Contacts of the strand formed by residues 496 - 504 (chain A) in PDB entry 2P2F
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 TYR 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.8 10.3 - - + -
413A TRP* 5.7 0.7 - + - -
415A GLN* 2.7 29.5 + - - -
417A GLU* 3.1 32.5 - - + +
418A THR* 4.4 11.2 - - + -
465A VAL* 3.1 7.1 - - - -
466A ILE* 2.8 64.8 + - + +
470A TRP* 4.0 4.9 - + + -
473A GLN* 3.9 12.6 - - - +
484A PHE* 5.7 2.0 - + - -
488A TYR* 3.6 33.0 - + + -
489A PHE* 3.8 29.2 - + + -
495A MET* 1.3 69.7 - - - +
497A PHE* 1.3 62.6 + - - +
498A SER* 3.9 12.5 + - - -
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Residues in contact with PHE 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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463A ASN* 3.7 18.6 - - + -
464A LEU 3.8 6.5 - - - -
465A VAL* 3.9 4.9 - - + -
487A THR 5.0 5.5 - - - +
488A TYR* 3.0 41.2 + - - +
491A THR* 3.9 24.0 - - + -
492A PHE* 3.5 43.7 - + + +
495A MET 3.5 1.9 + - - +
496A TYR* 1.3 72.9 - - - +
498A SER* 1.3 65.6 + - - +
499A GLY* 3.4 20.0 + - - -
500A ASP 4.1 9.0 - - - -
516A VAL* 3.6 24.7 - - + -
517A ASP* 5.7 5.6 - - + -
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Residues in contact with SER 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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413A TRP* 3.8 22.9 - - - -
415A GLN* 2.6 43.7 + - - +
464A LEU* 2.6 29.7 + - - +
465A VAL* 5.4 0.2 - - - -
466A ILE* 5.7 0.7 - - - -
488A TYR* 5.7 3.6 - - - -
496A TYR* 3.8 10.6 + - - -
497A PHE* 1.3 71.7 - - - +
499A GLY* 1.3 55.3 + - - +
500A ASP* 2.9 23.5 + - - +
515A ARG* 3.5 10.6 + - - -
526A ARG* 5.4 0.3 + - - -
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Residues in contact with GLY 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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497A PHE* 3.3 24.5 + - - -
498A SER* 1.3 75.9 - - - +
500A ASP* 1.3 53.0 + - - +
515A ARG* 3.3 24.1 + - - -
516A VAL* 2.7 37.6 + - - +
517A ASP* 3.5 12.7 + - - -
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Residues in contact with ASP 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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413A TRP* 3.1 28.5 + - + +
415A GLN* 3.6 2.9 + - - -
463A ASN* 3.8 4.3 - - - -
464A LEU* 2.9 29.2 + - + +
497A PHE* 4.1 1.2 - - - -
498A SER* 2.9 11.0 + - - +
499A GLY* 1.3 81.2 - - - +
501A GLY* 1.3 63.9 + - - +
512A ILE* 4.3 4.9 - - + +
514A GLY* 3.3 19.9 - - - +
515A ARG* 3.4 5.0 - - - -
516A VAL* 3.9 5.0 - - - +
999A AMP 2.5 47.5 + - - -
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Residues in contact with GLY 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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462A GLY 3.5 9.4 - - - -
464A LEU* 4.6 0.2 - - - -
500A ASP* 1.3 76.5 - - - +
502A ALA* 1.3 62.4 + - - +
512A ILE* 3.7 5.2 - - - +
513A THR* 3.0 30.2 + - - -
514A GLY 2.8 14.4 + - - +
516A VAL* 3.6 19.3 - - - +
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Residues in contact with ALA 502 (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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448A LEU* 3.7 21.9 - - + +
461A GLU* 3.4 5.6 - - - +
462A GLY 2.9 33.4 + - - +
464A LEU* 4.0 20.4 - - + +
501A GLY* 1.3 74.3 - - - +
503A ARG* 1.3 61.0 + - - +
510A TYR* 4.5 9.2 - - + -
511A TRP 3.3 12.3 - - - +
512A ILE* 4.2 5.8 - - + -
513A THR* 3.6 5.7 + - - -
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Residues in contact with ARG 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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448A LEU* 4.4 1.3 - - - -
460A THR 3.6 8.3 - - - +
461A GLU* 3.4 30.5 - - + +
502A ALA* 1.3 73.5 - - - +
504A ARG* 1.3 63.1 + - - +
505A ASP* 3.5 29.1 - - - +
509A TYR 3.5 1.0 - - - +
510A TYR* 3.3 4.1 - - - +
511A TRP* 2.6 91.2 + - + +
513A THR* 4.6 8.7 + - + -
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Residues in contact with ARG 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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446A PRO 5.3 0.2 + - - -
447A ALA* 4.8 3.0 - - - +
448A LEU* 3.7 26.3 - - + +
456A GLN 2.9 26.5 + - - -
457A GLU* 3.8 1.6 + - - +
458A GLY* 2.6 37.2 + - - +
459A ALA* 3.0 4.2 - - - +
460A THR* 2.9 42.3 + - - +
503A ARG* 1.3 77.2 + - - +
505A ASP* 1.3 63.9 + - - +
508A GLY* 3.6 33.7 - - - +
509A TYR 3.3 3.1 - - - +
510A TYR* 3.3 41.9 + - + -
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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