Contacts of the strand formed by residues 506 - 517 (chain A) in PDB entry 2WIN
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 SER 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A MET 4.2 1.7 - - - +
474A ASN* 3.8 13.7 + - - -
475A LYS 4.5 2.9 + - - -
503A PHE 3.5 4.7 - - - +
505A PRO* 1.3 82.9 - - - +
507A PHE* 1.3 60.5 + - - +
508A ARG* 5.9 0.3 + - - -
530A TRP* 3.1 34.3 + - - -
531A VAL 3.6 8.3 - - - -
532A ASP* 4.3 9.6 - - - -
533A VAL 4.4 0.4 - - - +
599A GLU* 4.1 20.7 + - - +
602A ASP* 5.1 3.8 + - - -
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Residues in contact with PHE 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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443A LEU* 3.8 10.8 - - + -
449A LEU* 4.0 19.7 - - + -
472A ILE* 4.4 7.9 - - + -
473A MET 3.1 13.9 - - - +
474A ASN* 4.7 1.8 - - + -
497A LEU* 4.1 14.4 - - + -
499A ILE* 3.7 16.6 - - + -
503A PHE* 3.3 44.2 - + + +
506A SER* 1.3 74.6 - - - +
508A ARG* 1.3 72.1 + - - +
509A LEU* 4.9 7.4 - - + -
529A VAL 4.3 0.3 - - - +
530A TRP* 4.5 0.9 - - - -
531A VAL* 3.2 42.5 + - + +
533A VAL* 3.5 32.3 - - + -
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Residues in contact with ARG 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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471A LEU 4.4 0.2 - - - -
472A ILE* 3.5 6.1 - - - +
473A MET* 3.0 45.6 + - + +
506A SER* 5.9 0.4 + - - -
507A PHE* 1.3 83.7 - - - +
509A LEU* 1.3 64.8 + - - +
510A VAL* 4.3 1.3 - - + -
528A SER* 5.8 2.5 - - - -
529A VAL 3.4 7.6 - - - +
530A TRP* 4.0 39.5 - - + +
599A GLU* 5.3 2.4 + - - -
602A ASP* 2.8 33.1 + - - -
604A GLY* 3.8 28.5 + - - -
605A CYS* 4.9 0.2 - - - +
606A THR 3.4 30.8 + - - +
607A PRO 5.1 0.4 - - - -
620A ALA* 4.0 32.1 + - + +
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Residues in contact with LEU 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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436A LEU* 3.6 23.1 - - + +
451A VAL* 4.1 24.0 - - + -
453A PHE* 4.8 1.1 - - + -
470A TYR* 3.8 25.8 - - + -
471A LEU 3.3 17.0 - - - +
472A ILE* 3.5 20.6 - - + -
495A LEU* 5.6 1.3 - - + -
497A LEU* 5.1 8.3 - - + -
507A PHE* 4.9 8.1 - - + -
508A ARG* 1.3 76.5 - - - +
510A VAL* 1.3 65.1 + - - +
511A ALA* 4.5 4.7 - - + -
527A ASP 3.8 1.0 - - - +
528A SER* 3.4 2.1 - - - -
529A VAL* 3.0 43.0 + - + +
531A VAL* 6.2 1.1 - - + -
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Residues in contact with VAL 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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469A THR 3.7 0.8 - - - +
470A TYR* 3.0 5.7 - - - +
471A LEU* 2.8 61.5 + - + +
473A MET* 5.4 2.7 - - + -
508A ARG* 5.4 2.7 - - + -
509A LEU* 1.3 76.1 - - - +
511A ALA* 1.3 60.8 + - - +
512A TYR* 5.8 0.4 - - + -
526A ALA* 6.1 0.9 - - + -
527A ASP 3.6 4.5 - - - +
528A SER* 3.5 23.3 - - - -
616A VAL* 4.9 8.1 - - + +
617A PHE* 4.8 11.9 - - + -
620A ALA* 3.7 21.1 - - + -
622A LEU* 3.7 20.9 - - + -
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Residues in contact with ALA 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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434A LEU* 3.4 9.5 - - + +
436A LEU* 3.6 16.4 - - + -
453A PHE* 3.4 35.2 - - + -
468A TYR* 5.0 1.8 - - + -
