Contacts of the helix formed by residues 465 - 472 (chain A) in PDB entry 1OVM
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 TYR 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A ILE* 5.0 3.5 - - + +
436A GLY* 3.8 17.1 + - - -
439A GLN* 5.2 1.4 + - - -
440A LEU* 5.6 2.5 - - + +
464A GLY* 1.3 72.2 - - - -
466A THR* 1.3 65.7 + - - +
467A VAL 3.2 2.5 - - - -
468A GLU* 3.1 10.2 + - + +
469A ARG* 3.0 25.1 + - - +
478A TYR 3.8 6.7 - - - -
479A ASN* 3.2 26.2 + - - +
480A ASP 4.3 2.2 + - - -
481A ILE* 3.4 27.9 - - + +
600A TPP 3.3 50.9 - - + +
26B VAL* 4.8 4.3 - - - +
27B PRO* 3.3 39.1 - - + +
49B CYS 4.3 13.7 + - - -
50B ALA 5.4 1.9 + - - -
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Residues in contact with THR 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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385A THR* 3.3 15.9 - - - +
462A ASN* 2.9 42.8 + - + +
464A GLY 4.1 1.1 - - - +
465A TYR* 1.3 72.6 - - - +
467A VAL* 1.3 57.9 + - - -
469A ARG* 3.2 11.3 + - - +
470A ALA* 2.8 29.6 + - - +
531A PRO 4.5 1.1 - - - +
532A LYS 2.9 28.3 - - - +
533A ALA* 5.0 0.2 - - - -
534A ASP 4.1 1.0 + - - -
535A ILE* 3.1 24.4 - - - +
600A TPP 2.7 11.5 + - - -
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Residues in contact with VAL 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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384A GLY* 3.3 21.5 - - - -
388A PHE* 4.8 1.6 - - + -
465A TYR 4.5 0.4 - - - -
466A THR* 1.3 77.3 + - - +
468A GLU* 1.3 68.6 + - - +
470A ALA* 3.1 8.7 + - - +
471A ILE* 3.0 29.6 + - + +
539A LEU* 3.2 41.7 - - + -
543A THR* 3.8 1.4 + - - +
600A TPP 3.1 52.7 + - + +
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Residues in contact with GLU 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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465A TYR* 3.1 23.0 + - + +
467A VAL* 1.3 81.7 - - - +
469A ARG* 1.3 56.3 + - - +
471A ILE* 2.9 20.8 + - - +
472A HIS 2.8 32.1 + - - +
479A ASN* 3.1 22.4 - - - +
600A TPP 3.8 37.5 + - + -
27B PRO* 5.2 1.1 - - + -
28B GLY* 3.3 14.0 + - - -
29B ASP* 3.1 28.1 + - - +
32B LEU* 3.8 14.1 - - + +
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Residues in contact with ARG 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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463A GLU 2.9 27.5 + - - -
464A GLY* 3.9 1.0 - - - -
465A TYR 3.0 22.1 + - - +
466A THR* 3.4 14.6 - - - +
468A GLU* 1.3 77.2 - - - +
470A ALA* 1.3 60.8 + - - +
471A ILE 3.4 0.3 + - - -
472A HIS* 3.5 6.6 + - - -
474A ALA* 3.1 55.8 + - + +
475A GLU* 4.9 2.2 - - - +
476A GLN 4.7 2.0 + - - -
479A ASN* 3.2 35.9 + - + +
480A ASP* 3.0 27.8 + - - -
532A LYS* 3.6 43.3 - - - +
533A ALA* 5.8 2.2 - - - +
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Residues in contact with ALA 470 (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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466A THR 2.8 13.4 + - - +
467A VAL* 3.3 7.9 - - - +
469A ARG* 1.3 76.7 - - - +
471A ILE* 1.3 61.5 + - - +
535A ILE* 4.2 21.3 - - + -
539A LEU* 5.5 0.4 - - + -
543A THR* 3.2 37.8 - - + +
547A GLU* 5.7 0.2 - - - +
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Residues in contact with ILE 471 (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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467A VAL* 3.0 15.9 + - + +
468A GLU* 2.9 29.4 + - - +
470A ALA* 1.3 81.2 - - - +
472A HIS* 1.3 52.9 + - + +
543A THR* 3.4 22.7 - - - +
546A LEU* 3.5 29.4 - - + -
547A GLU* 2.7 48.3 - - - +
550A ASN* 4.0 22.9 - - - +
29B ASP* 4.5 9.6 - - + +
32B LEU* 4.1 12.8 - - + -
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Residues in contact with HIS 472 (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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468A GLU 2.8 14.9 + - - +
469A ARG 3.5 3.2 + - - -
471A ILE* 1.3 81.9 - - + +
473A GLY* 1.3 80.2 + - - +
474A ALA 3.5 2.2 - - - -
478A TYR* 3.2 14.2 + - - -
479A ASN* 3.2 8.7 + - - -
547A GLU* 3.0 31.6 - - - +
550A ASN* 5.5 0.2 - - - +
32B LEU* 4.1 24.1 - - + +
33B GLN* 3.9 22.8 + - + -
36B ASP* 2.6 39.5 + - - -
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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