Contacts of the helix formed by residues 456 - 471 (chain G) in PDB entry 6NRB
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 ASP 456 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451G ASP* 4.4 2.5 - - - -
454G GLY 3.8 1.6 + - - -
455G PHE* 1.3 72.7 - - - +
457G ALA* 1.3 69.9 + - - +
458G THR* 3.0 7.5 + - - -
459G ASN* 2.7 35.9 + - + +
460G ILE* 3.0 22.9 - - + +
110I GLN* 5.0 1.9 + - - -
433I ARG* 2.8 35.2 + - - +
472L ASN* 5.6 2.4 - - - +
474L ILE* 5.8 5.0 - - + +
475L SER* 3.6 12.0 + - - +
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Residues in contact with ALA 457 (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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447G ARG* 3.2 51.6 - - + +
450G CYS* 3.5 12.5 - - - +
451G ASP* 4.0 4.9 + - - +
455G PHE 3.4 4.4 + - - -
456G ASP* 1.3 77.7 + - - +
458G THR* 1.3 58.1 + - - +
460G ILE* 3.0 1.4 + - - +
461G LEU* 2.4 41.1 + - + +
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Residues in contact with THR 458 (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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447G ARG* 5.6 3.1 + - - +
456G ASP* 3.0 10.1 + - - -
457G ALA* 1.3 78.0 - - - +
459G ASN* 1.3 53.0 + - - +
461G LEU* 2.9 12.0 + - + +
462G ASN* 2.3 61.8 + - - +
110I GLN* 5.8 0.7 - - - -
433I ARG* 4.0 7.4 - - - -
436I LEU* 3.5 26.9 - - + -
472L ASN* 5.6 6.9 + - - +
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Residues in contact with ASN 459 (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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456G ASP* 2.7 14.2 + - + +
458G THR* 1.3 70.9 - - - +
460G ILE* 1.3 52.2 + - + +
462G ASN* 3.4 6.8 + - - +
463G LYS* 2.4 69.8 + - - +
432I SER* 3.1 19.3 - - - -
433I ARG* 3.3 50.8 - - - +
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Residues in contact with ILE 460 (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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450G CYS* 3.7 10.8 - - - -
455G PHE* 3.5 24.2 - - + -
456G ASP* 3.0 23.2 + - + +
457G ALA 3.0 0.6 + - - -
459G ASN* 1.3 76.2 - - + +
461G LEU* 1.3 57.2 + - - +
463G LYS* 3.3 23.2 + - + +
464G LEU* 2.7 34.5 + - + +
477G VAL* 3.6 20.9 - - + -
484G ILE* 3.4 36.7 - - + +
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Residues in contact with LEU 461 (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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414G MET* 3.1 42.5 - - + +
443G GLU* 3.5 16.6 - - + +
446G PRO* 3.9 7.2 - - + -
447G ARG* 3.4 37.2 - - + +
450G CYS* 3.7 21.8 - - - -
457G ALA* 2.4 49.7 + - + +
458G THR* 3.2 13.2 - - + +
460G ILE* 1.3 66.7 - - - +
462G ASN* 1.3 59.9 + - - +
464G LEU* 3.2 1.3 + - - -
465G ARG* 2.8 26.5 + - - +
477G VAL* 4.4 3.4 - - + -
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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
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458G THR* 2.3 55.2 + - - +
459G ASN 3.5 1.1 - - - +
461G LEU* 1.3 68.3 - - - +
463G LYS* 1.3 54.2 + - - +
465G ARG* 3.0 2.9 + - - +
466G ALA* 2.7 34.1 + - - +
431I GLY* 3.6 0.2 - - - -
432I SER 2.9 33.8 - - - +
435I GLN* 2.7 44.8 - - + +
436I LEU* 3.2 13.3 - - - +
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Residues in contact with LYS 463 (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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459G ASN* 2.4 59.9 + - - +
460G ILE* 3.3 18.2 - - + +
462G ASN* 1.3 70.1 - - - +
464G LEU* 1.3 50.5 - - - +
466G ALA* 2.7 10.9 + - - +
467G ARG* 2.2 43.6 + - + +
484G ILE* 3.8 25.6 - - + -
432I SER* 3.1 25.9 + - - +
