Contacts of the helix formed by residues 457 - 472 (chain Y) in PDB entry 5G04
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 457 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452Y LEU* 2.9 51.1 + - - +
455Y PRO* 3.2 22.3 - - + +
456Y VAL* 1.3 70.9 - - - +
458Y GLN* 1.3 63.8 + - - +
459Y GLU 3.3 3.7 + - - -
460Y LYS* 3.4 23.8 + - + -
461Y ALA* 3.3 4.0 + - - +
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Residues in contact with GLN 458 (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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452Y LEU 6.0 0.2 - - - -
453Y GLU* 5.2 3.1 - - + +
456Y VAL* 2.8 27.9 + - - +
457Y THR* 1.3 72.3 - - - +
459Y GLU* 1.3 57.1 + - + +
461Y ALA* 3.9 6.1 - - - +
462Y LYS* 3.1 40.0 + - + +
485Y LEU* 4.8 8.2 - - + +
488Y ARG* 3.4 51.7 + - - +
489Y GLU* 3.8 25.3 + - - +
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Residues in contact with GLU 459 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457Y THR 3.3 0.6 - - - -
458Y GLN* 1.3 78.3 - - + +
460Y LYS* 1.3 76.4 + - + +
462Y LYS* 3.5 15.7 + - + +
463Y THR* 3.5 20.4 + - - +
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Residues in contact with LYS 460 (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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452Y LEU* 3.3 23.5 - - + +
457Y THR* 3.4 31.8 + - + -
459Y GLU* 1.3 87.9 + - + +
461Y ALA* 1.3 61.8 + - - +
463Y THR* 3.4 16.9 + - - -
464Y LEU* 3.4 16.7 - - + +
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Residues in contact with ALA 461 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449Y THR* 3.3 22.0 - - - +
452Y LEU* 3.4 28.6 - - + +
453Y GLU* 3.3 26.2 - - - +
457Y THR 3.3 12.4 + - - +
458Y GLN* 3.9 4.9 - - - +
459Y GLU 3.3 0.6 - - - -
460Y LYS* 1.3 77.5 - - - +
462Y LYS* 1.3 61.8 + - - +
464Y LEU* 3.3 3.6 + - - +
465Y LEU* 3.1 17.9 + - - +
485Y LEU* 5.2 0.7 - - + -
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Residues in contact with LYS 462 (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* 3.1 28.2 + - + +
459Y GLU* 3.5 7.1 + - - +
461Y ALA* 1.3 74.6 - - - +
463Y THR* 1.3 59.3 + - + +
465Y LEU* 3.2 2.8 + - - +
466Y ASP* 2.9 50.9 + - - +
482Y LYS* 4.9 4.8 - - - +
485Y LEU* 3.6 31.6 - - + +
486Y LEU* 4.1 20.2 - - - +
489Y GLU* 3.5 40.4 - - - +
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Residues in contact with THR 463 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459Y GLU 3.5 13.4 + - - +
460Y LYS* 3.4 15.2 + - - -
462Y LYS* 1.3 75.0 - - + +
464Y LEU* 1.3 67.6 + - - +
466Y ASP* 3.5 10.9 + - - +
467Y LYS* 3.0 37.3 + - - +
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Residues in contact with LEU 464 (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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434Y TYR* 4.8 10.3 - - + +
445Y THR* 4.0 33.2 - - + +
448Y ALA* 4.9 11.9 - - + -
449Y THR* 3.7 13.2 - - + +
452Y LEU* 5.4 7.6 - - + -
460Y LYS* 3.4 17.0 + - + +
461Y ALA* 3.3 10.3 + - - +
462Y LYS 3.3 0.2 - - - -
463Y THR* 1.3 89.5 + - - +
465Y LEU* 1.3 55.8 + - - +
467Y LYS* 3.3 20.4 + - + +
468Y ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 465 (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* 4.9 5.6 - - - -
449Y THR* 3.4 33.4 - - + +
