Contacts of the helix formed by residues 361 - 373 (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 THR 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359B SER* 3.7 12.8 - - - +
360B LEU* 1.3 81.4 - - - +
362B GLN* 1.3 65.5 + - - +
363B GLU* 3.3 13.4 - - - +
364B ASN* 2.8 26.8 + - - +
365B PHE* 2.8 22.9 + - - +
530B LEU* 3.6 9.2 - - - -
531B PRO* 4.4 4.0 - - + -
534B ASP* 3.3 15.7 - - - +
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Residues in contact with GLN 362 (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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361B THR* 1.3 70.3 - - - +
363B GLU* 1.3 65.4 + - - +
365B PHE* 4.3 3.8 - - - -
366B TRP* 2.9 60.6 + - + +
385B THR* 3.3 28.2 + - - +
460B LEU* 4.4 2.9 - - - +
462B ASN* 4.7 3.5 + - - -
530B LEU* 3.8 24.0 - - + +
534B ASP* 3.0 47.7 + - + +
535B ILE 4.1 2.5 - - - +
536B PRO* 3.2 30.5 - - + +
537B PRO* 6.1 0.7 - - + -
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B THR* 3.0 12.1 - - - +
362B GLN* 1.3 82.9 - - - +
364B ASN* 1.3 63.9 + - + +
366B TRP* 3.6 2.6 + - - +
367B ARG* 2.9 55.9 + - - +
534B ASP* 4.9 0.8 + - - -
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Residues in contact with ASN 364 (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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356B PRO* 5.0 9.0 - - + +
357B ASP 4.4 12.8 + - - +
358B GLY 4.7 0.8 + - - -
359B SER 2.8 28.6 + - - -
360B LEU* 3.1 15.4 - - - +
361B THR* 2.8 29.4 + - - +
363B GLU* 1.3 79.2 - - + +
365B PHE* 1.3 75.6 + - - +
367B ARG* 3.8 17.3 - - - +
368B THR* 2.7 35.0 + - - -
507B ALA* 4.4 11.2 - - + -
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.4 9.2 - - + -
361B THR 2.8 17.5 + - - +
362B GLN* 3.7 4.9 - - - +
364B ASN* 1.3 82.8 + - - +
366B TRP* 1.3 108.4 + + - +
368B THR* 3.2 7.2 + - - -
369B LEU* 3.0 35.4 + - + +
432B LEU* 4.3 3.1 - - + -
458B LEU* 3.8 29.6 - - + -
460B LEU* 3.7 23.1 - - + -
510B LEU* 4.0 15.7 - - + +
528B VAL* 3.8 29.6 - - + -
530B LEU* 4.5 7.2 - - + -
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Residues in contact with TRP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLN* 2.9 51.8 + - + +
363B GLU* 4.2 2.2 - - - +
365B PHE* 1.3 95.7 - + - +
367B ARG* 1.3 64.6 + - - +
369B LEU* 3.4 31.1 + - + +
370B GLN* 3.0 22.5 + - - +
385B THR 3.6 8.1 - - - -
386B SER* 3.2 35.2 - - - -
389B GLY* 3.5 24.3 - - - +
390B ALA* 3.4 26.2 - - + -
392B ASP* 6.2 2.7 - - + -
393B LEU* 4.2 15.3 - - + +
432B LEU* 3.7 13.7 - - + -
460B LEU* 4.3 4.9 - - + -
536B PRO* 4.9 2.9 - - + -
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Residues in contact with ARG 367 (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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356B PRO* 3.0 42.6 - - + +
363B GLU* 2.9 53.5 + - - +
364B ASN* 3.8 12.6 - - - +
365B PHE 3.2 0.6 - - - -
366B TRP* 1.3 78.7 - - - +
368B THR* 1.3 64.1 + - - +
370B GLN* 3.2 20.2 - - + +
371B THR* 3.7 10.5 + - + +
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Residues in contact with THR 368 (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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356B PRO* 5.4 5.2 - - - +
360B LEU* 5.4 0.2 - - - +
364B ASN 2.7 19.9 + - - -
365B PHE 3.2 8.0 + - - -
367B ARG* 1.3 75.5 - - - +
369B LEU* 1.3 65.7 + - - +
371B THR* 3.0 29.3 + - - +
372B PHE* 3.5 4.3 + - - +
507B ALA* 4.3 15.5 + - - +
510B LEU* 3.3 28.6 - - + +
511B ALA* 4.2 22.2 - - + +
514B LEU* 4.1 10.5 - - + +
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Residues in contact with LEU 369 (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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365B PHE* 3.0 22.1 + - + +
366B TRP* 3.5 31.0 - - + +
367B ARG 3.4 0.2 - - - -
368B THR* 1.3 78.7 - - - +
370B GLN* 1.3 61.8 + - - +
372B PHE* 3.0 36.0 + - + +
373B ILE* 3.3 20.4 + - + +
379B ILE* 6.1 0.2 - - + -
393B LEU* 4.3 11.4 - - + -
430B ILE* 5.2 5.8 - - + -
432B LEU* 3.4 33.4 - - + -
458B LEU* 4.2 22.9 - - + -
510B LEU* 4.9 0.8 - - + +
514B LEU* 4.3 8.7 - - + -
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Residues in contact with GLN 370 (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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253B ARG* 3.7 15.9 + - - +
366B TRP 3.0 12.6 + - - +
367B ARG* 3.2 15.7 - - + +
368B THR 3.1 0.2 - - - -
369B LEU* 1.3 78.4 - - - +
371B THR* 1.3 63.2 + - + +
372B PHE 3.3 0.9 + - - -
373B ILE* 3.5 14.9 + - - +
392B ASP 4.1 2.3 - - - +
393B LEU* 3.4 17.0 - - + +
394B ARG* 2.7 55.9 + - - +
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Residues in contact with THR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ARG* 3.7 14.8 - - + +
368B THR* 3.0 16.8 + - - +
370B GLN* 1.3 77.8 - - + +
372B PHE* 1.3 53.4 + - - +
374B ARG* 2.4 28.6 + - - -
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Residues in contact with PHE 372 (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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368B THR 3.5 2.2 + - - +
369B LEU* 3.0 28.0 + - + +
371B THR* 1.3 80.5 + - - +
373B ILE* 1.3 70.7 + - + +
374B ARG* 3.5 8.6 + - - +
428B ARG* 3.0 52.5 + - - -
430B ILE* 4.1 21.1 - - + -
456B ILE* 4.5 9.0 - - + -
514B LEU* 3.2 69.3 - - + -
517B VAL* 4.6 6.7 - - + -
518B ALA* 4.0 9.6 - - + -
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Residues in contact with ILE 373 (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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253B ARG* 4.4 3.2 + - - +
369B LEU* 3.3 17.5 + - + +
370B GLN* 3.5 23.4 - - - +
372B PHE* 1.3 81.9 - - + +
374B ARG* 1.3 70.8 + - - +
377B ASP* 3.5 9.0 - - + +
379B ILE* 3.7 26.0 - - + -
393B LEU* 4.4 18.6 - - + -
394B ARG 3.6 27.4 - - - +
395B LEU* 4.2 12.3 - - + -
396B PRO* 3.7 23.7 - - + +
428B ARG* 3.9 0.4 - - - +
430B ILE* 5.6 4.5 - - + -
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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