Contacts of the helix formed by residues 457 - 471 (chain A) in PDB entry 1BHG
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 GLU 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A HIS 3.6 4.3 + - - +
456A LEU* 1.3 75.8 - - + +
458A SER* 1.3 68.8 + - - +
460A GLY* 3.2 10.2 + - - -
461A TYR* 3.6 8.3 + - - +
491A LYS* 2.9 40.0 + - + +
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Residues in contact with SER 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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415A PRO* 4.8 4.3 + - - +
418A PHE* 4.4 21.5 - - - +
456A LEU* 4.1 17.7 - - - +
457A GLU* 1.3 76.7 - - - +
459A ALA* 1.3 63.5 + - - +
461A TYR* 3.1 19.7 + - - +
462A TYR* 3.1 13.7 + - - +
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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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418A PHE* 3.4 39.4 - - + -
452A PRO* 5.7 0.2 - - + -
453A ALA 3.5 28.5 - - - +
454A SER* 4.1 4.7 - - - -
456A LEU* 3.7 8.2 + - + +
457A GLU 3.2 0.6 - - - -
458A SER* 1.3 81.1 + - - +
460A GLY* 1.3 56.2 + - - +
462A TYR* 3.5 2.1 - - - +
463A LEU* 2.8 36.2 + - + +
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Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A SER 4.8 0.8 + - - -
456A LEU 3.5 4.8 + - - -
457A GLU 3.2 8.7 + - - -
459A ALA* 1.3 77.5 - - - +
461A TYR* 1.3 56.0 + - - +
463A LEU* 3.6 2.3 + - - +
464A LYS* 3.1 28.4 + - - +
491A LYS* 4.0 21.8 - - - -
492A GLY* 4.2 13.0 - - - -
495A TYR* 4.0 11.0 - - - -
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Residues in contact with TYR 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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420A ASN* 6.0 0.4 - - - -
423A LEU* 3.9 13.0 - - + -
457A GLU 3.6 6.1 + - - +
458A SER* 3.1 13.4 + - - +
460A GLY* 1.3 73.8 - - - +
462A TYR* 1.3 72.4 + - + +
464A LYS* 3.1 20.3 + - - +
465A MET* 2.9 64.8 + - + +
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Residues in contact with TYR 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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181A LEU* 4.4 5.7 - - - +
412A LEU* 3.9 14.9 - - + +
417A PHE 3.7 8.0 + - - -
418A PHE* 3.3 52.9 - + + +
422A SER* 4.2 5.2 + - - -
423A LEU* 4.1 36.8 - - + -
426A HIS* 3.8 29.8 - + + +
458A SER 3.1 9.1 + - - +
459A ALA* 3.5 10.1 - - - +
461A TYR* 1.3 85.9 - - + +
463A LEU* 1.3 75.5 + - + +
465A MET* 2.9 13.2 + - - +
466A VAL* 2.9 35.9 + - + -
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Residues in contact with LEU 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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412A LEU* 5.7 0.9 - - + -
418A PHE* 5.2 3.6 - - + -
448A VAL* 4.6 16.6 - - + -
449A ALA* 4.6 12.3 - - + -
452A PRO* 4.1 9.4 - - + -
454A SER* 3.8 17.0 - - - -
459A ALA* 2.8 21.4 + - + +
460A GLY* 3.7 6.1 - - - +
461A TYR 3.1 0.2 - - - -
462A TYR* 1.3 92.7 - - + +
464A LYS* 1.3 58.2 + - - +
466A VAL* 4.0 2.6 - - + +
467A ILE* 2.8 41.8 + - + +
481A PHE* 3.5 43.7 - - + -
492A GLY* 4.2 11.0 - - - +
495A TYR* 5.5 0.4 - - + -
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Residues in contact with LYS 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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460A GLY 3.1 15.2 + - - +
461A TYR* 3.5 21.0 - - - +
