Contacts of the helix formed by residues 456 - 468 (chain A) in PDB entry 2FY5
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 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A CYS* 6.4 0.4 - - - +
34A HIS* 3.5 5.2 + - - -
432A LEU* 4.3 1.2 - - - +
453A ARG 3.6 17.7 - - - +
454A SER 2.9 10.2 + - - +
455A ALA* 1.3 75.6 - - - +
457A PRO* 1.3 75.3 - - + +
458A GLU* 3.4 12.9 + - - +
459A ALA* 3.1 25.2 + - - +
460A LEU* 3.3 15.4 + - - +
485A ALA 5.1 2.6 + - - -
488A ALA* 4.4 18.3 - - + +
489A GLN* 4.3 10.5 - - - +
492A TYR* 5.1 9.4 - - + -
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Residues in contact with PRO 457 (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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30A GLN* 3.9 33.0 - - + +
31A CYS* 5.6 3.1 - - - -
34A HIS* 3.6 29.8 - - + +
456A THR* 1.3 85.5 - - + +
458A GLU* 1.3 78.0 + - - +
460A LEU* 3.3 7.8 + - + +
461A ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 458 (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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456A THR* 3.4 10.0 - - - +
457A PRO* 1.3 94.1 - - + +
459A ALA* 1.3 62.4 + - - +
461A ALA* 3.8 6.7 + - - +
462A PHE* 3.4 20.1 + - - +
481A LEU* 4.3 3.6 - - - +
484A ASP* 3.3 27.5 - - - +
485A ALA* 3.7 15.9 - - - +
487A ARG* 4.0 11.5 + - - +
488A ALA* 3.4 29.2 - - + +
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Residues in contact with ALA 459 (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 VAL* 5.7 5.4 - - + -
422A GLN* 4.3 18.4 - - + -
432A LEU* 4.2 5.6 - - + -
454A SER 4.1 13.7 - - - +
456A THR* 3.1 24.2 + - - +
457A PRO 3.2 0.2 - - - -
458A GLU* 1.3 75.6 - - - +
460A LEU* 1.3 62.1 + - - +
462A PHE* 3.3 3.1 + - + +
463A VAL* 3.0 34.5 + - - +
485A ALA* 4.3 12.5 - - + +
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Residues in contact with LEU 460 (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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34A HIS* 3.9 35.2 - - + +
426A TYR* 4.2 14.6 - - + -
432A LEU* 3.8 30.5 - - + +
456A THR 3.3 10.0 + - - +
457A PRO* 3.3 11.6 + - + +
459A ALA* 1.3 79.9 - - - +
461A ALA* 1.3 57.6 + - - +
463A VAL* 3.1 6.5 - - - +
464A ARG* 3.0 74.4 + - - +
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Residues in contact with ALA 461 (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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457A PRO 3.2 12.2 + - - +
458A GLU* 4.1 7.0 - - - +
459A ALA 3.3 0.2 - - - -
460A LEU* 1.3 79.9 - - - +
462A PHE* 1.3 61.4 + - - +
464A ARG* 4.2 6.8 - - - +
465A ALA* 3.3 23.2 + - - +
481A LEU* 3.6 22.7 - - + +
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Residues in contact with PHE 462 (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 VAL* 3.8 30.7 - - + -
423A LEU* 3.8 26.5 - - + -
458A GLU 3.4 15.2 + - - +
459A ALA 3.3 4.4 + - - +
460A LEU 3.2 0.6 - - - -
461A ALA* 1.3 77.9 - - - +
463A VAL* 1.3 73.8 + - + +
465A ALA* 3.2 2.8 + - + +
466A VAL* 3.1 48.3 + - + +
478A LYS* 3.7 8.3 - - - -
481A LEU* 3.9 16.6 - - + +
482A LEU* 3.6 46.9 - - + -
485A ALA* 4.2 3.4 - - + -
600A MET* 4.3 5.4 - - + -
603A LEU* 3.7 15.5 - - + -
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Residues in contact with VAL 463 (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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422A GLN* 3.9 12.6 - - + +
423A LEU* 3.5 46.7 - - + +
426A TYR* 3.8 32.5 - - + -
432A LEU* 4.3 3.6 - - + -
459A ALA* 3.0 22.5 + - - +
460A LEU* 3.1 20.9 - - + +
462A PHE* 1.3 82.2 - - + +
464A ARG* 1.3 57.5 + - - +
467A THR* 2.8 36.5 + - - +
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Residues in contact with ARG 464 (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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426A TYR* 3.4 27.9 + - + +
460A LEU* 3.0 55.9 + - + +
461A ALA* 4.2 5.8 - - - +
463A VAL* 1.3 76.1 - - - +
465A ALA* 1.3 65.7 + - - +
467A THR* 3.9 4.7 - - - -
468A ASP* 3.0 33.5 + - + +
471A ALA* 5.5 0.2 - - - +
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Residues in contact with ALA 465 (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 ALA 3.3 17.4 + - - +
462A PHE 3.2 5.0 + - - +
464A ARG* 1.3 82.3 - - - +
466A VAL* 1.3 61.4 + - + +
468A ASP 4.1 8.1 + - - +
471A ALA* 5.9 0.2 - - - -
473A VAL* 4.0 32.5 + - + +
478A LYS* 3.3 23.1 - - + -
481A LEU* 3.5 22.0 - - + -
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Residues in contact with VAL 466 (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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423A LEU* 4.1 19.5 - - + -
427A ARG* 5.4 3.6 - - - +
462A PHE* 3.1 49.6 + - + +
463A VAL 4.1 2.9 - - - +
465A ALA* 1.3 79.4 - - - +
467A THR* 1.3 62.4 + - + +
468A ASP 5.0 0.9 - - - -
469A HIS* 4.9 9.5 + - - -
478A LYS* 3.9 30.3 + - + +
599A ASP* 4.4 21.5 - - + +
603A LEU* 4.6 4.9 - - + -
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Residues in contact with THR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.3 11.0 - - + -
426A TYR* 3.2 30.5 - - + -
427A ARG* 4.0 28.7 - - + +
463A VAL 2.8 22.5 + - - +
464A ARG* 3.8 1.9 + - - -
466A VAL* 1.3 79.7 - - + +
468A ASP* 1.3 61.0 + - - +
469A HIS* 3.2 25.4 + - - -
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Residues in contact with ASP 468 (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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464A ARG* 3.0 22.8 + - + +
465A ALA 4.1 8.2 + - - +
466A VAL 3.6 1.5 - - - -
467A THR* 1.3 75.3 + - - +
469A HIS* 1.3 62.4 + - - +
470A LYS* 3.7 19.4 + - - +
471A ALA* 3.1 40.4 + - + +
472A ALA* 3.7 2.4 + - - -
473A VAL 4.9 0.5 + - - -
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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