Contacts of the helix formed by residues 459 - 473 (chain G) in PDB entry 6V3O
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 SER 459 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458G GLU* 1.3 74.0 - - - +
460G GLU* 1.3 71.1 + - - +
462G HIS* 3.1 21.4 + - - +
463G THR* 3.4 9.5 + - - +
534G ILE* 3.7 13.9 - - - +
535G SER 2.8 19.7 + - - -
536G MET* 3.5 18.6 - - - -
538G THR* 5.5 0.3 + - - +
542G ASP* 2.6 36.7 + - - +
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Residues in contact with GLU 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458G GLU* 3.3 21.0 - - + +
459G SER* 1.3 83.3 + - - +
461G ARG* 1.3 65.8 + - - +
463G THR* 3.4 22.9 + - - +
464G ASP* 3.1 35.7 + - - +
479G ARG* 5.0 9.4 + - - +
486G ARG* 5.3 4.9 + - - -
536G MET* 6.3 1.3 - - + -
542G ASP* 5.5 0.3 - - - +
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Residues in contact with ARG 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ARG 5.4 3.0 + - - -
295G GLY* 5.7 3.2 - - - +
457G GLN* 3.5 38.2 + - + +
458G GLU* 3.7 24.4 - - - +
459G SER 3.3 0.8 - - - -
460G GLU* 1.3 77.5 - - + +
462G HIS* 1.3 61.6 + - - +
464G ASP* 3.8 8.5 + - - +
465G VAL* 3.3 25.1 + - - +
510G GLU* 2.8 57.0 + - - +
511G ILE* 5.7 0.3 - - - +
513G ASP* 3.9 12.5 + - - +
514G VAL* 3.8 16.2 - - + +
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Residues in contact with HIS 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G GLN* 3.7 18.1 - - + +
458G GLU 3.3 21.5 + - - -
459G SER* 3.1 12.2 + - - +
461G ARG* 1.3 77.4 - - - +
463G THR* 1.3 63.5 + - + +
465G VAL* 3.0 21.5 + - - +
466G ILE* 3.1 16.3 + - - +
514G VAL* 4.2 17.3 - - + -
518G PHE* 4.6 1.1 - + - -
532G TYR* 2.7 38.7 + + - -
534G ILE* 4.2 7.5 - - + +
542G ASP* 5.0 1.7 + - - +
545G ALA* 4.8 8.5 - - + -
546G VAL* 3.5 30.7 - - + +
549G LEU* 4.2 18.6 - - + +
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Residues in contact with THR 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459G SER 3.5 17.0 - - - +
460G GLU* 3.4 26.2 + - - +
462G HIS* 1.3 76.8 - - + +
464G ASP* 1.3 61.4 + - - +
466G ILE* 3.8 3.7 - - - +
467G ASP* 2.8 30.1 + - - +
478G TYR* 3.7 28.9 - - + +
479G ARG* 4.7 7.8 + - - +
486G ARG* 4.0 24.4 + - - +
542G ASP* 4.6 11.4 - - - +
545G ALA* 5.5 4.5 - - + -
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Residues in contact with ASP 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460G GLU* 3.1 23.8 + - - +
461G ARG* 4.0 10.5 - - - +
462G HIS 3.2 0.2 - - - -
463G THR* 1.3 77.0 + - - +
465G VAL* 1.3 64.5 + - - +
467G ASP* 3.8 1.0 - - - +
468G ALA* 3.0 23.4 + - - +
479G ARG* 2.3 43.7 + - - +
511G ILE* 3.9 15.9 - - + +
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Residues in contact with VAL 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461G ARG 3.3 17.2 + - - +
462G HIS* 3.0 8.6 + - - +
464G ASP* 1.3 77.1 - - - +
466G ILE* 1.3 62.9 + - - +
468G ALA* 3.2 6.2 + - - +
469G ILE* 3.1 29.6 + - + +
501G LEU* 4.9 0.7 - - + -
505G LEU* 5.1 1.0 - - + +
511G ILE* 3.8 34.3 - - + +
514G VAL* 3.9 26.2 - - + -
515G ILE* 4.6 13.9 - - + -
549G LEU* 3.7 27.6 - - + -
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Residues in contact with ILE 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462G HIS 3.1 13.3 + - - +
463G THR 4.0 2.9 - - - +
465G VAL* 1.3 76.1 - - - +