469A THR 3.6 5.6 - - - +
470A TYR* 4.3 7.0 - - + -
509A LEU* 4.5 0.7 - - + -
510A VAL* 1.3 76.7 - - - +
512A TYR* 1.3 61.2 + - - +
526A ALA* 3.3 1.7 - - - -
527A ASP 2.9 32.2 + - - -
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Residues in contact with TYR 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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5A SER* 3.5 10.0 + - - -
7A ILE* 3.7 17.4 - - + +
23A GLU* 2.6 29.5 + - - -
25A HIS* 4.0 3.5 + + - -
434A LEU* 4.1 3.1 - - - +
468A TYR* 3.8 2.4 - - - +
469A THR* 3.0 71.8 + - + +
471A LEU* 4.4 1.8 - - + -
510A VAL 5.7 0.7 - - - -
511A ALA* 1.3 76.5 - - - +
513A TYR* 1.3 69.8 + - - +
514A THR* 4.7 16.4 - - + -
524A VAL* 3.9 17.0 - - + -
525A VAL 3.1 15.5 - - - +
526A ALA* 3.5 14.8 - - + -
617A PHE* 3.6 17.7 - + + -
624A PHE* 3.6 21.9 - + - -
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Residues in contact with TYR 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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433A TYR 2.8 27.4 + - - -
434A LEU* 3.5 30.3 - - + -
455A LEU* 3.4 18.8 - - + +
457A MET* 3.4 26.8 - - + +
465A ILE* 3.4 26.9 - - + -
467A TYR* 4.0 19.3 - - - +
468A TYR* 3.5 22.2 - + + -
512A TYR* 1.3 79.7 - - - +
514A THR* 1.3 60.6 + - - +
515A LEU* 4.1 6.5 - - + -
523A GLU 4.1 0.5 - - - +
524A VAL* 3.8 1.7 - - - -
525A VAL* 3.1 47.9 + - + +
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Residues in contact with THR 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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3A MET* 3.1 17.9 - - - +
25A HIS* 3.6 46.0 - - + +
464A LYS 5.5 0.9 - - - +
465A ILE* 4.4 4.1 - - - +
467A TYR* 4.9 8.2 + - + +
512A TYR* 4.7 7.0 - - + -
513A TYR* 1.3 77.7 - - - +
515A LEU* 1.3 64.0 + - - +
522A ARG* 2.9 26.3 + - - +
523A GLU 3.3 8.0 + - - -
524A VAL* 4.2 8.5 - - - -
624A PHE* 6.3 0.2 - - + -
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Residues in contact with LEU 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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432A ASN* 5.1 2.0 - - - +
457A MET* 4.4 8.7 - - + -
461A HIS* 3.4 40.2 - - + +
464A LYS* 3.7 18.4 - - + +
465A ILE* 3.6 28.5 - - + -
513A TYR* 4.1 15.3 - - + -
514A THR* 1.3 78.8 + - - +
516A ILE* 1.3 67.1 + - - +
517A GLY* 4.2 1.4 + - - +
522A ARG* 3.4 18.2 + - - +
523A GLU* 3.4 43.8 + - + +
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Residues in contact with ILE 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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1A SER* 5.1 11.2 - - - +
26A ASP* 3.8 17.0 - - - +
461A HIS* 3.9 8.8 + - - +
464A LYS* 5.1 5.1 - - - +
515A LEU* 1.3 86.8 - - - +
517A GLY* 1.3 61.6 + - - +
520A GLY* 4.0 29.8 - - - +
521A GLN 4.1 4.7 - - - +
522A ARG* 3.2 39.3 - - - +
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Residues in contact with GLY 517 (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 HIS* 3.6 20.0 - - - -
515A LEU* 4.2 2.3 + - - +
516A ILE* 1.3 79.1 - - - +
518A ALA* 1.3 62.2 + - - +
519A SER 2.6 16.9 + - - -
520A GLY 3.4 3.0 + - - -
521A GLN 3.4 21.6 + - - +
523A GLU* 5.8 5.8 + - - +
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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