Contacts of the helix formed by residues 485 - 489 (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 ASN 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491C GLN 3.4 26.0 - - - +
492C ALA 3.0 15.9 + - - +
494C SER 3.7 12.2 - - - +
495C LEU* 3.9 13.1 - - + +
484D TRP* 1.3 69.2 - - - +
486D TRP* 1.3 65.3 + - - +
487D THR* 3.8 3.4 + - - -
488D HIS* 2.9 45.6 + - - +
489D ILE 3.9 1.6 + - - -
503D ARG* 3.4 27.7 - - - +
527D GLU* 4.9 1.0 + - - -
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Residues in contact with TRP 486 (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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435D ASP* 3.3 45.3 + - + +
438D ALA* 3.6 26.0 - - + -
439D GLN* 3.9 6.5 - - + -
442D ILE* 4.3 5.8 - - + -
459D VAL* 3.9 27.4 - - + -
461D ASN* 3.9 12.1 - - - +
481D ILE* 5.5 0.7 - - + -
484D TRP* 3.4 52.7 + + + +
485D ASN* 1.3 71.0 - - - +
487D THR* 1.3 63.1 + - - +
488D HIS 3.0 1.7 + - - -
489D ILE* 3.1 42.3 + - + +
525D LEU* 3.5 19.5 - - + +
527D GLU* 3.1 41.3 + - + -
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Residues in contact with THR 487 (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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485D ASN* 3.8 6.1 + - - -
486D TRP* 1.3 74.2 - - - +
488D HIS* 1.3 79.0 + - - +
489D ILE 3.4 0.2 - - - -
491D GLN* 3.2 18.7 + - - +
501D CYS* 3.3 27.7 - - + +
502D TRP* 3.5 37.7 - - - +
503D ARG* 4.1 12.3 + - + +
525D LEU* 5.0 3.6 - - + +
527D GLU* 3.6 19.9 + - + +
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Residues in contact with HIS 488 (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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488C HIS* 5.1 1.1 - - - +
491C GLN* 4.3 16.8 - - + +
492C ALA* 3.8 6.6 - - - +
485D ASN* 2.9 35.6 + - - +
487D THR* 1.3 105.4 + - - +
489D ILE* 1.3 64.3 + - - +
490D PRO* 3.5 1.8 - - - -
491D GLN* 3.3 31.0 + - + +
492D ALA* 3.6 10.2 + - - +
503D ARG* 5.6 2.0 - - - -
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Residues in contact with ILE 489 (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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492C ALA* 4.1 23.3 - - + +
493C LEU* 4.9 3.6 - - + -
442D ILE* 3.9 18.2 - - + -
445D LEU* 3.4 26.7 - - + -
484D TRP* 4.0 12.8 - - + -
486D TRP* 3.4 49.1 - - + +
488D HIS* 1.3 76.1 - - - +
490D PRO* 1.3 73.8 - - + +
492D ALA* 2.8 14.7 + - + +
493D LEU* 3.0 27.9 + - + +
525D LEU* 4.8 1.3 - - + -
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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