Contacts of the helix formed by residues 487 - 499 (chain A) in PDB entry 2WOK
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 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A VAL 5.4 0.2 + - - -
485A LEU* 3.9 8.9 - - + +
486A ASP* 1.3 72.7 - - - +
488A PRO* 1.3 69.6 - - - +
489A GLU* 2.8 26.4 + - - +
490A VAL* 3.0 28.0 + - + +
491A ASN* 2.9 26.0 + - - +
516A ARG* 4.1 8.7 + - - +
520A HIS* 2.7 37.7 + - + +
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Residues in contact with PRO 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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486A ASP* 3.3 11.2 - - - +
487A ASP* 1.3 88.3 - - - +
489A GLU* 1.3 62.7 + - + +
491A ASN* 3.8 12.5 - - + +
492A ALA* 2.9 30.3 + - - +
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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 ASP* 2.8 15.6 + - - +
488A PRO* 1.3 81.8 - - + +
490A VAL* 1.3 64.3 + - - +
492A ALA* 3.5 5.9 + - - +
493A LEU* 3.0 31.7 + - - +
516A ARG* 3.3 34.4 + - - +
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Residues in contact with VAL 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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468A VAL* 4.2 22.0 - - + +
485A LEU* 4.6 6.5 - - + -
487A ASP* 3.0 33.2 + - + +
489A GLU* 1.3 76.6 - - - +
491A ASN* 1.3 66.1 + - - +
493A LEU* 3.2 9.7 + - - +
494A ILE* 3.0 41.1 + - + +
513A VAL* 4.0 15.7 - - + +
516A ARG* 4.0 24.5 - - + -
517A VAL* 4.5 11.0 - - + -
520A HIS* 4.7 1.6 - - + +
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Residues in contact with ASN 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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468A VAL 4.5 0.7 - - - +
469A ASP* 3.6 6.9 - - - +
470A GLY 3.0 21.1 + - - +
471A ARG* 3.2 46.5 + - - +
486A ASP* 2.8 27.9 + - - -
487A ASP 2.9 23.3 + - - +
488A PRO* 3.8 9.1 - - + +
490A VAL* 1.3 78.4 - - - +
492A ALA* 1.3 57.9 + - - +
494A ILE* 3.4 4.8 + - - +
495A ASP* 3.0 26.4 + - - -
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Residues in contact with ALA 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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488A PRO 2.9 19.7 + - - +
489A GLU* 3.9 9.0 - - - +
491A ASN* 1.3 74.7 - - - +
493A LEU* 1.3 63.6 + - - +
495A ASP* 3.3 11.2 + - - +
496A GLU* 3.0 22.1 + - - +
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Residues in contact with LEU 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 3.0 23.1 + - - +
490A VAL* 3.6 3.4 - - - +
492A ALA* 1.3 71.2 - - - +
494A ILE* 1.3 66.8 + - - +
496A GLU* 3.1 14.3 + - - +
497A THR* 3.0 27.3 + - - +
509A LEU* 3.8 27.4 - - + +
512A ALA* 4.1 24.2 - - + -
513A VAL* 3.4 31.0 - - + +
516A ARG* 4.1 25.8 - - + +
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Residues in contact with ILE 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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461A TYR* 3.7 30.1 - - + -
465A ALA* 4.5 3.4 - - - -
468A VAL* 4.3 8.3 - - + -
469A ASP* 3.6 42.2 - - + +
471A ARG* 4.3 3.4 - - - +
490A VAL* 3.0 29.5 + - + +
491A ASN 3.6 7.4 - - - +
493A LEU* 1.3 76.5 - - - +
495A ASP* 1.3 62.2 + - - +
497A THR* 2.7 28.0 + - - -
498A LEU* 3.2 9.7 + - + +
510A TRP* 3.8 27.4 - - + -
513A VAL* 4.3 5.8 - - + -
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Residues in contact with ASP 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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179A PRO* 5.6 0.3 - - - +
471A ARG* 2.7 39.3 + - - -
491A ASN 3.0 16.8 + - - +
492A ALA* 3.5 12.2 - - - +
494A ILE* 1.3 74.8 - - - +
496A GLU* 1.3 62.8 + - - +
498A LEU* 3.1 27.7 + - - +
499A HIS* 3.4 14.2 + - + +
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Residues in contact with GLU 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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492A ALA 3.0 13.5 + - - +
493A LEU* 3.1 16.4 + - - +
495A ASP* 1.3 74.8 - - - +
497A THR* 1.3 58.6 + - - +
498A LEU 3.2 0.7 + - - -
499A HIS* 3.3 28.7 + - + +
500A THR* 2.6 31.7 + - - +
509A LEU* 3.6 34.3 - - + +
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Residues in contact with THR 497 (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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181A SER* 3.8 1.7 + - - -
493A LEU 3.0 17.8 + - - +
494A ILE* 2.7 16.4 + - - +
496A GLU* 1.3 75.2 - - - +
498A LEU* 1.3 66.2 + - - +
500A THR* 3.1 12.7 + - - +
506A ARG* 3.1 34.0 - - - +
509A LEU* 3.6 27.3 - - + +
510A TRP* 3.3 51.0 + - + +
513A VAL* 5.1 0.4 - - + -
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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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96A GLY* 5.5 1.9 - - - -
178A ARG* 5.7 6.5 - - - -
179A PRO* 3.5 21.6 - - + +
180A PHE* 3.6 32.3 + - + -
181A SER* 2.9 41.9 + - - +
182A ASP 5.2 0.4 - - - +
461A TYR* 3.7 43.3 - - + +
471A ARG* 5.8 0.4 - - - +
494A ILE* 3.4 17.7 - - + +
495A ASP* 3.1 19.6 + - - +
497A THR* 1.3 84.8 + - - +
499A HIS* 1.3 57.2 + - - +
500A THR 3.5 0.2 - - - -
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Residues in contact with HIS 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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95A GLY 4.0 11.8 - - - +
96A GLY* 5.8 0.7 - - - -
179A PRO* 3.5 29.0 - - + +
495A ASP* 3.4 14.2 + - + +
496A GLU* 3.5 36.3 + - + +
497A THR 3.2 0.2 - - - -
498A LEU* 1.3 77.3 - - - +
500A THR* 1.3 64.7 + - - +
501A THR* 3.6 11.4 + - - +
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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