
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Residues in contact with MET 491 (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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445B GLY* 3.9 13.5 - - - +
448B LEU* 3.6 25.7 - - + +
449B TRP* 3.9 30.3 - - - -
452B ALA* 4.1 5.6 - - + -
480B PRO* 4.2 4.9 - - + -
483B CYS* 3.9 27.8 - - - -
487B VAL* 3.1 21.6 + - + +
488B TYR* 3.0 24.6 + - + +
490B LEU* 1.3 76.6 - - - +
492B ARG* 1.3 63.2 + - - +
494B CYS* 3.1 9.3 + - - +
495B TRP* 3.1 52.8 + - + -
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Residues in contact with ARG 492 (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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474B ASP* 4.2 23.0 + - - -
476B ARG* 3.6 32.2 + - - +
488B TYR* 2.9 60.5 + - + +
489B GLU* 3.6 10.1 - - - +
490B LEU 3.2 0.2 - - - -
491B MET* 1.3 76.0 - - - +
493B ALA* 1.3 63.0 + - - +
495B TRP* 3.3 26.8 + - - +
496B GLN* 3.0 27.3 + - - +
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Residues in contact with ALA 493 (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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489B GLU 2.9 12.9 + - - +
490B LEU* 3.1 14.3 + - + +
492B ARG* 1.3 77.4 - - - +
494B CYS* 1.3 63.1 + - - +
496B GLN* 3.2 26.4 + - - +
502B ARG* 3.6 2.9 - - - -
503B PRO* 3.3 32.2 - - + +
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Residues in contact with CYS 494 (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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441B VAL* 3.5 31.2 - - - +
442B TRP* 3.5 11.4 - - - -
444B PHE* 4.2 7.6 - - - -
445B GLY* 3.8 20.9 - - - -
448B LEU* 5.8 1.1 - - - -
490B LEU* 3.0 21.7 + - - -
491B MET* 3.4 9.4 - - - +
493B ALA* 1.3 79.3 - - - +
495B TRP* 1.3 56.6 + - + +
496B GLN 3.3 0.4 - - - -
502B ARG* 3.1 24.8 + - - -
503B PRO* 4.3 2.0 - - - -
508B ILE* 3.9 28.9 - - - -
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Residues in contact with TRP 495 (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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442B TRP* 3.2 40.3 + + + -
445B GLY* 3.4 25.5 - - - -
446B VAL* 3.4 23.1 - - + +
449B TRP* 4.2 7.2 - + + -
459B TYR* 5.3 3.4 - - - -
476B ARG* 2.9 45.7 + - + +
477B MET* 3.8 54.1 - - + -
488B TYR* 4.4 2.7 - + - -
491B MET* 3.1 41.1 + - + +
492B ARG* 3.3 26.9 + - - +
493B ALA 3.2 1.0 - - - -
494B CYS* 1.3 78.8 - - - +
496B GLN* 1.3 66.2 + - - +
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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