Contacts of the strand formed by residues 489 - 500 (chain A) in PDB entry 2WKP
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 LYS 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A GLU* 3.2 33.8 + - - +
481A ILE* 3.9 28.5 - - + +
482A ASN 3.4 6.5 - - - +
483A TYR* 4.1 16.8 - - + -
487A GLY 3.4 3.8 + - - +
488A LYS* 1.3 75.6 - - - +
490A PHE* 1.3 67.7 + - - +
491A TRP* 4.2 18.4 - - - +
517A THR* 5.3 4.9 - - - +
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Residues in contact with PHE 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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437A LEU* 4.0 35.2 - - + -
438A THR* 4.8 9.6 - - + -
453A LEU* 4.9 5.2 - - + -
481A ILE* 3.5 3.5 - - - +
482A ASN* 2.8 56.9 + - + +
483A TYR 3.7 26.7 - - - -
484A THR* 3.9 15.7 - - + -
488A LYS 3.9 9.0 - - - -
489A LYS* 1.3 80.5 - - - +
491A TRP* 1.3 75.2 + - - +
492A ASN* 4.0 14.1 - - + -
513A GLN* 5.6 0.9 - - + -
515A ASP* 3.8 14.8 - - + +
516A GLY 3.7 11.4 - - - +
517A THR* 5.6 0.9 - - + +
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Residues in contact with TRP 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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479A GLN* 3.8 30.3 - - + +
480A LEU* 3.8 23.8 - - - -
481A ILE* 3.5 33.2 - - + +
489A LYS* 4.2 15.6 - - - +
490A PHE* 1.3 75.3 - - - +
492A ASN* 1.3 59.9 + - - +
493A LEU 4.1 0.7 - - - -
514A LEU 3.8 0.3 - - - +
515A ASP* 3.3 5.5 - - - -
516A GLY* 2.8 38.9 + - - +
517A THR 3.7 8.5 + - - -
518A GLU* 3.4 34.4 - - - +
519A HIS* 3.6 46.3 - + + +
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Residues in contact with ASN 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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478A VAL 3.7 0.2 - - - +
479A GLN* 3.2 4.6 - - - -
480A LEU* 2.8 44.2 + - + +
482A ASN* 2.8 29.2 + - - +
490A PHE* 4.0 13.1 - - + -
491A TRP* 1.3 75.1 - - - +
493A LEU* 1.3 72.8 + - - +
494A PHE* 3.4 14.5 + - - +
513A GLN* 3.4 24.9 - - - +
514A LEU 3.8 3.3 + - - -
1725A FMN 3.1 23.6 + - - -
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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
----------------------------------------------------------
477A THR* 4.2 18.2 - - + -
478A VAL 3.6 8.5 - - - +
479A GLN* 3.5 31.8 - - + +
491A TRP 4.1 0.8 - - - -
492A ASN* 1.3 68.7 - - - +
494A PHE* 1.3 58.4 + - - +
512A VAL 3.7 2.9 - - - +
514A LEU* 2.9 50.2 + - + +
520A VAL* 4.6 15.0 - - + -
525A GLU* 4.4 6.5 - - + +
528A GLY* 3.6 38.4 - - - +
529A VAL* 3.8 9.0 - - + +
532A ILE* 3.7 9.8 - - + +
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Residues in contact with PHE 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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466A ILE* 3.9 29.2 - - + -
476A VAL* 5.1 2.0 - - + -
477A THR* 3.2 4.9 - - - +
478A VAL* 2.8 57.0 + - + +
480A LEU* 4.2 3.4 - - + -
492A ASN* 3.4 19.5 + - - +
493A LEU* 1.3 73.5 - - - +
495A HIS* 1.3 62.4 + - - +
496A LEU* 3.7 28.3 - - + -
511A GLY* 3.7 14.6 - - - -
512A VAL 3.4 14.1 - - - -
513A GLN* 3.9 4.3 - - + -
532A ILE* 4.2 1.6 - - - -
1725A FMN 3.1 61.0 - + - -
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Residues in contact with HIS 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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475A GLU* 3.4 26.9 + - - -
476A VAL 3.2 5.1 + - - -
477A THR* 2.7 24.3 + - - +
494A PHE* 1.3 78.6 - - - +
496A LEU* 1.3 72.8 + - - +
497A GLN* 2.8 28.8 + - - -
510A ILE 3.8 0.3 - - - +
511A GLY* 3.3 3.1 - - - -
512A VAL* 2.8 39.1 + - + +
532A ILE* 3.5 27.3 - - + +
533A LYS* 3.9 24.9 - - + +
536A ALA* 3.7 20.2 - - + -
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Residues in contact with LEU 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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466A ILE* 4.6 2.2 - - + -
469A ALA* 4.5 2.0 - - + -
470A ILE* 3.7 21.8 - - + -
474A THR 3.5 22.4 - - - +
475A GLU* 3.1 7.4 - - - +
476A VAL* 2.8 46.1 + - + +
494A PHE* 3.7 18.8 - - + -
495A HIS* 1.3 77.6 - - - +
497A GLN* 1.3 65.5 + - - +
509A PHE* 3.9 20.4 - - + -
510A ILE 3.3 6.5 - - - +
1725A FMN 3.5 45.8 - - + -
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Residues in contact with GLN 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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475A GLU* 3.5 16.9 - - + +
495A HIS* 2.8 24.3 + - - +
496A LEU* 1.3 76.9 - - - +
498A PRO* 1.3 81.1 + - + +
499A MET 3.7 0.2 + - - -
509A PHE* 4.0 4.7 - - - -
510A ILE* 2.8 46.9 + - + +
533A LYS* 4.7 2.8 - - - +
536A ALA* 3.5 32.9 + - + +
537A GLU* 3.0 29.4 + - - +
540A ASP* 4.7 9.5 + - - +
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Residues in contact with PRO 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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473A GLN 3.5 30.5 - - - +
474A THR* 4.0 2.9 - - - +
475A GLU* 4.0 15.3 - - + +
497A GLN* 1.3 99.5 + - + +
499A MET* 1.3 59.7 + - - +
500A ARG* 4.2 12.7 + - - +
506A VAL* 4.0 24.9 - - + -
508A TYR 3.5 6.3 - - - +
509A PHE* 3.8 14.5 - - + -
510A ILE* 5.6 0.4 - - - -
540A ASP* 4.6 3.8 - - - +
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Residues in contact with MET 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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417A ILE* 4.6 2.7 - - + -
497A GLN 3.7 0.4 + - - -
498A PRO* 1.3 74.5 - - - +
500A ARG* 1.3 63.2 + - - +
506A VAL* 3.6 1.6 - - - -
507A GLN* 2.7 34.3 + - + +
508A TYR* 2.7 45.7 + - + +
510A ILE* 3.1 38.6 - - + -
540A ASP* 3.4 30.3 - - - +
543A ALA* 3.4 36.6 - - + -
544A LYS* 4.7 5.2 - - + -
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Residues in contact with ARG 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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473A GLN* 3.5 29.3 + - - +
498A PRO* 4.2 11.2 + - + +
499A MET* 1.3 86.0 - - - +
501A ASP* 1.3 65.3 + - - +
504A GLY* 3.1 33.2 + - - +
505A ASP* 3.1 10.7 - - - +
506A VAL* 3.7 25.0 - - + +
507A GLN* 4.7 2.0 - - - +
540A ASP* 4.7 2.0 + - - +
544A LYS* 5.6 7.1 - - - +
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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