Contacts of the helix formed by residues 384 - 391 (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 GLY 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B GLN* 1.3 77.2 - - - +
385B THR* 1.3 66.1 + - - -
386B SER 3.1 3.6 + - - -
387B ALA* 3.4 0.9 + - - +
388B PHE* 3.2 31.6 + - - -
467B VAL* 3.4 32.3 - - - +
600B TPP 3.5 7.1 - - - -
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Residues in contact with THR 385 (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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362B GLN* 3.3 30.2 + - - +
366B TRP* 3.6 5.4 - - - -
384B GLY* 1.3 72.1 - - - -
386B SER* 1.3 63.1 + - - +
388B PHE* 3.7 0.6 - - - +
389B GLY* 2.9 23.0 + - - -
460B LEU* 3.7 9.9 - - - +
462B ASN* 4.0 3.0 + - - +
466B THR* 3.3 24.9 - - - +
467B VAL* 3.9 0.4 - - - +
534B ASP 4.0 1.6 - - - +
535B ILE* 4.0 4.0 - - + -
536B PRO* 3.6 21.4 - - + +
539B LEU* 3.8 12.3 - - + -
600B TPP 2.6 26.5 + - - +
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TRP* 3.2 12.4 - - - -
381B ALA* 4.0 4.3 - - - -
382B ASP 3.4 15.5 - - - -
383B GLN 5.1 1.1 - - - -
384B GLY 3.1 0.4 - - - -
385B THR* 1.3 79.9 + - - +
387B ALA* 1.3 60.1 + - - +
390B ALA* 2.9 32.1 + - - +
432B LEU* 3.6 20.9 + - - +
433B THR* 3.5 29.0 + - - -
434B GLY* 3.6 3.8 + - - -
460B LEU* 3.8 11.9 - - - +
600B TPP 4.6 0.8 + - - -
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Residues in contact with ALA 387 (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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244B LEU* 4.5 11.8 - - + +
381B ALA* 3.9 10.3 - - - +
382B ASP 2.9 23.4 + - - +
383B GLN* 4.2 8.3 - - - +
384B GLY 3.4 4.2 + - - +
386B SER* 1.3 79.4 - - - +
388B PHE* 1.3 66.8 + - + +
389B GLY 3.1 0.2 - - - -
390B ALA* 4.0 1.4 - - - +
391B ILE* 3.2 26.7 + - - +
401B PHE* 5.3 0.6 - - - -
403B VAL* 4.0 23.6 - - + -
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Residues in contact with PHE 388 (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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244B LEU* 3.8 24.9 - - + -
290B THR* 4.7 18.2 - - + -
383B GLN* 4.0 21.3 - - + -
384B GLY* 3.2 37.0 + - - +
385B THR 3.7 1.8 - - - +
387B ALA* 1.3 79.0 - - + +
389B GLY* 1.3 56.8 + - - +
391B ILE* 3.5 17.3 - - - +
392B ASP* 4.4 2.6 - - - +
467B VAL* 5.2 0.9 - - + -
536B PRO* 3.6 12.8 - - - +
538B LEU* 3.8 29.6 - - + +
539B LEU* 3.3 39.0 - - + -
542B LEU* 3.4 30.5 - - + -
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Residues in contact with GLY 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TRP* 3.5 32.8 - - - +
385B THR 2.9 16.5 + - - -
388B PHE* 1.3 78.1 - - - +
390B ALA* 1.3 63.6 + - - +
391B ILE 3.0 5.3 + - - -
392B ASP* 3.2 20.4 + - - +
393B LEU 4.3 1.2 + - - -
536B PRO* 4.1 8.3 - - - -
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Residues in contact with ALA 390 (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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247B LYS* 3.5 7.4 - - - -
366B TRP* 3.4 23.1 - - + -
381B ALA* 4.1 4.5 - - + -
386B SER 2.9 18.3 + - - +
387B ALA 4.0 2.9 - - - +
389B GLY* 1.3 71.8 - - - +
391B ILE* 1.3 63.5 + - - +
392B ASP 3.0 3.1 - - - -
393B LEU* 3.0 23.5 + - + +
401B PHE* 3.9 24.3 - - + -
432B LEU* 4.0 12.8 - - + -
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Residues in contact with ILE 391 (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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244B LEU* 3.7 33.9 - - + +
247B LYS* 3.2 26.5 + - + +
260B THR* 3.6 36.3 + - + +
262B SER* 4.6 13.9 - - - +
387B ALA 3.2 13.7 + - - +
388B PHE* 3.5 23.3 - - - +
390B ALA* 1.3 77.2 - - - +
392B ASP* 1.3 73.4 + - - +
393B LEU 3.3 0.2 - - - -
538B LEU* 3.5 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