Contacts of the helix formed by residues 465 - 472 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.8 4.3 - - - +
27C PRO* 3.3 39.5 - - + +
49C CYS 4.2 14.6 + - - -
50C ALA* 5.3 2.4 + - - -
410D ILE* 5.0 4.0 - - + +
436D GLY* 3.8 17.6 + - - -
439D GLN* 5.2 1.7 + - - -
440D LEU* 5.7 1.9 - - - +
464D GLY* 1.3 71.8 - - - -
466D THR* 1.3 65.7 + - - +
467D VAL 3.2 2.5 - - - -
468D GLU* 3.1 9.6 + - + +
469D ARG* 3.0 24.3 + - - +
478D TYR 3.8 6.7 - - - -
479D ASN* 3.2 25.9 + - - +
480D ASP 4.4 2.2 + - - -
481D ILE* 3.3 28.8 - - + +
600D TPP 3.3 52.3 - - + -
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Residues in contact with THR 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D THR* 3.4 13.0 - - - +
462D ASN* 3.0 42.3 + - + +
464D GLY 4.1 1.1 - - - +
465D TYR* 1.3 72.6 - - - +
467D VAL* 1.3 57.5 + - - -
469D ARG* 3.2 12.1 + - - +
470D ALA* 2.8 29.5 + - - +
531D PRO 4.4 0.9 - - - +
532D LYS 2.8 28.3 - - - +
533D ALA* 5.0 0.2 - - - -
534D ASP 4.1 1.9 + - - +
535D ILE* 3.1 25.0 - - - +
600D TPP 2.7 15.2 + - - -
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Residues in contact with VAL 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D GLY* 3.3 24.7 - - - -
388D PHE* 4.9 1.3 - - + -
465D TYR 4.5 0.2 - - - -
466D THR* 1.3 76.9 + - - +
468D GLU* 1.3 67.2 + - - +
470D ALA* 3.3 8.7 + - - +
471D ILE* 3.1 29.5 + - + +
539D LEU* 3.1 42.2 - - + -
543D THR* 3.7 0.7 + - - -
600D TPP 3.2 51.6 + - + +
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Residues in contact with GLU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PRO* 5.1 1.1 - - + -
28C GLY* 3.2 16.8 + - - -
29C ASP* 3.1 26.1 + - - +
32C LEU* 3.7 12.2 - - + +
465D TYR* 3.1 22.6 + - + +
467D VAL* 1.3 75.8 - - - +
469D ARG* 1.3 60.4 + - - +
471D ILE* 2.9 22.2 + - - +
472D HIS 2.9 32.3 + - - +
479D ASN* 3.1 22.4 - - - +
600D TPP 3.7 38.0 + - + -
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Residues in contact with ARG 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D ASN 4.1 3.4 + - - -
463D GLU 3.3 22.6 + - - -
464D GLY* 4.1 6.5 - - - -
465D TYR 3.0 20.1 + - - +
466D THR* 3.4 12.2 - - - +
468D GLU* 1.3 76.3 - - - +
470D ALA* 1.3 61.4 + - - +
471D ILE 3.4 0.7 + - - -
472D HIS* 3.5 7.7 + - - -
474D ALA* 3.1 54.7 + - + +
476D GLN 5.1 0.4 + - - -
479D ASN* 3.2 31.9 + - + +
480D ASP* 2.3 32.5 + - - -
532D LYS* 3.0 49.9 + - - +
533D ALA* 6.0 1.8 - - - +
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Residues in contact with ALA 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D THR 2.8 16.3 + - - +
467D VAL* 3.4 7.2 - - - +
468D GLU 3.1 0.2 - - - -
469D ARG* 1.3 78.7 - - - +
471D ILE* 1.3 58.5 + - - +
535D ILE* 4.2 20.0 - - + -
543D THR* 3.1 37.7 - - + +
547D GLU* 5.7 0.3 - - - +
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Residues in contact with ILE 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 4.5 10.8 - - + +
32C LEU* 3.9 14.6 - - + -
467D VAL* 3.1 13.4 + - + +
468D GLU* 2.9 30.7 + - - +
469D ARG 4.2 0.2 - - - -
470D ALA* 1.3 80.3 - - - +
472D HIS* 1.3 52.7 + - + +
543D THR* 3.5 20.0 - - - +
546D LEU* 3.4 32.3 - - + -
547D GLU* 2.6 49.0 - - + +
550D ASN* 4.0 21.5 - - - +
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Residues in contact with HIS 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.1 23.1 - - + +
33C GLN* 3.9 22.6 + - + -
36C ASP* 2.5 40.6 + - - -
468D GLU 2.9 18.1 + - - +
469D ARG 3.5 3.6 + - - -
471D ILE* 1.3 81.8 - - + +
473D GLY* 1.3 80.1 + - - +
474D ALA 3.5 2.0 - - - -
478D TYR* 3.3 13.6 + - - -
479D ASN* 3.3 9.0 + - - -
547D GLU* 2.9 33.0 - - - +
550D ASN* 5.5 0.2 - - - +
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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