Contacts of the strand formed by residues 499 - 509 (chain A) in PDB entry 2PY5
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 THR 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A TYR* 3.8 0.2 - - - -
495A LEU* 2.9 30.0 + - + +
496A ARG* 3.0 25.6 + - + +
497A GLN 3.1 10.6 + - - -
498A LYS* 1.3 78.5 + - - +
500A TYR* 1.3 62.7 + - - +
529A LYS 3.1 2.9 - - - -
530A CYS* 3.5 29.3 - - - -
531A ALA* 4.3 2.8 + - - +
546A PHE* 3.8 16.8 - - + -
574A ILE* 4.1 20.4 - - + -
1Y G 4.1 8.7 + - - +
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A TYR* 3.8 26.0 - + - -
461A HIS* 3.6 16.2 + + - -
493A LYS 3.2 11.9 - - - +
494A TYR* 3.3 38.1 - + + -
498A LYS* 5.0 0.9 - - - -
499A THR* 1.3 82.2 - - - +
501A ILE* 1.3 69.3 + - - +
502A GLN* 3.6 35.0 + - + -
527A SER* 5.5 2.7 - - - -
529A LYS* 2.7 80.7 + - + +
546A PHE* 3.7 4.8 - - - -
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Residues in contact with ILE 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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492A ALA* 3.2 3.5 - - - +
493A LYS* 2.9 38.1 + - + +
500A TYR* 1.3 79.8 - - - +
502A GLN* 1.3 67.9 + - - +
526A PHE* 4.0 8.3 - - + -
527A SER 3.2 13.5 - - - +
528A VAL* 4.0 19.5 - - + -
541A VAL* 4.1 3.4 - - + -
542A THR 4.2 0.2 - - - +
543A PHE* 3.6 47.8 - - + +
546A PHE* 3.5 50.3 - - + -
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Residues in contact with GLN 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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247A VAL* 3.7 9.2 - - - +
461A HIS* 3.3 19.0 + - - -
487A SER* 4.8 0.5 + - - -
489A PHE* 3.5 24.7 - - + -
491A ARG 3.6 5.2 - - - -
492A ALA* 3.9 10.3 - - + -
494A TYR* 2.9 24.2 + - - -
500A TYR* 3.6 18.8 + - + -
501A ILE* 1.3 81.5 - - - +
503A ASP* 1.3 60.6 + - - +
504A ILE* 3.5 32.1 + - + +
525A LYS 3.5 1.7 - - - +
526A PHE* 3.6 3.5 - - - -
527A SER* 2.8 36.6 + - - +
543A PHE* 4.1 3.6 - - - -
9014A EDO 5.4 1.6 - - - -
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Residues in contact with ASP 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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489A PHE* 3.2 2.4 - - - +
490A LYS* 2.8 36.5 + - + +
491A ARG* 2.8 50.8 + - + +
502A GLN* 1.3 68.4 - - - +
504A ILE* 1.3 61.6 + - - +
524A ILE* 3.5 25.3 - - + +
525A LYS 3.7 2.9 - - - -
526A PHE* 3.4 16.1 - - - +
543A PHE* 3.2 21.5 - - - -
8010A EDO 5.1 2.4 + - - -
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Residues in contact with ILE 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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487A SER* 4.0 20.0 - - - +
488A THR 3.6 11.7 - - - +
489A PHE* 4.1 4.5 - - + +
502A GLN* 3.5 35.7 - - + +
503A ASP* 1.3 72.5 - - - +
505A TYR* 1.3 77.3 + - - +
506A MET* 3.5 13.2 - - - +
515A GLU* 4.8 0.9 - - + -
524A ILE* 3.4 6.2 - - - -
525A LYS* 2.8 49.2 + - + +
527A SER* 3.9 19.5 - - - +
9014A EDO 3.7 31.0 - - - +
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Residues in contact with TYR 505 (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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244A GLU* 2.6 29.0 + - - -
488A THR* 3.0 30.7 + - + +
489A PHE 3.7 20.6 - - - -
490A LYS* 3.1 30.8 - - + +
504A ILE* 1.3 81.1 - - - +
506A MET* 1.3 59.7 + - - +
515A GLU* 3.9 0.9 - - - +
516A GLY 2.9 33.8 + - - +
517A SER 3.9 5.4 - - - +
518A PRO* 3.7 28.1 + - + +
521A TYR* 3.7 37.7 - + + -
523A ASP 4.0 2.2 - - - -
524A ILE* 4.0 8.7 - - + -
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Residues in contact with MET 506 (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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504A ILE* 3.5 15.3 - - - +
505A TYR* 1.3 79.5 - - - +
507A LYS* 1.3 61.2 - - - +
513A LEU* 3.8 33.7 - - + +
514A VAL* 3.2 34.3 - - - +
515A GLU* 3.9 15.7 - - - +
516A GLY* 3.6 3.6 - - - +
521A TYR* 3.3 3.3 - - - +
522A THR* 2.8 22.6 + - - -
523A ASP 2.9 19.0 + - - +
525A LYS* 3.5 52.5 - - + +
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Residues in contact with LYS 507 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A MET* 1.3 75.6 - - - +
508A GLU* 1.3 63.8 + - - +
509A VAL* 4.1 13.9 - - + +
513A LEU* 3.5 4.2 - - - -
514A VAL* 2.7 48.5 + - + +
515A GLU 3.4 24.7 - - - +
516A GLY* 3.9 5.2 - - - -
520A ASP* 3.0 45.8 + - - +
521A TYR* 4.2 4.9 - - - -
522A THR* 3.5 10.5 - - + +
9012A EDO 5.5 3.5 + - - -
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Residues in contact with GLU 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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507A LYS* 1.3 72.7 - - - +
509A VAL* 1.3 64.7 + - - +
511A GLY* 4.1 25.2 - - - +
512A LYS* 3.3 17.7 - - - +
513A LEU* 3.2 25.6 + - - +
522A THR* 3.1 24.1 + - + +
523A ASP* 4.9 3.3 - - - +
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Residues in contact with VAL 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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507A LYS* 3.6 19.7 + - + +
508A GLU* 1.3 78.2 - - - +
510A ASP* 1.3 87.6 + - - +
511A GLY 3.2 0.7 - - - -
512A LYS* 2.7 26.7 + - - +
514A VAL* 3.8 29.1 - - + +
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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