Contacts of the helix formed by residues 485 - 489 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484C TRP* 1.3 69.6 - - - +
486C TRP* 1.3 63.4 + - - +
487C THR* 3.6 8.3 + - - -
488C HIS* 2.9 52.9 + - - +
489C ILE 3.8 1.9 + - - -
503C ARG* 4.5 12.7 - - - +
527C GLU* 5.0 0.8 + - - -
491D GLN 3.5 21.8 - - - +
492D ALA 2.9 16.7 + - - +
494D SER 3.7 11.8 - - - +
495D LEU* 4.0 15.6 - - + +
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Residues in contact with TRP 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C ASP* 3.3 44.6 - - + +
438C ALA* 3.6 26.5 - - + -
439C GLN* 4.0 7.2 - - + -
442C ILE* 4.4 5.4 - - + -
459C VAL* 3.9 28.7 - - + -
461C ASN* 3.8 13.2 - - - +
481C ILE* 5.5 0.9 - - + -
484C TRP* 3.5 50.5 + + + +
485C ASN* 1.3 72.2 - - - +
487C THR* 1.3 62.6 + - - +
488C HIS 3.0 1.4 + - - -
489C ILE* 3.1 41.2 + - + +
490C PRO* 3.7 0.2 - - - +
525C LEU* 3.5 21.2 - - + +
527C GLU* 3.2 39.1 + - + -
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Residues in contact with THR 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C ASN* 3.6 6.9 + - - -
486C TRP* 1.3 73.7 - - - +
488C HIS* 1.3 78.2 + - - +
489C ILE 3.5 0.2 - - - -
491C GLN* 3.3 19.8 + - - +
501C CYS* 3.4 31.0 - - + +
502C TRP* 3.2 35.2 - - - +
503C ARG* 4.2 9.4 + - + -
525C LEU* 4.9 2.5 - - + +
527C GLU* 3.7 20.8 + - + +
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Residues in contact with HIS 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C ASN* 2.9 37.0 + - - +
487C THR* 1.3 96.1 + - - +
489C ILE* 1.3 63.4 + - - +
490C PRO 3.5 1.8 - - - -
491C GLN* 3.2 30.2 + - + +
492C ALA* 3.6 10.6 + - - +
488D HIS* 5.1 1.3 - - - +
491D GLN* 4.3 15.9 - - + +
492D ALA* 3.8 6.5 - - + +
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Residues in contact with ILE 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ILE* 4.0 15.0 - - + -
445C LEU* 3.4 25.4 - - + -
484C TRP* 3.9 20.0 - - + -
485C ASN 4.1 3.6 - - - +
486C TRP* 3.1 46.9 + - + +
488C HIS* 1.3 75.7 - - - +
490C PRO* 1.3 73.8 - - + +
492C ALA* 2.8 14.4 + - + +
493C LEU* 3.0 27.9 + - + +
525C LEU* 4.9 1.1 - - + -
492D ALA* 4.1 19.7 - - + +
493D LEU* 4.9 4.3 - - + -
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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