Contacts of the strand formed by residues 429 - 434 (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 VAL 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A ILE* 3.3 24.2 - - + +
380A LEU* 3.5 28.7 - - + -
417A ALA* 4.3 8.3 - - + +
420A ALA* 4.8 0.4 - - + -
421A GLN* 3.4 51.4 - - + +
424A CYS 5.0 0.2 - - - +
427A ARG 3.4 4.6 + - - +
428A ARG* 1.3 77.1 - - - +
430A ILE* 1.3 62.1 + - - +
431A VAL* 4.0 13.6 + - + -
454A HIS 5.2 1.2 + - - -
455A PRO* 3.8 3.3 - - + +
456A ILE* 3.0 28.8 + - - +
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Residues in contact with ILE 430 (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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369A LEU* 5.2 8.7 - - + -
372A PHE* 4.1 20.2 - - + -
373A ILE* 5.6 3.4 - - + -
377A ASP* 3.8 15.9 - - + +
378A ILE 2.7 13.1 + - - +
379A ILE* 3.4 15.4 - - + -
380A LEU* 2.9 28.1 + - - +
428A ARG* 3.7 39.7 - - + +
429A VAL* 1.3 76.6 - - - +
431A VAL* 1.3 62.5 + - - +
432A LEU* 4.1 22.2 - - + -
456A ILE* 3.5 7.9 - - + -
458A LEU* 4.2 16.8 - - + -
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Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.7 5.4 - - + +
413A THR* 4.1 27.4 - - - +
414A LEU* 4.4 12.1 - - + -
417A ALA* 3.4 27.6 - - + -
429A VAL* 4.0 12.1 - - + +
430A ILE* 1.3 74.8 - - - +
432A LEU* 1.3 61.7 + - - +
433A THR* 4.3 15.0 - - + -
448A MET* 4.9 0.9 - - + -
455A PRO* 4.6 4.3 - - + -
456A ILE 3.0 7.8 + - - +
457A ILE* 4.1 23.1 - - + -
458A LEU* 2.8 33.8 + - - +
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Residues in contact with LEU 432 (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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365A PHE* 4.3 15.9 - - + -
366A TRP* 3.7 27.8 - - + -
369A LEU* 3.5 27.4 - - + -
379A ILE* 3.9 22.4 - - + -
380A LEU 2.7 13.1 + - - +
381A ALA* 3.1 9.7 - - + -
382A ASP 3.1 23.9 + - - -
386A SER* 3.6 11.9 + - - +
390A ALA* 4.0 12.6 - - + -
393A LEU* 4.6 1.1 - - + -
413A THR* 3.9 1.2 + - - -
430A ILE* 4.1 15.5 - - + -
431A VAL* 1.3 72.1 - - - +
433A THR* 1.3 58.8 + - - +
458A LEU* 3.9 15.3 - - + -
460A LEU* 5.5 2.9 - - + -
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Residues in contact with THR 433 (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* 4.2 4.5 + - - +
386A SER* 3.5 7.3 + - - -
413A THR* 3.9 15.0 + - - -
414A LEU* 5.1 7.8 - - + +
431A VAL* 4.3 14.1 - - + -
432A LEU* 1.3 75.5 - - - +
434A GLY* 1.3 74.2 + - - +
437A ALA* 3.7 7.6 - - - +
438A ALA* 3.6 26.0 + - + +
457A ILE* 4.4 6.3 - - + -
458A LEU 3.1 13.1 + - - +
459A VAL* 3.3 11.9 - - + -
460A LEU* 2.9 23.1 + - - +
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Residues in contact with GLY 434 (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* 4.8 2.2 - - - +
383A GLN 5.5 1.0 + - - -
386A SER* 3.6 8.5 + - - -
433A THR* 1.3 80.5 + - - +
435A ASP* 1.3 65.9 + - - -
436A GLY 3.2 2.5 - - - -
437A ALA* 3.5 2.5 + - - +
438A ALA* 3.1 22.3 + - - +
459A VAL* 4.3 0.4 - - - -
460A LEU* 4.0 9.2 - - - -
600A TPP 3.3 29.9 + - - -
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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