Contacts of the helix formed by residues 460 - 475 (chain K) 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 LYS 460 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422K GLU* 3.4 19.7 + - - +
455K CYS* 3.0 18.5 + - + +
458K LEU* 3.9 33.5 - - + +
459K LYS* 1.3 74.9 - - - +
461K TYR* 1.3 63.2 + - - +
462K ALA* 3.4 2.9 + - - -
463K GLU* 3.1 46.7 + - + +
464K ALA* 3.3 16.5 + - - +
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Residues in contact with TYR 461 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456K ARG* 4.0 28.3 - - + -
459K LYS* 3.2 55.0 + - + +
460K LYS* 1.3 70.9 - - - +
462K ALA* 1.3 65.8 + - - +
464K ALA* 3.3 3.4 + - - +
465K LEU* 3.0 27.0 + - - +
488K ILE* 3.8 27.7 - - + +
491K LEU* 3.9 24.0 - - + +
492K MET* 4.0 33.9 - - + -
22W ILE* 3.8 16.0 - - + +
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Residues in contact with ALA 462 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460K LYS 3.4 0.8 - - - -
461K TYR* 1.3 79.6 - - - +
463K GLU* 1.3 65.5 + - + +
465K LEU* 3.7 6.4 + - - +
466K ASP* 3.3 20.1 + - - +
492K MET* 5.6 1.3 - - - -
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Residues in contact with GLU 463 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422K GLU* 4.4 1.7 - - - +
455K CYS* 4.0 16.4 - - + -
460K LYS* 3.1 54.1 + - + +
461K TYR 3.3 0.2 - - - -
462K ALA* 1.3 81.0 - - + +
464K ALA* 1.3 64.6 + - - +
466K ASP* 3.2 12.0 + - - +
467K TYR* 3.0 36.2 + - + -
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Residues in contact with ALA 464 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452K GLY* 3.5 24.2 - - - +
455K CYS* 3.9 7.8 - - + +
456K ARG* 3.7 17.3 - - - +
460K LYS 3.3 8.0 + - - +
461K TYR* 3.6 9.4 - - - +
463K GLU* 1.3 75.1 - - - +
465K LEU* 1.3 65.9 + - - +
467K TYR* 3.2 2.8 + - - +
468K HIS* 2.8 30.8 + - - -
488K ILE* 3.8 17.0 - - + -
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Residues in contact with LEU 465 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461K TYR 3.0 12.5 + - - +
462K ALA* 3.9 5.6 - - - +
464K ALA* 1.3 78.6 - - - +
466K ASP* 1.3 61.4 + - - +
468K HIS* 3.4 4.7 + - - +
469K ARG* 3.2 46.0 + - - +
485K ILE* 3.7 47.1 - - + +
488K ILE* 3.8 15.7 - - + +
489K HIS* 3.4 31.6 - - + +
492K MET* 4.1 22.7 - - + -
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Residues in contact with ASP 466 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H GLN* 5.9 0.3 + - - -
462K ALA 3.3 11.7 + - - +
463K GLU* 3.2 14.7 + - - +
465K LEU* 1.3 79.0 - - - +
467K TYR* 1.3 70.3 + - - +
469K ARG* 3.4 10.7 + - - +
470K GLN* 3.1 41.4 + - - +
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Residues in contact with TYR 467 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426K LEU* 4.0 17.4 - - + +
429K LEU* 4.1 18.8 - - + +
448K LEU* 3.6 29.6 - - + +
451K LEU* 3.7 27.6 - - + -
452K GLY* 3.8 13.5 - - - -
455K CYS* 4.0 21.5 - - - -
463K GLU* 3.0 27.2 + - + -
464K ALA 3.2 0.6 + - - +
466K ASP* 1.3 82.9 - - - +
468K HIS* 1.3 68.1 + - - +
470K GLN* 3.1 28.6 + - - +
471K ALA* 2.9 21.1 + - - +
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Residues in contact with HIS 468 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448K LEU 5.4 0.9 - - - -
449K ASN* 4.0 16.5 + - - -
452K GLY* 3.5 29.4 - - - -
453K HIS* 3.8 17.6 + - - -
456K ARG* 4.9 1.3 - - - -
464K ALA 2.8 23.1 + - - -
465K LEU* 3.8 4.1 + - - +
467K TYR* 1.3 77.0 - - - +
