Contacts of the strand formed by residues 506 - 516 (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 VAL 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A PRO* 4.1 19.1 - - + +
421A ARG* 4.2 17.3 + - - +
473A GLN* 3.6 39.6 + - + +
498A PRO* 4.0 15.0 - - + -
499A MET 3.6 5.8 - - - +
500A ARG* 3.7 25.5 - - - +
501A ASP* 5.1 0.4 - - - +
504A GLY 4.1 0.4 + - - -
505A ASP* 1.3 72.9 - - - +
507A GLN* 1.3 60.8 + - - +
508A TYR 3.7 20.0 - - - +
509A PHE* 4.2 13.0 - - + -
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Residues in contact with GLN 507 (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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419A ASP* 3.9 6.2 - - - +
420A PRO* 3.3 16.1 - - - +
421A ARG* 3.9 19.5 + - - +
499A MET* 2.7 15.8 + - + +
500A ARG 4.8 0.8 - - - -
501A ASP* 3.8 28.2 - - + +
505A ASP 3.3 1.0 + - - -
506A VAL* 1.3 75.6 - - - +
508A TYR* 1.3 107.4 + - + +
548A LYS* 4.8 4.6 - - - +
617A GLN* 3.4 35.5 + - + +
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Residues in contact with TYR 508 (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* 3.6 21.1 - - + -
418A THR 3.3 19.7 - - - +
419A ASP* 4.2 7.2 - - + -
420A PRO* 3.7 2.2 - - - -
428A ILE* 3.9 15.9 - - + -
498A PRO* 3.5 3.3 - - - +
499A MET* 2.7 61.8 + - + +
506A VAL* 3.7 4.4 - - - +
507A GLN* 1.3 119.9 + - + +
509A PHE* 1.3 62.9 + - - +
543A ALA* 4.9 8.5 - - + -
546A LEU* 4.2 17.8 + - + +
548A LYS* 4.2 9.8 - - + +
599A TRP* 3.5 31.3 - + - -
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Residues in contact with PHE 509 (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* 3.3 6.9 - - - +
418A THR* 2.9 41.6 + - - +
420A PRO* 3.7 36.1 - - + -
425A ASN* 3.9 9.4 - - - -
470A ILE* 3.6 45.3 - - + -
473A GLN* 4.3 13.7 - - + -
474A THR 4.8 0.2 - - - -
496A LEU* 3.9 21.3 - - + -
497A GLN 3.6 1.3 - - - -
498A PRO* 3.8 32.1 - - + -
506A VAL* 4.2 11.2 - - + -
508A TYR* 1.3 75.0 - - - +
510A ILE* 1.3 61.9 + - - +
1725A FMN 3.7 17.4 - - + +
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Residues in contact with ILE 510 (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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416A VAL 3.7 5.6 - - - +
417A ILE* 4.5 3.4 - - + -
495A HIS* 3.8 0.7 - - - +
496A LEU* 3.3 3.8 - - - +
497A GLN* 2.8 45.6 + - + +
499A MET* 3.1 43.1 - - + -
509A PHE* 1.3 75.1 - - - +
511A GLY* 1.3 61.5 + - - +
512A VAL* 4.2 8.7 - - + -
536A ALA* 3.9 12.3 - - + +
539A ILE* 3.8 38.1 - - + -
540A ASP* 3.6 33.0 - - + +
1725A FMN 3.6 3.5 - - - +
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Residues in contact with GLY 511 (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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415A PHE* 3.1 6.4 - - - +
416A VAL 3.0 34.3 + - - -
494A PHE* 3.7 12.6 - - - -
495A HIS 3.3 7.0 - - - -
510A ILE* 1.3 75.1 - - - +
512A VAL* 1.3 63.3 + - - -
513A GLN* 3.8 5.3 + - - +
1725A FMN 3.4 16.3 - - - +
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Residues in contact with VAL 512 (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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413A LYS* 5.3 2.2 - - + -
414A ASN 3.5 11.9 - - - +
415A PHE* 4.2 0.4 - - + -
493A LEU 3.7 1.9 - - - +
494A PHE* 3.4 5.6 - - - -
495A HIS* 2.8 37.2 + - + +
510A ILE* 4.2 2.0 - - + -
511A GLY* 1.3 76.7 - - - -
513A GLN* 1.3 65.8 + - - +
532A ILE* 3.8 32.4 - - + +
535A THR* 4.0 15.5 - - + -
536A ALA* 4.0 25.6 - - + +
539A ILE* 3.7 27.6 - - + -
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Residues in contact with GLN 513 (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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414A ASN* 3.0 47.0 + - + +
415A PHE* 3.5 3.1 - - - -
416A VAL* 4.2 6.3 - - - +
434A PHE* 3.3 34.7 - - + -
437A LEU* 4.6 12.8 - - + -
453A LEU* 5.2 1.1 - - + -
490A PHE* 5.6 1.3 - - + -
492A ASN* 3.4 22.4 - - - +
494A PHE* 3.9 4.5 - - + -
511A GLY 3.8 11.7 + - - -
512A VAL* 1.3 79.9 - - - +
514A LEU* 1.3 61.3 + - - +
515A ASP 3.8 0.2 - - - -
1725A FMN 3.0 42.3 + - - +
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Residues in contact with LEU 514 (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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414A ASN* 5.8 0.4 - - - +
491A TRP 3.8 0.9 - - - +
492A ASN* 3.8 1.5 + - - -
493A LEU* 2.9 52.5 + - + +
512A VAL 4.2 0.2 + - - -
513A GLN* 1.3 72.3 - - - +
515A ASP* 1.3 74.5 + - - +
516A GLY 3.8 0.2 + - - -
528A GLY* 3.7 35.4 - - - +
531A LEU* 4.6 15.7 - - + -
532A ILE* 3.7 14.1 - - + +
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Residues in contact with ASP 515 (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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414A ASN* 3.1 19.8 + - - -
437A LEU* 3.7 35.1 - - + +
490A PHE* 3.8 15.9 - - + -
491A TRP 3.3 6.3 - - - -
492A ASN* 4.7 0.7 - - - +
513A GLN* 3.8 2.2 - - + -
514A LEU* 1.3 86.1 - - - +
516A GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 516 (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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490A PHE* 3.7 9.4 - - - +
491A TRP* 2.8 33.6 + - - -
514A LEU 3.8 0.6 + - - -
515A ASP* 1.3 76.6 - - - +
517A THR* 1.3 64.4 + - - +
518A GLU* 3.5 6.5 - - - -
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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