Contacts of the helix formed by residues 475 - 490 (chain Y) in PDB entry 5A31
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 475 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F PHE* 5.7 8.7 - + - -
442Y GLN* 3.8 25.1 - - + -
443Y THR* 3.6 24.4 - - + +
446Y LEU* 3.8 14.4 - - + +
468Y ALA 5.3 0.9 - - - +
469Y LEU* 4.5 0.2 - - - +
472Y GLU* 3.0 44.4 + - + +
473Y PRO 3.3 3.8 + - - -
474Y ASP* 1.3 73.0 - - - +
476Y ILE* 1.3 70.4 + - + +
477Y LYS* 3.3 42.8 + - + +
478Y ALA* 3.7 20.2 - - + -
479Y VAL* 3.0 26.6 + - - +
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Residues in contact with ILE 476 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288Y LYS* 5.7 8.5 - - - +
474Y ASP 3.3 2.0 + - - +
475Y TYR* 1.3 77.8 - - + +
477Y LYS* 1.3 61.9 + - + +
479Y VAL* 3.4 4.6 + - - +
480Y VAL* 2.9 32.5 + - + +
507Y SER* 3.3 44.4 - - - +
508Y ASP 5.3 2.5 - - - +
509Y CYS* 6.0 4.0 - - + -
510Y VAL* 4.1 25.1 - - + -
511Y LEU* 4.3 9.5 - - + +
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Residues in contact with LYS 477 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411Y GLU* 4.8 14.5 + - - -
446Y LEU* 3.5 20.2 - - + -
475Y TYR* 3.3 30.4 + - + +
476Y ILE* 1.3 83.7 - - + +
478Y ALA* 1.3 53.1 + - - +
480Y VAL* 3.8 5.7 - - - +
481Y LYS* 2.7 45.1 + - + +
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Residues in contact with ALA 478 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446Y LEU* 3.5 17.0 - - + +
465Y LEU* 3.4 10.8 - - + +
468Y ALA* 4.3 16.6 - - + -
469Y LEU* 3.4 27.5 - - + +
475Y TYR* 3.4 18.2 + - + +
476Y ILE 3.3 0.4 - - - -
477Y LYS* 1.3 75.0 - - - +
479Y VAL* 1.3 60.7 + - - +
481Y LYS 3.4 0.2 + - - -
482Y LYS* 2.9 31.0 + - - +
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Residues in contact with VAL 479 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469Y LEU* 3.2 24.0 - - + -
474Y ASP* 4.2 11.4 - - - +
475Y TYR 3.0 22.2 + - - +
476Y ILE* 4.0 2.9 - - - +
478Y ALA* 1.3 75.1 - - - +
480Y VAL* 1.3 53.1 + - - +
482Y LYS* 3.3 1.7 + - - +
483Y ALA* 2.8 33.0 + - - +
498Y LEU* 4.2 18.6 - - + -
499Y LEU* 3.4 29.2 - - + -
502Y ALA* 3.8 27.1 - - + -
511Y LEU* 4.4 5.2 - - + -
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Residues in contact with VAL 480 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476Y ILE* 2.9 21.6 + - + +
477Y LYS* 3.8 6.3 - - - +
479Y VAL* 1.3 72.4 - - - +
481Y LYS* 1.3 71.1 + - + +
483Y ALA* 3.3 8.0 + - - +
484Y GLU* 2.9 31.4 + - + +
510Y VAL* 3.8 24.7 - - + -
511Y LEU* 3.5 22.4 - - + -
514Y ILE* 4.4 18.5 - - + +
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Residues in contact with LYS 481 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446Y LEU* 3.2 52.7 + - + +
447Y LEU* 4.5 5.3 - - - +
449Y THR* 4.3 0.9 - - - +
450Y VAL* 3.2 42.0 - - + +
453Y GLU* 5.2 4.4 - - - +
465Y LEU* 3.5 25.3 - - + +
477Y LYS* 2.7 27.0 + - - +
480Y VAL* 1.3 76.8 - - + +
482Y LYS* 1.3 62.0 + - - +
484Y GLU* 3.2 25.3 + - - +
485Y LEU* 3.4 5.4 + - - +
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Residues in contact with LYS 482 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465Y LEU* 3.4 17.8 - - + +
466Y ASN* 4.0 35.2 + - - +
469Y LEU* 3.3 23.5 - - + +
478Y ALA 2.9 17.2 + - - +
479Y VAL 3.6 4.0 - - - +
