Contacts of the helix formed by residues 361 - 373 (chain A) 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 THR 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A SER* 3.7 12.8 - - - +
360A LEU* 1.3 81.2 - - - +
362A GLN* 1.3 67.0 + - - +
363A GLU* 3.1 11.9 + - - +
364A ASN* 2.9 27.0 + - - +
365A PHE* 2.9 22.5 + - - +
530A LEU* 3.7 8.5 - - - -
531A PRO* 4.4 4.9 - - + -
534A ASP* 3.2 15.3 - - - +
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Residues in contact with GLN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A THR* 1.3 69.7 - - - +
363A GLU* 1.3 63.4 + - - +
365A PHE* 4.3 4.0 - - - -
366A TRP* 2.8 62.9 + - + +
385A THR* 3.3 29.5 + - - +
460A LEU* 4.4 2.4 - - - +
462A ASN* 4.6 3.8 + - - -
530A LEU* 3.8 24.3 - - + +
534A ASP* 2.8 47.3 + - + +
535A ILE 4.5 1.1 - - - +
536A PRO* 3.1 32.2 - - + +
537A PRO* 6.1 0.7 - - + -
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 5.6 2.2 - - - +
361A THR* 3.0 12.0 + - - +
362A GLN* 1.3 82.6 - - - +
364A ASN* 1.3 63.9 + - + +
366A TRP* 3.6 2.9 + - - +
367A ARG* 2.8 59.5 + - - +
534A ASP* 4.9 0.8 + - - -
537A PRO* 6.0 3.3 - - - +
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Residues in contact with ASN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASP* 3.7 40.4 + - + +
359A SER 2.8 27.5 + - - -
360A LEU* 3.1 17.2 - - - +
361A THR* 2.9 31.1 + - - +
363A GLU* 1.3 79.4 - - + +
365A PHE* 1.3 59.9 + - - +
367A ARG* 3.8 12.8 - - + +
368A THR* 2.7 34.6 + - - +
507A ALA* 4.5 6.7 - - + -
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Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.4 8.5 - - + -
361A THR 2.9 19.8 + - - +
362A GLN* 3.6 4.7 - - - +
363A GLU 3.2 0.2 - - - -
364A ASN* 1.3 79.1 + - - +
366A TRP* 1.3 108.6 + + - +
368A THR* 3.2 5.6 + - - -
369A LEU* 3.0 31.8 + - + +
432A LEU* 4.3 8.5 - - + -
458A LEU* 3.8 28.9 - - + -
460A LEU* 3.7 23.3 - - + -
510A LEU* 3.6 21.9 - - + +
528A VAL* 3.8 26.9 - - + -
530A LEU* 4.6 7.9 - - + -
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLN* 2.8 52.0 + - + +
363A GLU* 4.2 2.2 - - - +
365A PHE* 1.3 94.4 - + - +
367A ARG* 1.3 65.5 + - - +
369A LEU* 3.3 32.3 + - + +
370A GLN* 2.9 23.8 + - - +
385A THR 3.5 10.8 - - - -
386A SER* 3.2 35.4 - - - -
389A GLY* 3.4 28.1 - - - +
390A ALA* 3.4 14.4 - - - -
392A ASP* 6.2 2.2 - - + -
393A LEU* 4.4 11.6 - - + +
432A LEU* 3.7 17.3 - - + -
460A LEU* 4.3 4.9 - - + -
536A PRO* 4.7 3.6 - - + -
537A PRO* 6.3 1.1 - - + -
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Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PRO* 5.9 2.2 - - - +
357A ASP* 4.2 20.6 + - - -
363A GLU* 2.8 54.2 + - - +
364A ASN* 3.8 11.4 - - - +
365A PHE 3.2 0.4 - - - -
366A TRP* 1.3 77.6 - - - +
368A THR* 1.3 62.3 + - - +
370A GLN* 3.3 19.6 - - + +
371A THR* 3.6 11.6 - - + +
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASN* 2.7 22.7 + - - +
365A PHE 3.5 4.9 - - - -
366A TRP 3.2 0.2 - - - -
367A ARG* 1.3 75.1 - - - +
369A LEU* 1.3 66.7 + - - +
371A THR* 3.1 27.6 + - - +
372A PHE* 3.5 4.7 + - - +
507A ALA* 4.8 12.2 + - - +
510A LEU* 3.7 25.7 - - + +
511A ALA* 4.2 21.8 - - + +
514A LEU* 4.0 14.1 - - + +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A PHE* 3.0 18.8 + - + +
366A TRP* 3.5 31.6 - - + +
368A THR* 1.3 77.9 - - - +
370A GLN* 1.3 57.6 + - - +
372A PHE* 2.9 40.6 + - + +
373A ILE* 3.3 19.5 + - + +
393A LEU* 4.2 13.0 - - + -
430A ILE* 5.2 5.6 - - + -
432A LEU* 3.5 34.5 - - + -
458A LEU* 4.3 23.6 - - + -
510A LEU* 5.1 0.6 - - + +
514A LEU* 4.4 8.3 - - + -
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Residues in contact with GLN 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ARG* 3.6 16.1 + - - +
366A TRP 2.9 12.7 + - - +
367A ARG* 3.3 16.8 - - + +
369A LEU* 1.3 77.0 - - - +
371A THR* 1.3 62.7 + - + +
372A PHE 3.1 1.6 + - - -
373A ILE* 3.5 13.3 - - - +
392A ASP 4.2 2.4 - - - +
393A LEU* 3.4 18.2 - - + +
394A ARG* 2.7 56.0 + - - +
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Residues in contact with THR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG* 3.6 15.7 - - + +
368A THR* 3.1 16.4 + - - +
370A GLN* 1.3 78.0 - - + +
372A PHE* 1.3 52.9 + - - +
374A ARG* 2.4 29.5 + - - -
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Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR 3.5 1.8 + - - +
369A LEU* 2.9 29.7 + - + +
371A THR* 1.3 81.2 + - - +
373A ILE* 1.3 69.3 + - + +
374A ARG* 3.4 10.6 + - - +
428A ARG* 3.1 54.3 + - - -
430A ILE* 4.1 21.1 - - + -
456A ILE* 4.6 8.7 - - + -
514A LEU* 3.2 66.9 - - + -
515A GLU* 4.6 5.6 - - - -
517A VAL* 4.5 7.4 - - + -
518A ALA* 4.0 9.6 - - + -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 4.4 3.4 + - - +
369A LEU* 3.3 18.8 + - + +
370A GLN* 3.5 23.4 - - - +
372A PHE* 1.3 82.9 - - + +
374A ARG* 1.3 70.2 + - - +
375A PRO* 4.9 0.2 - - - +
377A ASP* 3.5 9.6 - - + +
379A ILE* 3.7 26.2 - - + -
393A LEU* 4.1 21.5 - - + -
394A ARG 3.6 26.7 - - - +
395A LEU* 4.2 9.4 - - + -
396A PRO* 3.8 23.0 - - + +
428A ARG* 3.9 0.7 - - - +
430A ILE* 5.6 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