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Residues in contact with LEU 464 (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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414G MET* 3.5 31.4 - - + -
460G ILE* 2.7 23.4 + - + +
461G LEU* 3.3 8.1 - - - +
463G LYS* 1.3 71.7 - - - +
465G ARG* 1.3 52.5 + - - +
467G ARG* 3.1 12.4 - - + -
468G HIS* 2.4 43.3 + - + -
475G TYR* 4.5 1.8 - - + -
476G GLY* 3.5 28.9 - - - +
477G VAL* 3.2 40.8 - - + +
484G ILE* 3.5 21.8 - - + -
485G ALA 4.5 1.6 - - - +
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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
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414G MET* 3.8 11.2 - - + -
417G SER* 3.8 3.4 + - - -
418G LYS* 3.2 48.0 + - - +
421G ARG* 3.1 40.2 - - - +
422G ASP* 4.3 2.8 + - - -
443G GLU* 3.0 36.1 + - - +
461G LEU 2.8 23.8 + - - +
462G ASN* 3.0 2.4 + - - +
464G LEU* 1.3 71.4 - - - +
466G ALA* 1.3 52.4 + - - +
468G HIS* 2.8 6.3 + - - -
469G ALA 2.6 30.0 + - - -
425I ASN* 5.1 0.2 + - - -
428I THR* 3.4 13.1 + - + +
435I GLN* 3.1 41.2 - - - +
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Residues in contact with ALA 466 (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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462G ASN 2.7 15.3 + - - +
463G LYS* 2.7 10.8 + - - +
465G ARG* 1.3 71.5 - - - +
467G ARG* 1.3 51.2 + - + +
469G ALA* 2.8 7.5 + - - +
470G GLN* 2.7 48.4 + - - +
428I THR 3.2 25.1 + - - +
429I SER 4.0 7.2 - - - +
430I MET 4.2 4.0 - - - +
431I GLY* 3.6 12.8 - - - +
432I SER* 5.9 0.2 - - - +
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Residues in contact with ARG 467 (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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463G LYS* 2.2 42.1 + - + +
464G LEU* 3.1 18.8 - - + +
466G ALA* 1.3 65.7 - - + -
468G HIS* 1.3 56.6 + - + +
469G ALA 3.5 0.2 - - - -
470G GLN* 3.2 25.1 + - - +
471G GLY* 2.6 33.5 + - - -
472G GLY 3.3 1.6 + - - -
475G TYR* 3.1 43.4 - - + +
484G ILE* 4.3 26.0 + - + +
485G ALA* 4.7 7.3 - - - +
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Residues in contact with HIS 468 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410G GLY 3.8 0.2 - - - -
414G MET* 3.0 45.6 + - + +
415G GLU* 3.2 18.5 + - + +
418G LYS* 3.4 28.8 + - + +
464G LEU* 2.4 34.1 + - + +
465G ARG 3.1 5.8 + - - +
467G ARG* 1.3 69.0 - - - +
469G ALA* 1.3 59.0 + - - +
470G GLN 3.3 0.7 - - - -
471G GLY 3.2 14.0 - - - +
472G GLY* 3.4 22.2 - - - -
475G TYR* 2.4 47.9 + - + +
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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
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418G LYS* 3.8 15.0 - - - +
465G ARG 2.6 15.4 + - - +
466G ALA* 2.8 13.9 + - - +
468G HIS* 1.3 71.1 - - - +
470G GLN* 1.3 61.3 + - + +
471G GLY 4.4 0.4 - - - -
428I THR* 4.2 10.1 - - + +
429I SER* 4.9 9.4 - - - +
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Residues in contact with GLN 470 (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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466G ALA* 2.7 27.8 + - + +
467G ARG* 3.2 38.8 + - - +
469G ALA* 1.3 77.7 - - + +
471G GLY* 1.3 62.3 + - - +
429I SER 5.6 3.3 + - - +
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Residues in contact with GLY 471 (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 ARG* 2.6 19.3 + - - -
468G HIS 3.2 16.5 - - - +
469G ALA 4.4 0.3 - - - -
470G GLN* 1.3 77.2 - - - +
472G GLY* 1.3 58.5 + - - -
473G THR* 3.7 1.1 - - - -
475G TYR* 3.4 23.1 - - - -
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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