Contacts of the helix formed by residues 463 - 472 (chain J) in PDB entry 6NR8
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 ALA 463 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425B ALA 5.0 0.2 - - - +
429B PRO* 3.3 29.5 - - + +
433B ALA 6.3 0.2 - - - -
434B VAL* 6.0 2.9 - - + -
437B GLU* 3.4 26.2 - - - +
444J ARG* 5.1 2.7 - - - +
459J ALA 4.5 7.7 + - - +
461J LEU 3.3 0.2 - - - -
462J VAL* 1.3 85.5 - - + +
464J GLN* 1.3 67.8 + - - +
465J LEU 3.6 0.2 - - - -
466J ARG* 3.9 15.8 + - - +
467J ALA* 3.5 16.6 + - - +
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Residues in contact with GLN 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B THR 5.5 1.3 - - - +
429B PRO* 3.2 32.0 + - + +
430B GLY* 4.6 8.0 - - - -
456J TYR* 3.7 12.5 + - - -
460J ASP* 2.9 25.1 + - - +
461J LEU 3.5 1.2 + - - +
463J ALA* 1.3 81.7 - - - +
465J LEU* 1.3 63.1 + - + +
467J ALA* 3.4 4.3 + - - +
468J ALA* 3.1 27.2 + - + +
485J ILE* 5.3 12.5 - - - +
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Residues in contact with LEU 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415J MET* 3.7 9.4 - - + -
461J LEU* 3.5 13.1 + - + +
464J GLN* 1.3 79.0 - - + +
466J ARG* 1.3 60.8 + - - +
468J ALA* 3.7 14.1 - - + -
469J HIS* 2.9 53.2 + - + +
476J ALA* 4.1 9.0 - - + +
477J GLY* 3.6 32.3 - - - +
478J LEU* 3.7 21.3 - - + -
485J ILE* 3.7 37.5 - - + -
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Residues in contact with ARG 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASN* 2.4 39.8 + - - +
437B GLU* 5.1 2.4 + - - -
415J MET* 3.3 41.1 - - + +
418J ALA* 3.8 11.3 + - - -
419J HIS* 3.4 46.0 + - + +
422J THR* 4.9 7.7 + - - +
423J GLN* 5.6 3.0 - - - +
444J ARG* 3.7 35.7 - - - +
462J VAL 3.4 15.0 + - - +
463J ALA* 3.9 16.8 + - - +
464J GLN 3.2 0.4 - - - -
465J LEU* 1.3 78.2 - - - +
467J ALA* 1.3 62.1 + - - +
469J HIS* 4.1 0.4 - - - -
470J SER* 2.8 28.8 + - - -
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Residues in contact with ALA 467 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASN* 3.2 37.9 - - + +
427B ARG* 4.7 4.9 - - - +
429B PRO* 4.8 2.9 - - + -
419J HIS* 4.1 11.7 - - + -
463J ALA 3.5 12.4 + - - +
464J GLN 3.4 4.5 + - - +
466J ARG* 1.3 81.5 - - - +
468J ALA* 1.3 62.7 + - - +
470J SER* 4.1 0.4 - - - -
471J GLU* 3.2 34.9 + - - +
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Residues in contact with ALA 468 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464J GLN* 3.1 20.5 + - + +
465J LEU* 3.0 19.9 + - + +
467J ALA* 1.3 79.3 - - - +
469J HIS* 1.3 63.2 + - - +
471J GLU* 3.4 3.8 + - - +
472J GLY 2.9 22.8 + - - +
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Residues in contact with HIS 469 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412J CYS* 3.5 23.6 + - - -
415J MET* 3.3 30.8 - - + +
416J LEU* 3.4 29.9 - - + +
465J LEU* 2.9 42.1 + - + -
466J ARG 4.1 0.7 - - - -
468J ALA* 1.3 76.1 - - - +
470J SER* 1.3 82.5 + - - +
472J GLY 3.2 17.7 + - - +
473J ASN 3.3 10.5 - - - +
474J THR* 3.3 24.0 + - - +
476J ALA* 3.2 30.5 - - + +
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Residues in contact with SER 470 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416J LEU* 3.8 12.2 - - - +
419J HIS* 3.3 42.1 - - - +
466J ARG 2.8 23.6 + - - -
467J ALA 4.2 0.2 - - - -
468J ALA 3.2 0.6 - - - -
469J HIS* 1.3 93.5 + - - +
471J GLU* 1.3 61.2 + - - +
472J GLY* 3.4 0.9 + - - -
474J THR* 4.8 4.2 - - - +
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Residues in contact with GLU 471 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ASN 3.6 18.7 - - - +
427B ARG* 3.8 19.4 - - - +
419J HIS* 4.9 11.8 - - + +
467J ALA* 3.2 23.4 + - - +
468J ALA* 4.1 3.9 - - - +
470J SER* 1.3 76.5 - - - +
472J GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 472 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468J ALA 2.9 17.6 + - - +
469J HIS* 3.2 4.9 - - - +
470J SER 3.2 4.0 - - - -
471J GLU* 1.3 80.7 - - - +
473J ASN* 1.3 72.6 + - - +
474J THR* 5.7 0.7 - - - -
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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