481Y LYS* 1.3 72.3 - - - +
483Y ALA* 1.3 64.8 + - - +
485Y LEU* 3.2 18.3 - - + +
486Y LEU* 3.0 36.3 - - + +
498Y LEU* 3.6 32.2 - - + +
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Residues in contact with ALA 483 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479Y VAL 2.8 21.5 + - - +
480Y VAL* 3.3 6.5 + - - +
482Y LYS* 1.3 69.5 - - - +
484Y GLU* 1.3 65.6 + - - +
486Y LEU* 3.0 20.8 + - - +
487Y SER* 3.1 14.5 + - - -
495Y GLY* 6.1 0.7 - - - +
498Y LEU* 4.6 6.9 - - + +
499Y LEU* 4.1 13.0 - - + -
514Y ILE* 4.1 26.7 - - + -
518Y PHE* 3.4 10.4 - - + -
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Residues in contact with GLU 484 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480Y VAL* 2.9 18.9 + - + +
481Y LYS* 3.3 19.0 - - - +
482Y LYS 3.2 0.4 - - - -
483Y ALA* 1.3 75.6 - - - +
485Y LEU* 1.3 64.0 + - - +
487Y SER* 2.9 24.7 + - - +
488Y ARG* 3.1 24.2 + - + +
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Residues in contact with LEU 485 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453Y GLU* 3.4 25.1 - - - +
458Y GLN* 4.6 6.3 - - + +
462Y LYS* 3.3 49.6 - - + +
465Y LEU* 3.7 22.0 - - + -
481Y LYS 3.4 7.1 + - - +
482Y LYS* 3.2 25.2 + - + +
484Y GLU* 1.3 77.0 - - - +
486Y LEU* 1.3 55.1 + - + +
488Y ARG* 2.9 27.1 + - - +
489Y GLU* 2.6 45.4 + - + +
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Residues in contact with LEU 486 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462Y LYS* 5.3 4.0 - - - -
482Y LYS* 3.0 42.8 - - + +
483Y ALA* 3.0 10.6 + - - +
485Y LEU* 1.3 86.3 - - + +
487Y SER* 1.3 53.0 + - - +
489Y GLU* 3.9 10.5 - - + -
490Y GLN* 2.8 29.8 + - - -
491Y LYS 3.4 15.8 + - - +
492Y TYR* 4.9 0.7 - - - -
494Y ASP* 3.4 24.9 - - + +
495Y GLY* 3.2 36.8 - - - +
498Y LEU* 4.2 11.9 - - + -
518Y PHE* 4.0 10.5 - - + -
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Residues in contact with SER 487 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483Y ALA 3.1 11.5 + - - -
484Y GLU* 2.9 18.3 + - - +
486Y LEU* 1.3 75.7 - - - +
488Y ARG* 1.3 63.7 + - - +
490Y GLN* 3.3 17.7 + - - +
492Y TYR* 4.1 17.7 + - - -
518Y PHE* 3.8 19.0 - - - -
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Residues in contact with ARG 488 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453Y GLU* 3.5 38.1 + - - +
456Y VAL* 4.3 12.7 - - - +
458Y GLN* 3.4 43.8 + - - +
484Y GLU* 3.1 26.8 + - + +
485Y LEU* 2.9 32.2 + - - +
487Y SER* 1.3 75.5 - - - +
489Y GLU* 1.3 66.6 + - - +
490Y GLN* 3.4 17.2 + - - +
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Residues in contact with GLU 489 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458Y GLN* 3.9 23.2 + - - +
462Y LYS* 3.4 36.2 + - - +
485Y LEU* 2.6 33.7 + - + +
486Y LEU* 3.6 13.9 - - + +
488Y ARG* 1.3 71.5 - - - +
490Y GLN* 1.3 70.9 + - - +
491Y LYS* 3.1 17.1 + - + +
494Y ASP* 5.6 0.4 - - - +
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Residues in contact with GLN 490 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486Y LEU 2.8 8.3 + - - -
487Y SER 3.3 11.2 + - - +
488Y ARG* 3.2 16.5 + - - +
489Y GLU* 1.3 80.0 + - - +
491Y LYS* 1.3 57.2 + - - +
492Y TYR* 3.3 36.6 + - + +
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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