Contacts of the helix formed by residues 458 - 474 (chain G) in PDB entry 2R6C
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 PRO 458 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASP* 3.9 11.7 - - + +
457G LEU* 1.3 90.7 - - + +
459G ALA* 1.3 68.8 + - - +
460G PHE* 3.6 21.5 - - + -
461G GLN* 3.2 29.4 + - + +
462G ASN* 3.3 9.6 + - - -
555G ARG* 5.8 0.7 - - - +
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Residues in contact with ALA 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP 2.8 21.1 + - - +
95B ALA 3.6 9.4 - - - -
96B VAL 3.5 17.5 - - - +
97B PRO* 3.7 4.1 - - + +
458G PRO* 1.3 71.8 - - - +
460G PHE* 1.3 57.3 + - - +
462G ASN* 2.7 27.2 + - - +
463G ALA 2.9 8.8 + - - -
551G HIS* 3.5 23.1 - - + +
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Residues in contact with PHE 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458G PRO* 4.3 20.9 - - + -
459G ALA* 1.3 77.3 - - - +
461G GLN* 1.3 82.7 + - + +
463G ALA* 3.1 3.4 + - - +
464G GLU* 2.8 48.1 + - - +
490G ASN* 4.1 17.3 - - + -
491G ILE* 4.5 12.3 - - + -
551G HIS* 3.7 36.2 + - + +
552G VAL* 4.6 1.8 - - - +
555G ARG* 3.1 60.8 - - + -
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Residues in contact with GLN 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G LEU* 3.2 32.2 - - + +
458G PRO* 3.2 21.7 + - + +
459G ALA 2.9 0.6 + - - -
460G PHE* 1.3 96.2 - - + +
462G ASN* 1.3 60.6 + - - +
464G GLU* 3.2 5.3 + - - +
465G ARG* 2.8 36.9 + - - +
491G ILE* 3.4 34.9 - - + +
494G HIS* 4.4 8.1 + - + +
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Residues in contact with ASN 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 2.7 29.4 + - - +
97B PRO* 4.0 11.4 - - + -
456G LEU 4.2 3.1 + - - +
457G LEU* 3.3 43.4 + - - +
458G PRO 3.3 5.4 + - - -
459G ALA 2.7 12.1 + - - +
461G GLN* 1.3 75.6 - - - +
463G ALA* 1.3 54.7 + - - +
465G ARG* 3.3 10.1 - - - +
466G LEU* 2.8 39.8 + - + +
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Residues in contact with ALA 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 3.9 8.7 - - + +
459G ALA 2.9 9.3 + - - +
460G PHE 3.1 10.1 + - - +
462G ASN* 1.3 75.1 - - - +
464G GLU* 1.3 64.4 + - - +
466G LEU* 3.9 1.0 - - - +
467G LEU* 3.0 28.1 + - - +
548G TYR* 3.7 48.7 - - + +
551G HIS* 4.1 8.1 - - + -
552G VAL* 4.6 4.0 - - + -
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Residues in contact with GLU 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460G PHE* 2.8 17.7 + - - +
461G GLN* 3.4 11.2 - - - +
463G ALA* 1.3 77.3 - - - +
465G ARG* 1.3 65.5 + - - +
467G LEU* 3.2 3.1 + - - +
468G LEU* 3.2 23.6 + - - +
489G PHE* 3.1 32.0 - - + -
490G ASN* 2.7 46.1 + - - +
491G ILE* 3.0 14.4 + - - +
494G HIS* 3.6 28.3 - - + +
552G VAL* 3.4 16.9 - - - +
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Residues in contact with ARG 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G LEU* 4.3 27.9 - - - +
461G GLN* 2.8 23.8 + - - +
462G ASN* 3.3 13.2 - - - +
464G GLU* 1.3 75.1 - - - +
466G LEU* 1.3 57.9 - - - +
468G LEU* 3.0 22.7 + - - +
469G ALA 3.1 10.0 + - - -
494G HIS* 4.3 19.5 + - + -
527G LEU* 3.9 23.6 - - - +
530G GLU* 5.1 6.3 + - - +
531G LEU* 3.3 33.9 - - + +
534G LEU* 4.1 28.6 - - + +
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Residues in contact with LEU 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 4.1 12.6 - - + -
101B ASN* 6.0 0.2 - - - +
105B TYR* 4.9 13.5 - - - +
462G ASN* 2.8 25.8 + - + +
463G ALA 4.1 2.9 - - - +
465G ARG* 1.3 70.3 - - - +
467G LEU* 1.3 65.4 + - - +
469G ALA* 3.3 7.4 + - - +
470G HIS* 3.0 31.0 + - + +
534G LEU* 4.1 17.0 - - + -
535G LEU 4.0 20.6 - - - +
536G ILE* 4.0 13.2 - - + -
548G TYR* 3.5 41.1 - - + +
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Residues in contact with LEU 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463G ALA 3.0 18.4 + - - +