463A LEU* 1.3 73.7 - - - +
465A MET* 1.3 77.0 + - + +
467A ILE* 4.4 3.8 - - - +
468A ALA* 2.8 40.4 + - + +
495A TYR* 2.9 62.3 + - + -
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Residues in contact with MET 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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423A LEU* 3.7 12.6 - - + -
427A MET* 3.5 22.4 - - + +
461A TYR* 2.9 62.0 + - + +
462A TYR 2.9 8.2 + - - +
464A LYS* 1.3 109.0 - - + +
466A VAL* 1.3 66.3 + - - +
468A ALA* 3.7 5.8 - - + +
469A HIS* 3.0 19.8 + - - +
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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* 4.3 10.3 - - + -
426A HIS* 3.0 45.8 - - + +
427A MET* 3.7 11.1 - - + +
430A MET* 4.1 6.9 - - + +
448A VAL* 3.6 19.3 - - + -
462A TYR* 2.9 42.5 + - + +
463A LEU* 4.0 5.2 - - + +
465A MET* 1.3 76.4 - - - +
467A ILE* 1.3 60.1 + - - +
469A HIS* 3.4 5.8 - - - +
470A THR* 3.0 26.9 + - - -
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Residues in contact with ILE 467 (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 VAL* 3.6 34.3 - - + -
463A LEU* 2.8 31.8 + - + +
464A LYS* 4.0 2.5 - - - +
466A VAL* 1.3 70.2 - - - +
468A ALA* 1.3 58.8 + - - +
469A HIS 3.0 4.7 - - - -
470A THR* 2.9 19.8 + - - -
471A LYS* 3.0 20.9 + - + +
479A VAL* 4.1 18.1 - - + +
480A THR* 4.6 2.2 - - - -
481A PHE* 4.2 8.5 - - + -
492A GLY 5.5 0.2 - - - +
495A TYR* 3.7 28.9 - - + +
496A VAL* 4.0 26.9 - - + -
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Residues in contact with ALA 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 LYS* 2.8 28.9 + - + +
465A MET* 3.8 6.3 - - + +
467A ILE* 1.3 75.8 - - + +
469A HIS* 1.3 58.7 + - - +
471A LYS* 3.4 12.5 + - - +
472A SER* 3.3 19.6 + - - -
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Residues in contact with HIS 469 (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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427A MET* 3.4 61.3 + - + +
430A MET* 5.1 4.7 - - + -
431A GLU* 3.5 16.8 + - - +
465A MET 3.0 11.0 + - - +
466A VAL 3.4 10.8 - - - +
468A ALA* 1.3 75.0 - - - +
470A THR* 1.3 54.3 + - - +
472A SER* 2.4 41.7 + - - +
473A LEU* 3.2 32.9 - - + +
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Residues in contact with THR 470 (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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430A MET* 3.0 39.9 - - + +
434A VAL* 4.0 17.9 - - + -
446A TRP* 4.1 13.9 - - + +
448A VAL* 3.8 2.4 - - - +
466A VAL 3.0 13.9 + - - -
467A ILE 2.9 7.8 + - - -
469A HIS* 1.3 73.3 - - - +
471A LYS* 1.3 59.8 + - - +
472A SER 2.6 18.9 - - - +
473A LEU* 4.8 4.5 - - - -
474A ASP* 3.1 16.5 + - + +
479A VAL* 3.8 23.7 - - + +
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Residues in contact with LYS 471 (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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467A ILE* 3.0 23.8 + - + +
468A ALA* 3.6 13.9 - - - +
469A HIS 3.2 0.2 - - - -
470A THR* 1.3 77.5 - - - +
472A SER* 1.3 57.4 + - - +
474A ASP 3.3 20.1 - - - +
475A PRO* 3.5 13.3 - - - +
477A ARG 5.9 0.9 - - - +
478A PRO* 4.9 3.3 - - - +
479A VAL* 4.0 15.9 - - + +
495A TYR 5.7 2.0 - - - +
497A ASP* 2.6 42.9 + - - +
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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