469K ARG* 1.3 57.1 + - - +
471K ALA* 3.1 8.6 + - + +
472K LEU* 2.8 24.6 + - - +
481K THR* 3.4 19.3 - - + +
484K ALA* 3.2 35.1 - - + +
485K ILE* 3.5 22.0 - - + -
488K ILE* 4.3 18.5 - - + +
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Residues in contact with ARG 469 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H THR* 3.9 7.7 - - - +
129H ASP* 3.7 36.6 + - + +
130H ARG* 4.3 23.5 + - + +
132H ALA* 6.1 3.8 - - - +
465K LEU* 3.2 42.7 + - - +
466K ASP* 3.8 10.5 - - - +
467K TYR 3.2 0.4 - - - -
468K HIS* 1.3 75.6 - - - +
470K GLN* 1.3 63.9 + - + +
472K LEU* 3.1 17.8 + - - +
473K VAL* 3.2 9.8 + - - +
485K ILE* 4.4 8.3 - - + +
489K HIS* 3.8 28.7 + - - -
501K TYR* 3.9 14.6 + - - -
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Residues in contact with GLN 470 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H VAL* 4.3 26.2 - - + +
97H PHE* 5.4 0.9 - - - -
100H GLN* 4.6 15.2 - - - +
130H ARG* 5.3 5.8 - - - +
429K LEU* 6.0 0.3 - - - +
433K LYS* 6.2 0.2 - - - +
448K LEU* 3.9 23.2 - - + +
466K ASP* 3.1 38.8 + - - +
467K TYR* 3.1 29.1 + - - +
469K ARG* 1.3 75.4 - - - +
471K ALA* 1.3 62.7 + - - +
473K VAL* 3.0 28.3 + - + +
474K LEU* 3.6 8.7 + - - +
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Residues in contact with ALA 471 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445K GLU* 4.1 16.9 - - - +
448K LEU* 3.9 21.9 - - + +
449K ASN* 4.1 14.6 - - + +
467K TYR 2.9 12.9 + - - +
468K HIS* 3.4 11.9 - - - +
470K GLN* 1.3 76.4 - - - +
472K LEU* 1.3 61.4 + - - +
474K LEU* 3.2 16.0 + - - +
475K ILE* 3.3 17.6 + - - +
481K THR* 4.7 7.6 - - + +
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Residues in contact with LEU 472 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H THR* 3.6 27.5 - - - +
129H ASP* 3.8 5.4 - - + -
468K HIS 2.8 6.9 + - - +
469K ARG* 3.1 11.8 + - - +
471K ALA* 1.3 73.4 - - - +
473K VAL* 1.3 62.5 + - - +
475K ILE* 2.8 22.4 - - - +
476K PRO* 3.5 28.8 - - - +
478K ASN* 3.8 20.4 - - + +
481K THR* 3.6 22.2 - - + +
482K TYR* 3.5 31.9 - - + +
485K ILE* 3.5 26.2 - - + -
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Residues in contact with VAL 473 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H LEU* 4.5 4.8 - - + +
86H ALA* 3.3 42.8 + - + +
89H GLU* 3.0 21.5 - - + +
96H VAL* 4.4 9.4 - - + -
124H VAL* 5.8 0.2 - - + -
128H THR* 3.5 10.7 - - + +
130H ARG* 2.9 33.9 - - - +
469K ARG 3.2 5.3 + - - +
470K GLN* 3.0 20.5 + - + +
472K LEU* 1.3 77.8 - - - +
474K LEU* 1.3 72.5 + - + +
476K PRO* 4.2 8.8 - - - +
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Residues in contact with LEU 474 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H ALA* 3.8 7.3 - - + +
96H VAL* 4.0 15.9 - - + -
97H PHE* 4.1 19.1 - - + -
441K VAL* 3.4 53.1 - - + +
442K ASP* 5.5 2.1 + - - -
445K GLU* 4.1 20.4 - - + +
448K LEU* 3.9 21.8 - - + -
470K GLN 3.8 9.6 - - - +
471K ALA 3.2 6.8 + - - +
473K VAL* 1.3 95.5 - - + +
475K ILE* 1.3 57.7 + - - +
476K PRO* 4.0 4.6 - - - +
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Residues in contact with ILE 475 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442K ASP* 5.9 2.2 - - - +
445K GLU* 3.9 18.6 - - + -
471K ALA 3.3 5.6 + - - +
472K LEU* 2.8 20.6 - - - +
474K LEU* 1.3 77.9 - - - +
476K PRO* 1.3 72.8 - - + +
477K GLN 3.3 19.8 + - - +
478K ASN* 3.3 37.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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