Contacts of the helix formed by residues 462 - 471 (chain I) 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 ASP 462 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458H VAL* 6.0 0.7 - - - +
462H GLU* 4.7 11.8 - - - +
486H VAL* 4.2 24.9 - - - +
458I GLN 4.9 7.4 + - - +
460I SER 4.8 0.6 - - - +
461I THR* 1.3 87.1 + - - +
463I LEU* 1.3 65.0 + - + +
464I VAL 3.4 0.2 - - - -
465I ALA* 3.4 9.1 - - + +
466I LYS* 3.0 38.6 + - + +
494I LYS* 4.4 22.4 + - + -
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Residues in contact with LEU 463 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449I PRO* 4.0 14.1 - - + +
450I ASN* 4.4 5.4 - - - +
453I ALA* 3.7 24.7 - - + -
458I GLN* 3.9 13.0 - - + +
460I SER* 4.0 16.6 - - - +
461I THR 3.2 0.4 - - - -
462I ASP* 1.3 85.0 - - + +
464I VAL* 1.3 61.2 + - + +
465I ALA 3.5 0.2 + - - -
467I LEU* 3.3 34.6 + - + +
488I LEU* 3.8 33.0 - - + -
493I GLY 3.3 26.9 - - - +
494I LYS* 4.9 2.7 - - + -
495I PRO* 3.8 16.8 - - + -
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Residues in contact with VAL 464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429G GLY 3.5 20.6 - - - +
430G LYS* 6.0 1.1 - - + -
432G GLN* 2.8 28.2 + - - +
433G LEU* 5.7 6.1 - - + -
446I LEU* 3.8 31.4 - - + -
449I PRO* 6.2 0.9 - - + -
450I ASN* 3.5 16.8 - - - +
460I SER 3.3 21.5 + - - +
461I THR* 3.4 15.7 - - - +
463I LEU* 1.3 75.5 - - - +
465I ALA* 1.3 61.5 + - - +
467I LEU 4.4 0.9 - - - +
468I ARG* 3.2 21.9 - - + +
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Residues in contact with ALA 465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G PRO* 3.4 16.8 - - + +
429G GLY* 3.3 21.5 - - - +
461I THR 3.3 18.3 + - - +
462I ASP* 3.2 15.9 + - + +
463I LEU 3.2 1.0 - - - -
464I VAL* 1.3 80.8 - - - +
466I LYS* 1.3 66.3 + - + +
469I ALA* 3.2 22.5 + - - +
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Residues in contact with LYS 466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462I ASP* 3.0 20.4 + - + +
463I LEU 4.7 0.2 - - - +
465I ALA* 1.3 78.4 - - + +
467I LEU* 1.3 58.6 + - - +
469I ALA* 2.9 22.1 + - - +
470I PHE* 2.9 39.2 + - + -
494I LYS* 3.9 18.6 - - - +
495I PRO* 3.7 52.5 + - + -
497I ASP* 5.4 1.4 + - - -
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Residues in contact with LEU 467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I GLY 4.8 4.7 - - - +
414I ALA* 5.2 0.7 - - - -
417I ALA* 4.1 26.2 - - + -
446I LEU* 6.6 0.2 - - + -
449I PRO* 4.9 11.0 - - + -
463I LEU* 3.3 24.3 + - + +
464I VAL* 5.5 0.4 - - - -
465I ALA 3.5 0.4 - - - -
466I LYS* 1.3 77.9 - - + +
468I ARG* 1.3 72.7 + - - +
470I PHE* 3.7 21.5 + - + +
471I HIS* 3.3 30.5 + - - +
486I ILE* 4.2 13.9 - - - +
487I GLY 4.1 17.3 - - - +
488I LEU* 4.3 24.5 - - + -
495I PRO* 4.9 5.2 - - + -
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Residues in contact with ARG 468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424G SER 5.7 0.2 - - - -
425G ARG* 2.9 38.9 - - - +
426G THR* 4.9 0.9 - - - -
427G ILE 4.3 3.1 - - - +
428G PRO* 6.1 0.2 - - - -
432G GLN* 3.2 28.0 - - - +
417I ALA* 2.8 38.2 + - - +
420I SER* 5.2 3.2 + - - -
421I ILE* 3.3 30.8 - - - +
446I LEU* 4.1 23.0 - - - +
464I VAL* 3.2 21.7 + - - +
465I ALA 3.8 1.9 + - - +
466I LYS 3.2 0.4 - - - -
467I LEU* 1.3 87.4 + - - +
469I ALA* 1.3 64.3 + - - +
470I PHE 3.2 0.8 + - - -
471I HIS* 3.2 40.7 + - - +
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Residues in contact with ALA 469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425G ARG 4.6 2.2 - - - -
426G THR* 5.3 6.3 - - - +
428G PRO* 4.9 8.7 - - + +
465I ALA 3.2 19.6 + - - +
466I LYS* 2.9 9.5 + - - +
468I ARG* 1.3 76.7 - - - +
470I PHE* 1.3 65.6 + - + +
471I HIS 5.0 0.5 - - - +
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Residues in contact with PHE 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466I LYS* 2.9 54.7 + - + -
467I LEU* 3.7 24.7 - - + +
468I ARG 3.2 0.6 - - - -
469I ALA* 1.3 81.2 - - + +
471I HIS* 1.3 63.8 + - - +
472I ASN* 3.1 4.9 + - - +
483I LEU 3.3 17.7 - - - +
484I LYS* 3.3 5.0 - - - +
485I TRP* 3.2 48.2 - + + +
487I GLY 4.5 2.9 - - - -
495I PRO* 4.8 1.6 - - + -
497I ASP* 3.2 36.6 - - - -
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Residues in contact with HIS 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425G ARG* 5.3 9.2 - - + +
417I ALA* 3.5 6.8 + - + +
418I ALA* 3.3 26.1 - - - -
421I ILE* 4.3 5.7 - - + +
422I TYR* 3.3 26.3 + + + +
467I LEU* 3.3 13.9 + - - +
468I ARG* 3.2 46.9 + - - +
469I ALA 3.5 1.7 - - - +
470I PHE* 1.3 71.5 - - - +
472I ASN* 1.3 63.0 + - - +
473I GLU* 3.7 7.3 + - - +
484I LYS* 3.6 14.5 + - - +
485I TRP 3.1 26.3 + - - -
486I ILE* 3.5 15.4 - - - +
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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