453Y GLU* 5.0 4.3 - - - +
461Y ALA 3.1 7.4 + - - +
462Y LYS* 3.2 10.5 + - - +
464Y LEU* 1.3 72.5 - - - +
466Y ASP* 1.3 66.9 + - - +
468Y ALA* 3.4 10.2 + - + +
469Y LEU* 3.3 22.3 + - - +
478Y ALA* 3.5 31.4 - - + +
481Y LYS* 3.7 15.0 - - + +
482Y LYS* 3.6 32.3 - - + +
485Y LEU* 3.6 21.8 - - + -
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Residues in contact with ASP 466 (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* 2.9 29.2 + - - +
463Y THR* 3.5 12.3 - - - +
465Y LEU* 1.3 75.7 - - - +
467Y LYS* 1.3 60.7 + - + +
469Y LEU* 3.4 6.3 + - - +
470Y THR* 3.3 26.8 + - + +
482Y LYS* 2.6 44.5 - - - +
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Residues in contact with LYS 467 (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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445Y THR* 5.4 6.5 - - + -
463Y THR* 3.0 22.2 + - - +
464Y LEU* 3.5 23.5 - - + +
465Y LEU 3.3 0.2 - - - -
466Y ASP* 1.3 75.0 - - + +
468Y ALA* 1.3 63.3 + - - +
470Y THR* 2.6 27.0 + - + +
471Y GLN* 3.3 19.5 + - - +
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Residues in contact with ALA 468 (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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442Y GLN* 4.2 16.2 - - + +
445Y THR* 3.3 28.2 + - - +
446Y LEU* 4.5 4.7 - - - +
464Y LEU 3.0 12.6 + - - +
465Y LEU* 3.5 19.7 - - + +
467Y LYS* 1.3 74.1 - - - +
469Y LEU* 1.3 62.5 + - - +
471Y GLN* 3.4 17.7 + - - +
472Y ARG* 3.4 11.1 + - - +
475Y TYR* 5.8 1.2 - - - +
478Y ALA* 4.8 9.6 - - + -
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Residues in contact with LEU 469 (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 3.3 8.0 + - - +
466Y ASP* 3.8 8.1 - - - +
467Y LYS 3.3 0.2 - - - -
468Y ALA* 1.3 76.6 - - - +
470Y THR* 1.3 63.1 + - + +
472Y ARG 3.0 22.6 - - - +
473Y PRO* 3.9 5.7 - - - +
474Y ASP 4.6 4.0 - - - +
475Y TYR* 4.1 13.0 - - + +
478Y ALA* 3.7 25.1 - - + +
479Y VAL* 3.5 40.2 - - + -
482Y LYS* 3.7 31.0 - - + +
498Y LEU* 4.2 13.5 - - + -
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Residues in contact with THR 470 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466Y ASP* 3.3 16.3 + - + +
467Y LYS* 2.6 25.7 + - - +
469Y LEU* 1.3 78.1 - - - +
471Y GLN* 1.3 62.7 + - - +
472Y ARG* 4.6 1.0 - - - -
473Y PRO* 4.9 4.7 - - - +
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Residues in contact with GLN 471 (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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440Y ASN* 3.5 42.1 - - + +
441Y ALA 3.8 13.2 + - - +
442Y GLN* 4.0 14.8 + - + +
445Y THR* 4.6 10.5 + - - +
467Y LYS* 3.3 18.3 + - - +
468Y ALA* 3.6 9.6 - - - +
469Y LEU 3.3 0.4 - - - -
470Y THR* 1.3 86.0 + - - +
472Y ARG* 1.3 58.0 + - - +
473Y PRO* 4.0 5.1 - - - +
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Residues in contact with ARG 472 (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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442Y GLN* 3.7 30.5 - - + +
468Y ALA 3.4 4.4 + - - +
469Y LEU* 3.0 20.2 - - - +
471Y GLN* 1.3 79.0 - - - +
473Y PRO* 1.4 70.1 - - + +
474Y ASP 3.4 2.8 + - - -
475Y TYR* 3.8 22.2 + - + +
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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