Contacts of the helix formed by residues 465 - 472 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.9 4.3 - - - +
27A PRO* 3.4 39.3 - - + +
49A CYS 4.3 13.9 + - - -
50A ALA 5.3 2.9 + - - -
410B ILE* 5.0 2.7 - - + -
436B GLY* 3.8 20.0 + - - -
439B GLN* 5.2 1.2 + - - -
440B LEU* 5.6 2.6 - - - +
464B GLY* 1.3 74.2 - - - -
466B THR* 1.3 63.4 + - - +
467B VAL 3.3 2.5 - - - -
468B GLU* 3.2 9.4 + - + +
469B ARG* 3.0 25.5 + - - +
478B TYR 3.7 7.0 - - - -
479B ASN* 3.2 26.7 + - - +
480B ASP 4.3 2.4 + - - -
481B ILE* 3.3 27.6 - - + +
600B TPP 3.3 49.6 - - + -
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Residues in contact with THR 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B THR* 3.3 8.7 - - - +
462B ASN* 3.0 39.9 - - + +
464B GLY 4.2 1.1 - - - +
465B TYR* 1.3 71.1 - - - +
467B VAL* 1.3 58.1 + - - -
469B ARG* 3.1 12.4 + - - +
470B ALA* 2.8 29.6 + - - +
531B PRO 4.4 0.9 - - - +
532B LYS 2.9 29.2 - - - +
533B ALA* 5.1 0.2 - - - -
534B ASP 4.1 1.4 + - - +
535B ILE* 3.2 23.1 - - - +
600B TPP 2.5 21.6 + - - -
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B GLY* 3.4 21.5 - - - -
388B PHE* 4.9 2.0 - - + -
465B TYR 4.6 0.2 - - - -
466B THR* 1.3 78.1 + - - +
468B GLU* 1.3 67.9 + - - +
470B ALA* 3.2 8.1 + - - +
471B ILE* 3.0 28.9 + - + +
539B LEU* 3.2 42.2 - - + -
543B THR* 3.8 1.1 + - - +
600B TPP 3.1 54.2 + - + +
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Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO* 5.3 1.3 - - + -
28A GLY* 3.4 15.1 + - - -
29A ASP* 3.2 26.8 + - - +
32A LEU* 3.8 13.4 - - + +
465B TYR* 3.2 23.5 + - + +
467B VAL* 1.3 78.5 - - - +
469B ARG* 1.3 56.7 + - - +
471B ILE* 2.9 21.9 + - - +
472B HIS 2.8 32.3 + - - +
479B ASN* 3.1 21.8 - - - +
600B TPP 3.8 38.6 + - + -
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Residues in contact with ARG 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B GLU 3.0 25.9 + - - -
464B GLY* 4.7 0.8 - - - -
465B TYR 3.0 22.6 + - - +
466B THR* 3.4 14.6 - - - +
468B GLU* 1.3 76.5 - - - +
470B ALA* 1.3 62.2 + - - +
471B ILE 3.3 0.5 + - - -
472B HIS* 3.5 7.2 + - - -
474B ALA* 3.0 59.7 + - + +
475B GLU* 4.9 2.2 - - - +
476B GLN 4.7 2.6 + - - -
479B ASN* 3.2 34.6 + - + +
480B ASP* 2.8 28.8 + - - +
532B LYS* 3.6 43.5 + - - +
533B ALA* 5.8 1.8 - - - +
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Residues in contact with ALA 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B THR 2.8 13.3 + - - +
467B VAL* 3.4 9.9 - - - +
469B ARG* 1.3 77.4 - - - +
471B ILE* 1.3 60.2 + - - +
535B ILE* 4.2 19.5 - - + -
539B LEU* 5.5 0.4 - - + -
543B THR* 3.2 37.3 - - + +
547B GLU* 5.7 0.3 - - - +
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 4.5 9.9 - - + +
32A LEU* 3.9 15.7 - - + -
467B VAL* 3.0 16.4 + - + +
468B GLU* 2.9 29.2 + - - +
470B ALA* 1.3 80.2 - - - +
472B HIS* 1.3 53.8 + - + +
543B THR* 3.4 23.8 - - - +
546B LEU* 3.3 31.4 - - + -
547B GLU* 2.6 48.2 - - + +
550B ASN* 4.1 21.1 - - - +
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Residues in contact with HIS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.1 23.9 - - + +
33A GLN* 4.0 22.3 + - + -
36A ASP* 2.6 39.4 + - - -
468B GLU 2.8 15.5 + - - +
469B ARG 3.5 3.1 + - - -
471B ILE* 1.3 81.3 - - + +
473B GLY* 1.3 78.4 + - - +
474B ALA 3.5 1.8 - - - -
478B TYR* 3.3 13.9 + - - -
479B ASN* 3.3 8.7 + - - -
547B GLU* 2.9 32.1 - - - +
550B 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