Contacts of the helix formed by residues 435 - 442 (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 ASP 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B GLY* 1.3 68.9 - - - -
436B GLY* 1.3 75.8 + - - -
439B GLN* 3.1 24.3 + - - +
459B VAL* 3.8 10.1 - - + +
460B LEU 3.2 13.6 + - - +
461B ASN* 3.4 8.6 - - - +
462B ASN 3.3 3.8 + - - -
463B GLU* 3.1 28.9 + - - -
464B GLY 3.1 7.8 + - - +
481B ILE* 3.8 13.1 - - + +
483B LEU* 5.7 0.3 - - - +
486B TRP* 3.3 32.7 - - + +
600B TPP 3.0 1.0 + - - -
601B MG 2.3 28.2 - - - -
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Residues in contact with GLY 436 (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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410B ILE* 4.7 1.1 - - - -
435B ASP* 1.3 87.7 + - - +
437B ALA* 1.3 61.2 + - - +
439B GLN* 3.4 14.0 + - - +
440B LEU* 3.0 19.2 - - - +
465B TYR* 3.8 26.2 + - - -
481B ILE* 4.0 9.0 - - - -
600B TPP 3.1 12.0 + - - -
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Residues in contact with ALA 437 (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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382B ASP* 3.8 15.9 - - + +
383B GLN 5.1 0.2 - - - +
410B ILE* 3.9 10.8 - - + -
411B GLY* 3.3 35.3 - - - +
433B THR* 3.7 14.1 - - - +
434B GLY 3.6 0.6 + - - +
436B GLY* 1.3 76.8 - - - +
438B ALA* 1.3 62.9 + - - +
439B GLN 3.1 1.2 + - - -
440B LEU* 3.1 18.4 + - - +
441B THR 4.1 0.5 + - - -
600B TPP 2.9 20.4 + - - +
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Residues in contact with ALA 438 (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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414B LEU* 4.0 17.7 - - + +
433B THR* 3.6 19.9 + - + +
434B GLY 3.1 15.9 + - - +
436B GLY 3.4 0.2 - - - -
437B ALA* 1.3 78.5 - - - +
439B GLN* 1.3 57.0 + - - +
441B THR* 3.4 3.5 + - - -
442B ILE* 3.0 33.1 + - + +
459B VAL* 5.0 2.7 - - + -
486B TRP* 3.6 27.4 - - + -
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Residues in contact with GLN 439 (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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50A ALA* 4.5 16.1 - - + +
443A GLN* 3.1 32.4 + - - +
435B ASP 3.1 18.3 + - - +
436B GLY 3.5 8.6 - - - +
437B ALA 3.1 1.0 + - - -
438B ALA* 1.3 78.8 - - - +
440B LEU* 1.3 58.6 + - + +
441B THR 3.4 0.2 + - - -
442B ILE 3.9 1.0 + - - -
465B TYR* 5.2 1.6 + - - -
481B ILE* 3.8 26.9 - - - +
482B ALA* 3.0 30.8 + - - +
484B TRP* 3.3 52.7 - - + +
486B TRP* 3.9 4.1 - - + -
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Residues in contact with LEU 440 (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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26A VAL* 5.6 2.5 - - + -
50A ALA 3.0 24.0 - - - +
51A ASN* 3.3 21.2 + - + +
52A GLU* 3.7 23.6 - - - +
443A GLN* 3.2 12.7 + - - +
51B ASN* 5.3 1.0 + - - -
53B LEU* 5.1 5.2 - - + +
54B ASN* 4.5 2.1 + - - -
410B ILE* 3.4 48.2 - - + +
411B GLY* 4.3 2.0 - - - -
436B GLY 3.0 28.7 - - - +
437B ALA 3.1 10.7 + - - +
439B GLN* 1.3 78.2 - - + +
441B THR* 1.3 64.9 + - + +
443B GLN* 3.8 1.2 - - - +
465B TYR* 5.6 3.8 - - - +
600B TPP 4.0 5.2 - - + +
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Residues in contact with THR 441 (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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53B LEU* 4.5 2.7 - - + -
54B ASN* 3.2 29.1 - - - +
57B TYR* 3.7 15.3 - - + -
411B GLY* 2.8 40.1 + - - +
414B LEU* 3.5 20.2 - - - +
415B ALA* 4.5 5.4 - - - -
437B ALA 4.4 0.3 + - - -
438B ALA 3.4 2.8 + - - -
440B LEU* 1.3 84.5 - - + +
442B ILE* 1.3 64.2 + - - +
443B GLN* 3.0 12.5 - - - +
444B GLU* 3.0 17.5 + - - +
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Residues in contact with ILE 442 (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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442A ILE* 4.1 15.5 - - + -
443A GLN* 4.0 15.9 - - + +
493A LEU* 5.5 4.3 - - + -
414B LEU* 3.8 11.2 - - + -
438B ALA* 3.0 19.3 + - + +
440B LEU 3.7 0.2 - - - -
441B THR* 1.3 76.2 - - - +
443B GLN* 1.3 64.0 + - - +
445B LEU* 2.7 42.9 + - + +
484B TRP* 3.9 24.9 - - + -
486B TRP* 4.2 13.5 - - + -
489B ILE* 3.9 38.6 - - + -
493B LEU* 3.9 5.2 - - + +
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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