Contacts of the helix formed by residues 361 - 373 (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 THR 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359C SER* 3.8 11.2 - - - +
360C LEU* 1.3 82.4 - - - +
362C GLN* 1.3 65.7 + - - +
363C GLU* 3.0 11.7 + - - +
364C ASN* 2.9 28.2 + - - +
365C PHE* 2.8 22.3 + - - +
530C LEU* 3.6 8.3 - - - -
531C PRO* 4.4 4.9 - - + -
534C ASP* 3.2 15.7 - - - +
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C THR* 1.3 70.5 - - - +
363C GLU* 1.3 62.9 + - - +
365C PHE* 4.2 4.4 - - - -
366C TRP* 2.7 71.2 + - + +
385C THR* 3.3 33.0 + - - +
460C LEU* 4.4 2.5 - - - +
462C ASN* 4.5 4.3 + - - -
530C LEU* 3.7 25.1 - - + +
531C PRO 5.8 0.2 - - - +
534C ASP* 2.8 49.0 + - + +
535C ILE 4.1 2.2 - - - +
536C PRO* 3.3 23.7 - - + +
537C PRO* 6.0 0.4 - - + -
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Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C THR* 3.0 11.1 - - - +
362C GLN* 1.3 83.1 - - - +
364C ASN* 1.3 64.6 + - + +
366C TRP* 3.6 2.6 + - - +
367C ARG* 2.8 56.8 + - - +
534C ASP* 4.7 0.8 + - - -
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Residues in contact with ASN 364 (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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356C PRO* 4.4 21.0 - - + +
357C ASP 5.8 1.0 - - - +
358C GLY 4.0 5.9 + - - +
359C SER 2.8 27.6 + - - -
360C LEU* 3.1 16.7 - - - +
361C THR* 2.9 29.2 + - - +
363C GLU* 1.3 79.5 - - + +
365C PHE* 1.3 75.5 + - - +
367C ARG* 3.7 15.7 - - - +
368C THR* 2.7 34.7 + - - -
507C ALA* 4.6 7.8 - - + +
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Residues in contact with PHE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 4.4 7.4 - - + -
361C THR 2.8 19.8 + - - +
362C GLN* 3.6 7.2 - - - +
363C GLU 3.2 0.2 - - - -
364C ASN* 1.3 81.3 + - - +
366C TRP* 1.3 106.7 + + - +
368C THR* 3.1 7.4 + - - -
369C LEU* 2.9 33.1 + - + +
432C LEU* 4.2 8.3 - - + -
458C LEU* 3.8 29.4 - - + -
460C LEU* 3.7 21.5 - - + -
510C LEU* 4.5 15.4 - - + +
528C VAL* 3.8 29.6 - - + -
530C LEU* 4.6 7.0 - - + -
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Residues in contact with TRP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 2.7 53.7 + - + +
363C GLU* 4.3 2.5 - - - +
365C PHE* 1.3 100.6 - + - +
367C ARG* 1.3 62.6 + - - +
369C LEU* 3.7 28.6 - - + +
370C GLN* 3.1 21.7 + - - +
385C THR 3.4 21.1 - - - -
386C SER* 3.1 26.9 - - - -
389C GLY* 3.4 27.0 - - - +
390C ALA* 3.5 20.6 - - + -
392C ASP* 6.2 2.0 - - + -
393C LEU* 4.0 13.2 - - + +
432C LEU* 3.8 9.4 - - + -
460C LEU* 4.2 4.3 - - + -
536C PRO* 4.2 3.6 - - + +
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Residues in contact with ARG 367 (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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356C PRO* 3.1 40.8 - - + +
363C GLU* 2.8 54.5 + - - +
364C ASN* 3.7 12.2 - - - +
365C PHE 3.1 0.4 - - - -
366C TRP* 1.3 78.1 - - - +
368C THR* 1.3 63.0 + - - +
370C GLN* 3.3 18.8 - - + +
371C THR* 3.7 11.5 + - + +
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Residues in contact with THR 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C PRO* 5.0 9.2 - - - +
360C LEU* 5.5 0.3 - - - +
364C ASN* 2.7 21.4 + - - +
365C PHE* 3.1 7.5 + - - -
367C ARG* 1.3 75.8 - - - +
369C LEU* 1.3 65.7 + - - +
371C THR* 3.2 27.1 + - - +
372C PHE* 3.5 5.2 + - - +
507C ALA* 4.6 9.7 + - - +
510C LEU* 3.0 31.3 - - + +
511C ALA* 4.0 21.7 - - + +
514C LEU* 3.6 10.3 - - + -
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Residues in contact with LEU 369 (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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365C PHE* 2.9 22.1 + - + +
366C TRP* 3.7 28.3 - - + +
367C ARG 3.4 0.2 - - - -
368C THR* 1.3 76.6 - - - +
370C GLN* 1.3 57.1 + - - +
372C PHE* 2.8 46.9 + - + +
373C ILE* 3.2 15.9 + - + +
379C ILE* 6.2 0.2 - - + -
393C LEU* 4.3 12.6 - - + -
430C ILE* 5.3 6.1 - - + -
432C LEU* 3.4 35.7 - - + -
458C LEU* 4.3 22.2 - - + -
510C LEU* 4.9 0.8 - - + +
514C LEU* 4.6 7.4 - - + -
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Residues in contact with GLN 370 (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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253C ARG* 3.6 16.7 + - - +
366C TRP 3.1 14.1 + - - +
367C ARG* 3.3 15.9 - - + +
368C THR 3.1 0.4 - - - -
369C LEU* 1.3 78.2 - - - +
371C THR* 1.3 63.8 + - + +
372C PHE 3.1 0.9 + - - -
373C ILE* 3.6 15.4 - - - +
392C ASP 4.2 2.3 - - - +
393C LEU* 3.4 17.0 - - - +
394C ARG* 2.8 55.3 + - - +
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Residues in contact with THR 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ARG* 3.7 15.0 - - + +
368C THR* 3.2 15.1 + - - +
370C GLN* 1.3 77.9 - - + +
372C PHE* 1.3 52.9 + - - +
373C ILE 4.8 0.2 - - - -
374C ARG* 2.4 29.2 + - - -
514C LEU* 5.9 0.2 - - - +
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Residues in contact with PHE 372 (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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368C THR 4.0 0.9 - - - +
369C LEU* 2.8 30.7 + - + +
371C THR* 1.3 78.9 + - - +
373C ILE* 1.3 69.2 + - + +
374C ARG* 3.4 10.3 + - - +
428C ARG* 3.1 49.2 + - - -
430C ILE* 4.0 25.4 - - + -
456C ILE* 4.5 9.9 - - + -
514C LEU* 3.6 64.8 - - + -
515C GLU* 5.4 3.6 - - - -
517C VAL* 4.5 9.0 - - + -
518C ALA* 3.9 11.7 - - + -
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Residues in contact with ILE 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ARG* 4.3 3.4 + - - +
369C LEU* 3.7 20.9 - - + +
370C GLN* 3.6 21.7 - - - +
371C THR 4.8 0.2 - - - -
372C PHE* 1.3 82.8 - - + +
374C ARG* 1.3 68.8 + - - +
375C PRO* 4.6 0.2 - - - +
377C ASP* 3.5 8.7 - - - +
379C ILE* 3.8 24.5 - - + -
393C LEU* 4.5 14.1 - - + -
394C ARG 3.5 25.6 - - - +
395C LEU* 3.9 18.2 - - + -
396C PRO* 3.8 19.6 - - + +
428C ARG* 4.0 0.9 - - - +
430C ILE* 5.7 5.6 - - + -
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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