Contacts of the helix formed by residues 488 - 504 (chain A) in PDB entry 2WTJ
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 ASP 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A LYS* 2.9 45.0 + - + +
486A LEU 2.9 10.6 + - - +
487A GLN* 1.3 74.2 - - - +
489A GLU* 1.3 65.2 + - - +
490A ASP* 3.2 10.9 + - - +
491A MET* 2.9 26.2 + - + +
492A LYS* 3.0 23.2 + - - +
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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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487A GLN* 4.1 2.7 - - - -
488A ASP* 1.3 77.3 + - - +
490A ASP* 1.3 58.5 + - - +
492A LYS* 3.5 27.1 + - - +
493A ARG* 2.9 29.1 + - - +
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Residues in contact with ASP 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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488A ASP* 3.5 7.4 - - - +
489A GLU* 1.3 77.0 - - - +
491A MET* 1.3 67.9 + - - +
493A ARG* 3.1 8.5 + - - +
494A LYS* 3.0 23.4 + - - +
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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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322A ALA 5.0 2.0 - - - +
325A LYS* 4.2 15.7 - - + -
326A LEU* 3.7 34.5 - - + +
329A TYR* 3.4 53.8 - - + -
486A LEU* 4.0 21.8 - - + +
488A ASP* 2.9 28.4 + - - +
490A ASP* 1.3 71.5 - - - +
492A LYS* 1.3 76.2 + - + +
494A LYS* 3.1 12.2 + - - +
495A PHE* 3.0 17.5 + - - +
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Residues in contact with LYS 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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329A TYR* 3.7 44.2 - - + +
481A LEU 5.0 4.0 + - - -
486A LEU* 3.5 23.7 + - - +
487A GLN* 4.0 19.4 + - - +
488A ASP 3.0 15.5 + - - +
489A GLU* 3.8 32.3 + - - +
491A MET* 1.3 82.6 - - + +
493A ARG* 1.3 56.0 + - - +
495A PHE* 3.2 6.4 + - - +
496A GLN* 2.9 36.3 + - + +
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Residues in contact with ARG 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 18.4 + - - +
490A ASP* 3.1 8.5 + - - +
492A LYS* 1.3 75.8 - - - +
494A LYS* 1.3 53.1 + - - +
496A GLN* 3.2 7.7 + - + +
497A ASP* 2.7 56.8 + - - +
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Residues in contact with LYS 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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326A LEU* 4.5 14.8 - - + -
361A ASP* 3.2 38.8 - - + +
490A ASP 3.0 11.7 + - - +
491A MET* 3.1 13.4 + - - +
493A ARG* 1.3 76.0 - - - +
495A PHE* 1.3 57.2 + - - +
497A ASP* 3.3 11.7 + - + +
498A LEU* 2.9 37.9 + - + +
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Residues in contact with PHE 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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282A HIS* 5.8 1.1 - + - -
283A PRO* 5.3 2.7 - - + -
284A CYS* 4.0 12.3 - - - -
326A LEU* 4.0 15.4 - - + +
329A TYR* 3.6 23.3 - + + -
330A GLN* 3.6 27.1 - - + -
333A LEU* 3.7 26.5 - - + -
363A LEU* 3.6 26.0 - - + -
491A MET 3.0 12.0 + - - +
492A LYS* 3.5 7.2 - - + +
494A LYS* 1.3 75.9 - - - +
496A GLN* 1.3 74.2 + - - +
498A LEU* 3.0 7.3 + - - +
499A LEU* 2.8 56.2 + - + +
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Residues in contact with GLN 496 (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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329A TYR* 5.2 4.8 + - - -
492A LYS* 2.9 23.6 + - + +
493A ARG* 3.6 7.6 - - + +
495A PHE* 1.3 98.9 - - - +
497A ASP* 1.3 63.3 + - - +
499A LEU* 3.4 18.7 + - - +
500A SER* 3.2 22.5 + - - -
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Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ARG* 2.7 40.9 + - - +
494A LYS* 3.4 10.3 - - + +
495A PHE 3.1 0.2 - - - -
496A GLN* 1.3 73.5 - - - +
498A LEU* 1.3 66.3 + - + +
500A SER* 3.0 21.9 + - - -
501A GLU* 3.1 11.5 + - - +
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Residues in contact with LEU 498 (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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326A LEU* 4.3 13.7 - - + -
361A ASP* 3.8 22.4 - - + +
362A CYS* 3.6 38.4 - - - +
363A LEU* 3.8 18.2 - - + +
494A LYS* 2.9 23.6 + - + +
495A PHE* 3.0 9.2 + - - +
497A ASP* 1.3 75.7 - - + +
499A LEU* 1.3 63.6 + - - +
501A GLU* 3.3 23.4 + - - +
502A GLU* 3.0 23.9 + - - +
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Residues in contact with LEU 499 (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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283A PRO* 3.6 35.9 - - + -
363A LEU* 4.2 11.4 - - + +
495A PHE* 2.8 46.8 + - + +
496A GLN* 3.5 26.9 - - - +
497A ASP 3.2 0.2 - - - -
498A LEU* 1.3 77.1 - - - +
500A SER* 1.3 63.8 + - - +
502A GLU* 3.2 15.7 + - - +
503A ASN* 3.0 36.8 + - - +
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Residues in contact with SER 500 (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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496A GLN 3.2 10.1 + - - -
497A ASP* 3.0 14.8 + - - -
499A LEU* 1.3 78.7 - - - +
501A GLU* 1.3 66.4 + - - +
503A ASN* 3.1 8.4 + - - +
504A GLU* 3.0 32.9 + - - +
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Residues in contact with GLU 501 (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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497A ASP 3.1 9.1 + - - +
498A LEU* 3.6 31.3 - - - +
500A SER* 1.3 84.8 + - - +
502A GLU* 1.3 64.2 + - - +
503A ASN 3.1 1.0 + - - -
504A GLU* 3.4 28.1 + - - +
505A SER 4.8 0.9 + - - -
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Residues in contact with GLU 502 (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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283A PRO* 4.7 5.6 - - - +
302A GLU* 4.9 2.9 - - - +
363A LEU* 3.7 22.6 - - + +
365A LYS* 3.1 30.3 + - - -
498A LEU 3.0 13.5 + - - +
499A LEU* 3.2 14.9 + - - +
501A GLU* 1.3 77.0 - - - +
503A ASN* 1.3 76.1 + - - +
504A GLU 3.6 0.2 - - - -
505A SER* 4.5 8.1 + - - -
506A THR* 5.1 3.6 + - - +
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Residues in contact with ASN 503 (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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499A LEU* 3.0 31.1 + - - +
500A SER* 3.1 8.2 + - - +
501A GLU 3.0 1.0 - - - -
502A GLU* 1.3 94.6 + - - +
504A GLU* 1.3 64.6 + - - +
505A SER 3.1 3.4 - - - -
506A THR* 2.9 25.0 + - - +
507A ALA* 3.1 16.4 + - + +
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Residues in contact with GLU 504 (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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500A SER* 3.0 21.7 + - - +
501A GLU* 3.4 23.6 + - - +
503A ASN* 1.3 76.5 - - - +
505A SER* 1.3 62.0 + - - +
506A THR 3.3 1.2 + - - -
507A ALA* 3.6 18.1 + - - +
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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