464G GLU 3.5 5.4 - - - +
465G ARG 3.2 0.2 - - - -
466G LEU* 1.3 76.8 - - - +
468G LEU* 1.3 56.7 + - - +
470G HIS* 3.1 7.4 + - + +
471G MSE 2.9 35.5 + - - +
477G VAL* 5.3 2.3 - - + +
481G VAL* 4.4 18.8 - - + -
485G ILE* 3.7 29.8 - - + -
489G PHE* 4.6 6.1 - - + -
545G LEU* 3.8 29.4 - - + -
548G TYR* 3.8 30.1 - - + -
549G ILE* 4.2 8.1 - - + -
552G VAL* 4.3 10.1 - - + -
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Residues in contact with LEU 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464G GLU 3.2 5.4 + - - +
465G ARG 3.0 9.5 + - - +
467G LEU* 1.3 75.3 - - - +
469G ALA* 1.3 58.0 + - - +
471G MSE 3.6 8.3 - - - -
472G MSE 2.8 42.3 + - + +
489G PHE* 3.8 33.4 - - + -
494G HIS* 3.6 35.2 - - + +
497G LEU* 3.7 33.7 - - + -
498G ALA* 5.0 1.3 - - + -
501G ILE* 3.8 21.5 - - + +
531G LEU* 4.0 13.5 - - + -
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Residues in contact with ALA 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465G ARG 3.1 11.2 + - - +
466G LEU* 3.5 14.6 - - - +
468G LEU* 1.3 74.9 - - - +
470G HIS* 1.3 59.2 + - - +
472G MSE 3.9 13.4 - - - +
473G ARG* 3.2 31.9 + - - +
531G LEU* 3.6 19.4 - - + +
534G LEU* 4.6 11.0 - - + -
536G ILE* 4.0 22.0 - - + +
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Residues in contact with HIS 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466G LEU* 3.0 24.4 + - + +
467G LEU* 3.6 10.3 - - + +
468G LEU 3.1 0.2 - - - -
469G ALA* 1.3 75.2 - - - +
471G MSE 1.3 53.9 + - - +
473G ARG* 2.9 4.7 + - - +
474G SER* 2.5 38.9 + - - -
477G VAL* 4.5 11.0 - - + +
536G ILE* 3.4 28.3 - - + +
537G ALA 3.0 29.3 + - - -
538G ASP* 4.5 9.2 + - - -
539G ASP 4.5 3.4 - - - -
540G VAL* 3.5 48.1 - - + +
544G GLU* 4.4 7.0 + - - -
548G TYR* 5.0 5.6 + + - -
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Residues in contact with MSE 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G LEU* 2.9 27.1 + - - +
468G LEU* 3.5 22.4 - - - +
470G HIS* 1.3 73.3 - - - +
472G MSE 1.3 56.9 + - - +
474G SER 3.3 12.3 - - - +
475G ARG* 3.0 32.7 + - - -
477G VAL* 4.5 3.5 - - + +
478G ALA* 3.4 27.6 - - + +
481G VAL* 3.7 33.2 - - + -
489G PHE* 4.4 4.7 - - + -
498G ALA* 5.3 1.8 - - - +
501G ILE* 4.1 21.1 - - + -
502G TYR* 3.5 36.3 - - + +
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Residues in contact with MSE 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468G LEU* 2.8 32.1 + - + +
469G ALA* 3.9 6.3 - - - +
471G MSE 1.3 79.0 - - - +
473G ARG* 1.3 60.4 + - + +
475G ARG* 4.3 5.4 - - - -
497G LEU* 5.1 8.1 - - + -
501G ILE* 4.5 5.8 - - + +
504G PHE* 5.8 0.2 - - - -
512G ASP* 4.2 5.0 - - - -
513G PRO* 3.8 29.9 - - + +
516G LEU* 3.6 33.9 - - + +
517G ILE* 4.6 7.4 - - - -
520G ILE* 5.8 0.4 - - - -
528G ALA* 3.6 24.7 - - - +
531G LEU* 3.6 22.7 - - + +
532G SER* 3.5 34.1 - - - +
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Residues in contact with ARG 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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469G ALA 3.2 19.0 + - - +
470G HIS* 2.9 4.9 + - - +
472G MSE 1.3 83.8 - - + +
474G SER* 1.3 58.7 + - - +
475G ARG* 4.2 1.1 + - - -
511G ALA* 5.2 6.8 - - - +
512G ASP* 4.4 10.6 + - - +
513G PRO* 3.9 32.3 - - + +
532G SER* 3.5 29.0 + - - +
533G LEU* 5.5 4.9 - - - +
536G ILE* 3.7 22.2 - - + -
538G ASP* 3.8 25.1 + - - +
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Residues in contact with SER 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470G HIS* 2.5 14.7 + - - -
471G MSE 3.3 13.8 - - - +
473G ARG* 1.3 76.4 - - - +
475G ARG* 1.3 58.2 + - - +
476G ASP* 3.1 22.4 + - - +
477G VAL* 3.1 23.7 + - - +
478G ALA 3.4 5.5 + - - -
511G ALA* 5.6 0.4 - - - -
538G ASP* 4.0 15.0 - - - -
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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