467G ASP* 1.3 58.1 + - - +
469G ILE* 3.1 11.2 + - + +
470G THR* 2.8 28.9 + - + +
478G TYR* 3.5 37.0 - - + -
489G TRP* 3.8 17.9 - - + -
490G LEU* 4.0 16.4 - - + -
500G LEU* 6.1 0.4 - - + -
545G ALA* 3.6 38.4 - - + +
548G LEU* 4.7 7.6 - - + -
549G LEU* 4.2 18.2 - - + -
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Residues in contact with ASP 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463G THR 2.8 19.3 + - - +
464G ASP 3.8 4.5 - - - +
465G VAL 3.2 0.2 - - - -
466G ILE* 1.3 77.3 - - - +
468G ALA* 1.3 54.9 + - - +
470G THR* 3.1 5.3 + - - -
471G THR* 2.6 43.2 + - - -
477G SER* 2.3 29.7 + - - -
478G TYR* 3.1 8.5 + - - +
479G ARG* 2.9 50.6 + - + +
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Residues in contact with ALA 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464G ASP 3.0 13.6 + - - +
465G VAL* 3.5 9.0 - - - +
467G ASP* 1.3 77.3 + - - +
469G ILE* 1.3 57.9 + - - +
471G THR* 4.1 4.5 - - - -
472G HIS* 3.0 30.7 + - - +
505G LEU* 4.7 11.1 - - + +
506G PRO* 4.7 11.3 - - - +
511G ILE* 3.8 20.6 - - + -
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Residues in contact with ILE 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465G VAL* 3.1 22.3 + - + +
466G ILE* 3.1 15.5 + - + +
468G ALA* 1.3 74.4 - - - +
470G THR* 1.3 69.4 + - + +
472G HIS* 3.2 3.6 + - - +
473G LEU* 3.1 33.6 + - + +
489G TRP* 5.2 1.1 - - + -
500G LEU* 3.9 43.7 - - + +
501G LEU* 3.5 30.1 - - + -
502G PRO* 4.5 3.8 - - + -
505G LEU* 3.4 24.7 - - + -
548G LEU* 6.3 0.2 - - + -
549G LEU* 4.6 8.3 - - + -
552G GLU* 6.4 0.7 - - + -
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Residues in contact with THR 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466G ILE* 2.8 19.4 + - + +
467G ASP 3.1 9.7 + - - -
469G ILE* 1.3 71.9 - - - +
471G THR* 1.3 62.0 + - - +
473G LEU 3.6 0.5 + - - -
474G GLY 3.1 2.8 + - - -
475G ILE* 3.0 37.7 + - + +
476G GLY 3.1 21.2 + - - +
477G SER* 3.9 0.2 - - - -
478G TYR* 3.2 28.5 + - + -
481G TRP* 4.2 11.7 - - + -
489G TRP* 3.9 32.5 - - + -
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Residues in contact with THR 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G ASP* 2.6 35.0 + - - -
468G ALA* 4.1 4.5 - - - -
470G THR* 1.3 77.7 + - - +
472G HIS* 1.3 62.1 + - - +
474G GLY* 3.0 14.8 + - - -
476G GLY 3.4 12.6 + - - +
477G SER* 4.3 4.6 + - - -
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Residues in contact with HIS 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497F LYS* 3.3 53.0 - - + +
468G ALA 3.0 21.4 + - - +
469G ILE* 3.7 5.4 - - - +
471G THR* 1.3 77.6 - - - +
473G LEU* 1.3 59.7 + - - +
474G GLY* 3.4 0.9 + - - -
502G PRO* 3.9 22.0 - - + -
504G ASP* 3.0 31.1 + - - +
505G LEU* 4.3 7.0 - - + -
506G PRO* 3.6 28.9 - - + +
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Residues in contact with LEU 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497F LYS* 3.2 49.1 - - + +
498F ARG* 3.5 21.1 - - + +
469G ILE* 3.1 18.0 + - + +
472G HIS* 1.3 75.7 - - - +
474G GLY* 1.3 61.5 + - - +
475G ILE* 3.3 32.0 + - + +
500G LEU* 3.9 33.0 - - + +
502G PRO* 4.1 8.3 - - + -
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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
------------------------------------------------------------
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