Contacts of the helix formed by residues 461 - 469 (chain A) in PDB entry 5VOT
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 ASN 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A ASP* 4.0 6.5 - - - +
449A LYS* 4.2 8.5 - - - +
451A GLY* 3.1 15.8 + - - -
452A ALA* 2.3 46.6 + - - +
454A ASP* 6.1 3.1 - - + +
459A ILE* 5.4 1.8 - - + +
460A TRP* 1.3 73.5 - - - +
462A GLY* 1.3 63.3 + - - +
464A VAL* 3.5 1.0 - - - +
465A GLY* 2.7 20.0 + - - -
652A SER* 3.8 20.8 + - - -
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Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A VAL* 3.6 8.5 - - - +
447A ASP* 3.0 31.9 + - - -
449A LYS* 3.7 9.6 - - - -
451A GLY* 4.3 2.9 - - - -
461A ASN* 1.3 76.5 - - - +
463A MET* 1.3 56.4 + - - -
465A GLY* 2.6 22.9 + - - -
466A GLU* 2.9 12.6 + - - +
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Residues in contact with MET 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A THR* 3.6 23.6 - - + +
399A THR* 3.5 34.3 - - - +
400A ILE* 3.8 24.7 - - + -
445A VAL* 3.7 15.0 - - + +
449A LYS 3.5 17.8 + - - +
450A TYR* 3.4 25.4 + - + +
462A GLY* 1.3 68.3 - - - -
464A VAL* 1.3 61.7 + - + +
466A GLU* 2.7 25.3 + - - +
467A LEU* 2.9 19.3 + - - +
475A ALA* 5.4 6.5 - - + -
477A ALA* 4.1 11.7 - - + -
478A PRO 5.9 0.7 - - - +
479A LEU* 5.0 13.5 - - + -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A TYR 3.7 5.4 - - - +
451A GLY* 3.6 24.5 - - - +
460A TRP* 3.5 39.3 - - + -
461A ASN 3.4 7.8 + - - +
462A GLY 3.2 0.2 - - - -
463A MET* 1.3 76.8 - - + +
465A GLY* 1.3 57.9 + - - +
467A LEU* 4.6 3.1 - - - +
468A VAL* 2.9 49.2 + - + +
479A LEU* 5.2 10.1 - - + -
485A ARG* 4.9 17.5 - - + +
488A VAL* 4.8 6.7 - - + -
489A ILE* 6.0 9.0 - - + -
491A PHE* 6.5 0.7 - - + -
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Residues in contact with GLY 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A TRP 3.6 10.5 + - - -
461A ASN* 2.7 14.1 + - - -
462A GLY 2.6 16.9 + - - -
464A VAL* 1.3 72.8 - - - +
466A GLU* 1.3 62.0 + - - -
469A TYR* 3.0 40.8 - - - +
471A LYS* 4.5 2.9 - - - +
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Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A THR* 3.9 13.2 - - + +
445A VAL* 3.6 24.4 - - + +
446A GLY 4.7 2.4 + - - -
462A GLY 2.9 13.2 + - - +
463A MET* 2.7 24.5 + - - +
465A GLY* 1.3 74.5 - - - +
467A LEU* 1.3 58.7 + - - +
470A GLY 3.4 1.6 + - - -
471A LYS* 2.6 56.7 + - - +
472A ALA* 3.0 18.6 + - + +
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A THR* 4.7 0.9 - - + -
463A MET 2.9 13.4 + - - +
464A VAL* 4.6 2.0 - - - +
466A GLU* 1.3 74.3 - - - +
468A VAL* 1.3 68.4 + - - +
470A GLY* 2.9 14.6 + - - -
472A ALA* 3.2 37.5 - - + +
473A ASP 3.6 3.6 - - - -
474A ILE* 3.5 17.7 - - - +
475A ALA* 3.7 20.2 - - + -
489A ILE* 4.1 20.8 - - + +
735A ALA* 3.7 34.1 - - + +
736A THR* 4.2 3.1 - - - +
737A PRO* 3.9 23.0 - - + +
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A TRP* 4.2 17.9 - - + -
464A VAL* 2.9 41.0 + - + +
467A LEU* 1.3 77.4 - - - +
469A TYR* 1.3 73.7 + - + +
470A GLY 3.4 2.4 + - - -
488A VAL* 4.1 15.0 - - + +
489A ILE* 3.9 24.2 - - + -
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Residues in contact with TYR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A LYS 4.1 3.5 + - - -
459A ILE* 3.2 23.2 - - + +
460A TRP* 3.1 49.3 + - + +
465A GLY* 3.0 32.4 + - - +
467A LEU 3.2 1.0 - - - -
468A VAL* 1.3 87.9 - - + +
470A GLY* 1.3 59.1 + - - +
471A LYS* 2.8 44.3 + - + +
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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