Contacts of the helix formed by residues 435 - 441 (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 ASP 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434C GLY* 1.3 69.9 - - - -
436C GLY* 1.3 79.8 + - - +
439C GLN* 3.1 24.4 + - - +
459C VAL* 3.8 9.8 - - + +
460C LEU 3.3 12.0 + - - +
461C ASN* 3.4 8.2 - - - +
462C ASN 3.2 5.5 + - - -
463C GLU* 3.1 28.9 + - - -
464C GLY 3.0 8.4 + - - +
481C ILE* 3.7 13.3 - - + +
483C LEU* 5.8 0.2 - - - +
486C TRP* 3.3 33.1 - - + +
600C TPP 3.0 1.9 + - - -
601C MG 2.3 26.1 - - - -
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Residues in contact with GLY 436 (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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410C ILE* 4.6 0.9 - - - -
435C ASP* 1.3 91.3 + - - +
437C ALA* 1.3 59.4 + - - +
439C GLN* 3.3 11.4 + - - +
440C LEU* 3.0 21.2 - - - +
465C TYR* 3.7 25.7 + - - -
481C ILE* 4.0 9.0 - - - -
600C TPP 3.1 12.2 + - - -
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Residues in contact with ALA 437 (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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382C ASP* 3.8 28.7 - - + +
383C GLN 5.1 0.2 - - - +
410C ILE* 4.0 11.2 - - + +
411C GLY* 3.4 19.6 - - - +
433C THR* 3.7 14.6 - - - +
434C GLY 4.2 0.4 - - - +
436C GLY* 1.3 76.5 - - - +
438C ALA* 1.3 62.2 + - - +
439C GLN 3.0 1.2 + - - -
440C LEU* 3.1 22.8 + - - +
441C THR 4.1 0.3 + - - -
600C TPP 2.9 19.0 + - - +
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Residues in contact with ALA 438 (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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414C LEU* 4.0 18.2 - - + +
433C THR* 3.5 19.0 + - + +
434C GLY 3.1 15.5 + - - +
436C GLY 3.4 0.4 - - - -
437C ALA* 1.3 78.3 - - - +
439C GLN* 1.3 58.4 + - - +
441C THR* 3.6 3.2 + - - -
442C ILE* 3.0 33.2 + - + +
459C VAL* 5.0 2.9 - - + -
486C TRP* 3.6 26.5 - - + -
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Residues in contact with GLN 439 (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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435C ASP 3.1 19.0 + - - +
436C GLY 3.5 7.4 - - - +
437C ALA 3.0 1.0 + - - -
438C ALA* 1.3 78.9 - - - +
440C LEU* 1.3 58.8 + - + +
441C THR 3.4 0.2 + - - -
442C ILE 3.8 1.4 + - - -
465C TYR* 5.2 1.4 + - - -
481C ILE* 3.7 27.3 - - - +
482C ALA* 3.0 29.9 + - - +
484C TRP* 3.2 52.0 - - + +
486C TRP* 4.0 5.2 - - + -
50D ALA* 4.4 17.4 - - + +
443D GLN* 2.9 32.7 + - - +
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Residues in contact with LEU 440 (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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51C ASN* 5.2 1.6 + - - -
53C LEU* 5.2 5.0 - - + +
54C ASN* 4.5 2.6 + - - -
410C ILE* 3.4 48.9 - - + +
411C GLY* 4.3 2.0 - - - -
436C GLY 3.0 28.7 - - - +
437C ALA 3.1 10.7 + - - +
439C GLN* 1.3 76.9 - - - +
441C THR* 1.3 64.5 + - + +
443C GLN* 3.8 1.0 - - - +
465C TYR* 5.7 2.7 - - - +
600C TPP 4.0 4.5 - - + +
26D VAL* 5.6 2.7 - - + -
50D ALA 3.0 25.1 - - - +
51D ASN* 3.3 20.9 + - + +
52D GLU* 3.6 24.2 - - - +
443D GLN* 3.1 13.3 + - - +
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Residues in contact with THR 441 (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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53C LEU* 4.5 2.7 - - + -
54C ASN* 3.3 27.3 - - - +
57C TYR* 3.7 15.5 - - + -
411C GLY* 2.8 40.2 + - - +
414C LEU* 3.4 22.2 - - - +
415C ALA* 4.5 4.7 - - - -
437C ALA 4.1 0.8 + - - -
438C ALA 3.6 2.7 + - - -
440C LEU* 1.3 82.1 - - + +
442C ILE* 1.3 66.1 + - - +
443C GLN* 3.1 9.4 - - - -
444C GLU* 3.1 18.0 + - - +
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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