Contacts of the helix formed by residues 384 - 391 (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 GLY 384 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D GLN* 1.3 78.0 - - - +
385D THR* 1.3 66.2 + - - -
386D SER 3.1 3.4 + - - -
387D ALA* 3.5 0.5 + - - +
388D PHE* 3.1 33.0 + - - -
467D VAL* 3.3 32.8 - - - -
600D TPP 3.5 6.6 - - - -
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Residues in contact with THR 385 (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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362D GLN* 3.3 30.4 + - - +
366D TRP* 3.6 5.7 - - - -
384D GLY* 1.3 71.5 - - - -
386D SER* 1.3 64.0 + - - +
388D PHE 4.7 0.2 - - - +
389D GLY* 2.9 23.2 + - - -
460D LEU* 3.7 9.3 - - - +
462D ASN* 4.0 3.4 + - - +
466D THR* 3.4 26.2 - - - +
467D VAL* 3.8 0.2 - - - +
534D ASP 4.0 3.4 - - - +
535D ILE* 4.1 0.4 - - + -
536D PRO* 3.6 21.5 - - + +
539D LEU* 3.8 13.0 - - + -
600D TPP 2.7 30.6 + - - +
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Residues in contact with SER 386 (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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366D TRP* 3.4 13.0 - - - -
381D ALA* 4.0 4.5 - - - -
382D ASP 3.4 15.3 - - - -
383D GLN 4.9 1.5 + - - -
384D GLY 3.1 0.8 - - - -
385D THR* 1.3 80.1 + - - +
387D ALA* 1.3 59.2 + - - +
390D ALA* 2.9 32.4 + - - +
432D LEU* 3.3 34.8 + - - +
433D THR* 3.5 14.8 + - - -
434D GLY* 3.6 3.6 + - - -
460D LEU* 3.7 12.0 - - - +
600D TPP 4.6 0.6 + - - -
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Residues in contact with ALA 387 (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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244D LEU* 4.5 11.8 - - + +
381D ALA* 3.9 10.7 - - - +
382D ASP 2.9 22.6 + - - +
383D GLN* 4.3 9.0 - - - +
384D GLY 3.5 4.4 + - - +
386D SER* 1.3 79.9 - - - +
388D PHE* 1.3 66.6 + - + +
389D GLY 3.1 0.2 - - - -
390D ALA* 3.5 1.6 + - - +
391D ILE* 3.2 27.2 + - - +
401D PHE* 5.3 0.7 - - - -
403D VAL* 4.0 22.9 - - + -
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Residues in contact with PHE 388 (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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244D LEU* 4.0 23.3 - - + -
290D THR* 4.6 17.5 - - + -
383D GLN* 4.0 22.4 - - + -
384D GLY* 3.1 37.3 + - - +
385D THR* 3.8 1.8 - - - +
387D ALA* 1.3 78.2 - - + +
389D GLY* 1.3 57.9 + - - +
391D ILE* 3.3 18.1 - - - +
392D ASP* 4.4 2.9 - - - +
467D VAL* 5.3 0.7 - - + -
536D PRO* 3.8 11.9 - - - +
538D LEU* 3.7 29.0 - - + +
539D LEU* 3.3 39.5 - - + +
542D LEU* 3.3 31.2 - - + -
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Residues in contact with GLY 389 (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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366D TRP* 3.5 35.0 - - - +
385D THR 2.9 16.4 + - - -
388D PHE* 1.3 77.2 - - - +
390D ALA* 1.3 63.8 + - - +
391D ILE 3.1 4.7 + - - -
392D ASP* 3.2 21.5 + - - +
393D LEU* 4.3 1.4 + - - +
536D PRO* 4.1 7.6 - - - -
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Residues in contact with ALA 390 (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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247D LYS* 3.5 7.6 - - - -
366D TRP* 3.6 20.9 - - + -
381D ALA* 4.1 4.9 - - + -
386D SER 2.9 17.4 + - - +
387D ALA 3.9 2.7 - - - +
389D GLY* 1.3 72.7 - - - +
391D ILE* 1.3 58.9 + - - +
392D ASP 3.0 5.8 - - - -
393D LEU* 3.0 29.4 + - + +
401D PHE* 3.9 22.1 - - + -
432D LEU* 4.0 12.8 - - + -
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Residues in contact with ILE 391 (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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244D LEU* 3.7 32.8 - - + +
247D LYS* 3.3 25.5 + - + +
260D THR* 3.5 35.2 + - + +
262D SER* 4.6 13.5 - - - +
387D ALA 3.2 12.5 + - - +
388D PHE 3.3 24.2 - - - +
390D ALA* 1.3 78.3 - - - +
392D ASP* 1.3 72.8 + - - +
393D LEU 3.4 0.2 - - - -
538D LEU* 3.4 29.4 - - + -
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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