Contacts of the helix formed by residues 474 - 485 (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 SER 474 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with ARG 475 (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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471G MSE 3.0 28.8 + - - -
472G MSE 4.3 10.5 - - - +
473G ARG 4.4 0.2 + - - -
474G SER* 1.3 69.0 + - - +
476G ASP* 1.3 60.8 + - - +
478G ALA* 3.4 19.7 - - - +
479G LEU* 3.6 26.0 + - - +
501G ILE* 2.6 43.8 + - - +
502G TYR* 3.7 6.5 + - - +
504G PHE* 3.3 16.8 - - + -
505G TYR* 2.5 66.1 - - + +
509G HIS 4.5 0.9 - - - +
510G GLU 4.4 1.3 - - - +
511G ALA* 3.2 35.2 - - + +
516G LEU* 5.1 0.7 - - - -
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Residues in contact with ASP 476 (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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474G SER* 3.1 11.5 + - - +
475G ARG* 1.3 76.7 - - - +
477G VAL* 1.3 66.1 + - + +
479G LEU* 3.7 22.8 + - - +
480G VAL* 3.9 11.6 - - - +
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Residues in contact with VAL 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G LEU* 5.3 1.8 - - + +
470G HIS* 4.5 14.6 - - + -
471G MSE 4.5 6.1 - - + +
474G SER* 3.1 24.3 + - - +
476G ASP* 1.3 77.6 - - + +
478G ALA* 1.3 57.0 + - - +
479G LEU 3.1 0.2 - - - -
480G VAL* 2.8 29.3 + - - +
481G VAL* 3.0 20.7 + - + -
540G VAL* 3.9 22.7 - - + -
545G LEU* 3.8 32.8 - - + -
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Residues in contact with ALA 478 (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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471G MSE 3.4 36.0 - - + +
474G SER 3.4 2.6 + - - -
475G ARG* 3.4 43.7 - - - +
476G ASP 3.4 0.2 - - - -
477G VAL* 1.3 78.8 - - - +
479G LEU* 1.3 58.7 + - - +
481G VAL* 3.6 3.1 + - - +
482G GLN* 3.2 24.1 + - - +
502G TYR* 3.8 6.0 - - + -
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Residues in contact with LEU 479 (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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475G ARG 3.6 17.5 + - - +
476G ASP* 3.8 19.7 - - - +
477G VAL 3.0 0.8 + - - -
478G ALA* 1.3 78.8 - - - +
480G VAL* 1.3 63.2 + - + +
482G GLN* 3.5 26.3 + - - +
483G GLU* 3.7 8.3 + - - +
505G TYR* 3.9 37.7 - - + +
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Residues in contact with VAL 480 (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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476G ASP* 3.9 14.4 - - - +
477G VAL* 2.8 14.0 + - - +
479G LEU* 1.3 71.8 - - + +
481G VAL* 1.3 64.8 + - - +
482G GLN 3.2 0.7 + - - -
483G GLU* 3.6 4.9 + - - +
484G ARG* 3.3 39.9 + - + +
545G LEU* 4.1 25.8 - - + -
549G ILE* 5.1 2.2 - - + -
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Residues in contact with VAL 481 (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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467G LEU* 4.4 14.1 - - + -
471G MSE 3.7 42.4 - - + -
477G VAL* 3.0 30.3 + - + +
478G ALA 3.8 1.3 - - - +
480G VAL* 1.3 77.5 - - + +
482G GLN* 1.3 50.1 + - - +
484G ARG* 4.8 2.5 - - - -
485G ILE* 2.7 61.7 + - + +
489G PHE* 4.1 6.5 - - + -
502G TYR* 3.8 7.6 - - - +
545G LEU* 5.1 3.4 - - + -
549G ILE* 5.1 7.6 - - + -
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Residues in contact with GLN 482 (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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478G ALA 3.2 12.2 + - - +
479G LEU* 3.7 21.2 - - - +
480G VAL 3.2 0.8 - - - -
481G VAL* 1.3 75.4 - - - +
483G GLU* 1.3 60.7 + - - +
485G ILE 2.9 15.6 - - - +
486G GLY* 4.3 4.5 - - - +
502G TYR* 3.5 56.5 + - + +
506G GLU* 4.6 12.4 + - - +
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Residues in contact with GLU 483 (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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479G LEU 3.7 8.0 + - - +
480G VAL* 3.6 7.0 + - - +
481G VAL 3.5 0.2 - - - -
482G GLN* 1.3 79.6 - - - +
484G ARG* 1.3 66.6 + - + +
485G ILE 5.0 0.2 - - - -
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Residues in contact with ARG 484 (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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480G VAL* 3.3 30.1 + - + +
481G VAL 4.2 0.9 - - - +
482G GLN 3.3 0.4 - - - -
483G GLU* 1.3 88.4 - - + +
485G ILE* 1.3 60.6 + - - +
486G GLY 4.3 0.2 + - - -
488G ARG* 4.4 8.3 + - - -
545G LEU* 4.7 2.0 - - - +
546G GLU* 3.2 48.7 + - - +
549G ILE* 3.9 45.8 - - + +
553G LEU* 3.6 25.0 - - + +
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Residues in contact with ILE 485 (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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467G LEU* 3.7 29.8 - - + -
481G VAL* 2.7 35.0 + - + +
482G GLN 2.9 12.2 - - - +
484G ARG* 1.3 76.7 - - + +
486G GLY* 1.3 70.5 + - - +
487G GLY* 3.6 16.2 - - - -
488G ARG* 3.7 14.6 - - + -
489G PHE* 3.8 15.3 - - + -
502G TYR* 3.2 2.1 + - - -
549G ILE* 3.8 26.9 - - + -
552G VAL* 4.0 24.9 - - + -
553G LEU* 4.4 10.5 - - + -
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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