Contacts of the helix formed by residues 384 - 391 (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 GLY 384 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C GLN* 1.3 78.5 - - - +
385C THR* 1.3 66.8 + - - -
386C SER 3.1 4.0 + - - -
387C ALA* 3.4 1.1 + - - +
388C PHE* 3.1 32.0 + - - -
467C VAL* 3.3 32.5 - - - -
600C TPP 3.6 6.7 - - - -
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Residues in contact with THR 385 (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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362C GLN* 3.3 30.3 + - - +
366C TRP* 3.4 9.0 - - - -
384C GLY* 1.3 71.2 - - - -
386C SER* 1.3 63.4 + - - +
388C PHE 3.8 0.4 - - - +
389C GLY* 2.9 19.8 + - - -
460C LEU* 3.6 9.6 - - - +
462C ASN* 4.0 2.8 + - - +
466C THR* 3.4 25.1 - - - +
467C VAL* 3.8 0.2 - - - +
534C ASP 4.0 4.7 - - - +
535C ILE* 4.0 0.2 - - + -
536C PRO* 3.6 24.4 - - + +
539C LEU* 3.8 10.5 - - + -
600C TPP 2.6 31.4 + - - +
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Residues in contact with SER 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C TRP* 3.1 17.1 - - - -
381C ALA* 4.0 4.0 - - - -
382C ASP 3.4 14.8 - - - -
383C GLN 5.2 1.1 - - - -
384C GLY 3.1 0.4 - - - -
385C THR* 1.3 79.7 + - - +
387C ALA* 1.3 58.4 + - - +
390C ALA* 2.9 29.6 + - - +
432C LEU* 3.5 22.1 + - - -
433C THR* 3.4 28.2 + - - -
434C GLY* 3.5 4.1 + - - -
460C LEU* 3.7 11.2 - - - +
600C TPP 4.7 0.4 + - - -
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Residues in contact with ALA 387 (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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244C LEU* 4.6 10.0 - - + +
381C ALA* 3.9 10.1 - - - +
382C ASP 2.9 28.5 + - - +
383C GLN* 4.3 8.1 - - - +
384C GLY 3.4 5.1 + - - +
386C SER* 1.3 74.0 - - - +
388C PHE* 1.3 67.0 - - + +
390C ALA* 3.4 1.9 + - - +
391C ILE* 3.1 27.0 + - - +
401C PHE* 5.3 0.6 - - - -
403C VAL* 4.0 23.3 - - + -
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Residues in contact with PHE 388 (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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244C LEU* 3.9 24.2 - - + -
290C THR* 4.6 18.8 - - + -
383C GLN* 4.0 22.0 - - + -
384C GLY* 3.1 37.5 + - - +
385C THR 3.8 1.3 - - - +
387C ALA* 1.3 78.1 - - + +
389C GLY* 1.3 58.1 + - - +
391C ILE* 3.3 17.9 - - - +
392C ASP* 4.4 2.4 - - - +
405C PRO* 5.9 0.2 - - + -
467C VAL* 5.2 1.6 - - + -
536C PRO* 3.7 12.6 - - - +
538C LEU* 3.7 29.3 - - + +
539C LEU* 3.4 38.1 - - + -
542C LEU* 3.4 30.1 - - + -
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Residues in contact with GLY 389 (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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366C TRP* 3.4 33.6 - - - +
385C THR 2.9 16.2 + - - -
388C PHE* 1.3 76.5 - - - +
390C ALA* 1.3 63.4 + - - +
391C ILE 3.1 5.3 + - - -
392C ASP* 3.2 20.5 + - - +
393C LEU* 4.3 1.4 + - - +
536C PRO* 4.1 8.3 - - - -
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Residues in contact with ALA 390 (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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247C LYS* 3.5 7.8 - - - -
366C TRP* 3.5 19.5 - - + -
381C ALA* 4.2 4.7 - - + -
386C SER 2.9 18.5 + - - +
387C ALA 3.9 2.5 - - - +
389C GLY* 1.3 71.8 - - - +
391C ILE* 1.3 64.4 + - - +
392C ASP 3.0 2.9 - - - -
393C LEU* 3.0 33.1 + - + +
401C PHE* 3.8 21.4 - - + -
432C LEU* 4.0 10.5 - - + -
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Residues in contact with ILE 391 (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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244C LEU* 3.9 29.4 - - + +
247C LYS* 3.2 27.8 + - + +
260C THR* 3.4 36.3 + - + +
262C SER* 4.4 15.5 - - - +
387C ALA 3.1 12.2 + - - +
388C PHE 3.3 24.2 - - - +
390C ALA* 1.3 78.4 - - - +
392C ASP* 1.3 71.9 + - - +
401C PHE* 4.7 0.2 - - - -
538C LEU* 3.5 31.0 - - + -
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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