Contacts of the helix formed by residues 435 - 442 (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 ASP 435 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A GLY* 1.3 71.1 - - - +
436A GLY* 1.3 76.0 + - - -
439A GLN* 3.1 23.0 + - - +
459A VAL* 3.8 5.8 - - + +
460A LEU 3.3 14.4 + - - +
461A ASN* 3.4 10.7 - - - +
462A ASN 3.4 0.2 + - - -
463A GLU* 3.1 28.2 + - - -
464A GLY 3.1 8.2 + - - +
481A ILE* 3.7 12.7 - - + +
483A LEU* 5.7 0.3 - - - +
486A TRP* 3.3 38.8 + - + +
600A TPP 3.0 0.7 + - - -
601A MG 2.3 29.8 - - - -
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Residues in contact with GLY 436 (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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410A ILE* 4.7 0.9 - - - -
435A ASP* 1.3 87.1 + - - +
437A ALA* 1.3 61.9 + - - +
439A GLN* 3.3 13.8 + - - +
440A LEU* 3.0 19.6 - - - +
465A TYR* 3.8 25.3 + - - -
481A ILE* 4.0 10.1 - - - -
600A TPP 3.0 12.0 + - - -
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Residues in contact with ALA 437 (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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382A ASP* 3.8 26.5 - - + +
383A GLN 5.1 0.2 - - - +
410A ILE* 3.9 11.4 - - + +
411A GLY* 3.3 24.7 - - - +
433A THR* 3.7 14.8 - - - +
434A GLY 3.8 0.9 - - - +
435A ASP 3.4 0.2 - - - -
436A GLY* 1.3 76.1 - - - +
438A ALA* 1.3 63.1 + - - +
439A GLN 3.0 1.4 + - - -
440A LEU* 3.1 17.8 + - - +
441A THR 4.1 0.2 + - - -
600A TPP 2.8 19.4 + - - +
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Residues in contact with ALA 438 (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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414A LEU* 3.9 17.8 - - + +
433A THR* 3.6 20.1 + - + +
434A GLY 3.1 14.6 + - - +
436A GLY 3.4 0.4 - - - -
437A ALA* 1.3 74.3 - - - +
439A GLN* 1.3 57.2 - - - +
441A THR* 3.5 3.2 + - - -
442A ILE* 3.0 32.6 + - + +
459A VAL* 4.9 1.8 - - + -
486A TRP* 3.5 31.4 - - + -
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Residues in contact with GLN 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ASP 3.1 18.8 + - - +
436A GLY 3.5 8.1 - - - +
437A ALA 3.0 1.2 + - - -
438A ALA* 1.3 77.8 - - - +
440A LEU* 1.3 64.5 + - + +
441A THR 3.4 0.5 + - - -
442A ILE 3.8 2.1 + - - -
465A TYR* 5.2 1.2 + - - -
481A ILE* 3.8 27.2 - - - +
482A ALA* 2.9 31.0 + - - +
484A TRP* 3.2 52.1 - - + +
486A TRP* 4.1 3.1 - - + -
50B ALA* 4.4 17.3 - - + +
443B GLN* 3.1 27.4 + - - +
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Residues in contact with LEU 440 (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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51A ASN* 5.3 1.7 + - - -
53A LEU* 5.2 5.4 - - + +
54A ASN* 4.5 2.6 + - - -
410A ILE* 3.4 49.1 - - + +
436A GLY 3.0 28.3 - - - +
437A ALA 3.1 10.9 + - - +
439A GLN* 1.3 77.5 - - - +
441A THR* 1.3 66.3 + - + +
443A GLN* 3.8 0.9 - - - +
465A TYR* 5.6 4.3 - - - +
600A TPP 4.1 8.1 - - + +
26B VAL* 5.6 2.5 - - + -
50B ALA 3.0 24.2 - - - +
51B ASN* 3.4 19.6 + - + +
52B GLU* 4.0 20.6 - - - +
443B GLN* 3.1 13.0 + - - +
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Residues in contact with THR 441 (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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53A LEU* 4.5 2.9 - - + -
54A ASN* 3.3 25.1 - - - +
57A TYR* 3.7 15.0 - - + -
411A GLY* 2.8 41.0 + - - +
414A LEU* 3.3 21.3 - - - +
415A ALA* 4.5 5.4 - - - -
437A ALA 4.4 0.3 + - - -
438A ALA 3.5 2.2 + - - -
439A GLN 3.3 0.2 - - - -
440A LEU* 1.3 83.1 - - + +
442A ILE* 1.3 67.1 + - - +
443A GLN* 3.1 10.5 - - - +
444A GLU* 3.0 19.4 + - - +
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Residues in contact with ILE 442 (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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414A LEU* 3.8 11.4 - - + -
438A ALA* 3.0 18.7 + - + +
439A GLN 3.9 10.8 - - - +
440A LEU 3.7 0.2 - - - -
441A THR* 1.3 75.8 - - - +
443A GLN* 1.3 65.9 + - - +
445A LEU* 2.8 47.9 + - + +
484A TRP* 3.9 26.2 - - + -
486A TRP* 4.3 9.6 - - + -
489A ILE* 3.9 33.7 - - + -
493A LEU* 4.0 5.9 - - + +
442B ILE* 4.1 16.2 - - + -
443B GLN* 4.0 6.1 - - + +
493B LEU* 5.6 3.6 - - + -
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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