Contacts of the helix formed by residues 435 - 442 (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 ASP 435 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434D GLY* 1.3 70.1 - - - -
436D GLY* 1.3 67.4 + - - -
439D GLN* 3.1 23.7 + - - +
459D VAL* 3.9 10.5 - - + +
460D LEU 3.3 14.7 + - - +
461D ASN* 3.3 9.7 - - - +
462D ASN* 4.0 0.9 - - - -
463D GLU* 3.2 25.5 + - - -
464D GLY 3.1 9.4 + - - +
481D ILE* 3.6 13.1 - - + +
483D LEU* 5.6 0.3 - - - +
486D TRP* 3.3 34.8 + - + +
600D TPP 3.1 1.2 + - - -
601D MG 2.3 30.2 - - - -
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Residues in contact with GLY 436 (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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410D ILE* 4.7 0.9 - - - -
435D ASP* 1.3 90.2 + - - +
437D ALA* 1.3 61.6 + - - +
439D GLN* 3.3 12.2 + - - +
440D LEU* 3.1 18.8 - - - +
465D TYR* 3.8 26.1 - - - -
481D ILE* 4.0 8.5 - - - -
600D TPP 3.0 12.0 + - - -
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Residues in contact with ALA 437 (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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382D ASP* 3.7 28.5 - - + +
410D ILE* 3.9 10.3 - - + +
411D GLY* 3.4 20.1 - - - +
433D THR* 3.6 14.8 - - - +
434D GLY 3.8 0.2 - - - +
436D GLY* 1.3 76.2 - - - +
438D ALA* 1.3 62.9 + - - +
439D GLN 3.0 1.6 + - - -
440D LEU* 3.1 21.0 + - - +
441D THR 4.1 0.2 + - - -
600D TPP 2.9 20.4 + - - +
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Residues in contact with ALA 438 (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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411D GLY* 5.4 0.2 - - - -
414D LEU* 4.0 17.5 - - + +
433D THR* 3.5 19.4 + - + +
434D GLY 3.1 15.5 + - - +
436D GLY 3.4 0.4 - - - -
437D ALA* 1.3 77.7 - - - +
439D GLN* 1.3 56.0 + - - +
440D LEU 3.2 0.6 + - - -
441D THR* 3.4 3.0 + - - -
442D ILE* 2.9 33.6 + - + +
459D VAL* 5.0 2.7 - - + -
486D TRP* 3.6 27.8 - - + -
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Residues in contact with GLN 439 (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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50C ALA* 4.4 15.5 - - + +
443C GLN* 3.1 32.3 + - - +
435D ASP 3.1 18.4 + - - +
436D GLY 3.5 8.1 - - - +
437D ALA 3.0 1.2 + - - -
438D ALA* 1.3 78.6 - - - +
440D LEU* 1.3 59.1 + - + +
441D THR 3.4 0.3 + - - -
442D ILE 3.8 2.1 + - - -
465D TYR* 5.2 1.7 + - - -
481D ILE* 3.7 26.3 - - - +
482D ALA* 2.9 30.9 + - - +
484D TRP* 3.2 53.4 - - + +
486D TRP* 3.9 3.2 - - + -
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Residues in contact with LEU 440 (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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26C VAL* 5.7 2.0 - - + -
50C ALA 2.9 23.8 - - - +
51C ASN* 3.5 19.1 + - + +
52C GLU* 3.6 23.6 - - - +
443C GLN* 3.0 13.9 + - - +
51D ASN* 5.3 1.6 + - - -
53D LEU* 5.3 4.5 - - + +
54D ASN* 4.6 2.3 + - - -
410D ILE* 3.4 48.9 - - + +
436D GLY 3.1 22.0 - - - +
437D ALA* 3.1 10.4 + - - +
439D GLN* 1.3 79.4 - - + +
441D THR* 1.3 66.6 + - + +
443D GLN* 3.8 0.9 - - - +
465D TYR* 5.7 3.4 - - - +
600D TPP 4.0 5.8 - - + +
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Residues in contact with THR 441 (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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53D LEU* 4.6 2.7 - - + -
54D ASN* 3.3 25.9 - - - +
57D TYR* 3.7 15.7 - - + -
411D GLY* 2.8 39.5 + - - +
414D LEU* 3.5 21.6 - - - +
415D ALA* 4.5 5.8 - - - -
437D ALA 4.5 0.2 + - - -
438D ALA 3.4 3.0 + - - -
440D LEU* 1.3 83.4 - - + +
442D ILE* 1.3 67.4 + - - +
443D GLN* 3.2 10.1 - - - -
444D GLU* 3.0 19.4 + - - +
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Residues in contact with ILE 442 (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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442C ILE* 4.1 15.9 - - + -
443C GLN* 4.0 15.9 - - + +
493C LEU* 5.5 4.7 - - + -
414D LEU* 3.8 11.0 - - + -
438D ALA* 2.9 18.6 + - + +
439D GLN 4.0 3.8 - - - +
440D LEU 3.7 0.4 - - - -
441D THR* 1.3 76.0 - - - +
443D GLN* 1.3 69.1 + - - +
445D LEU* 2.7 42.8 + - + +
484D TRP* 3.9 22.9 - - + -
486D TRP* 4.3 11.9 - - + -
489D ILE* 3.9 38.8 - - + -
493D LEU* 4.0 4.9 - - + +
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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