Contacts of the strand formed by residues 456 - 461 (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 ILE 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A PHE* 4.6 10.5 - - + -
428A ARG* 4.1 24.7 - - + -
429A VAL 3.0 16.1 + - - +
430A ILE* 3.5 14.5 - - + -
431A VAL 3.0 21.0 + - - -
454A HIS 4.7 3.1 - - - +
455A PRO* 1.3 75.4 - - + +
457A ILE* 1.3 60.6 + - - +
458A LEU* 3.1 29.8 - - + +
514A LEU* 4.7 1.8 - - + -
517A VAL* 4.4 14.6 - - + +
520A HIS* 4.8 6.7 - - + -
524A SER* 3.3 16.4 - - - +
526A ILE* 3.4 29.2 - - + -
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Residues in contact with ILE 457 (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* 4.3 12.3 - - + -
431A VAL* 3.7 21.8 - - + +
433A THR* 4.4 9.9 - - + -
445A LEU* 3.7 31.0 - - + -
448A MET* 3.9 17.0 - - - -
455A PRO* 3.8 15.0 - - + -
456A ILE* 1.3 72.9 - - - +
458A LEU* 1.3 63.4 + - - +
459A VAL* 4.3 9.9 - - + -
523A LEU* 4.2 12.1 - - + -
524A SER 2.8 13.4 + - - +
525A LEU* 3.4 20.8 - - + +
526A ILE* 2.8 28.8 + - - +
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Residues in contact with LEU 458 (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* 3.8 30.5 - - + -
369A LEU* 4.3 16.4 - - + -
372A PHE* 6.0 0.4 - - + -
430A ILE* 4.2 13.2 - - + -
431A VAL 2.8 15.8 + - - +
432A LEU* 3.9 9.4 - - + -
433A THR* 3.1 27.5 + - - +
456A ILE* 3.1 43.1 - - + +
457A ILE* 1.3 72.8 - - - +
459A VAL* 1.3 62.9 + - - +
460A LEU* 3.8 4.9 + - + +
510A LEU* 4.8 5.2 - - + -
514A LEU* 4.7 11.9 - - + -
526A ILE* 3.4 13.5 - - + +
528A VAL* 4.3 10.5 - - + -
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Residues in contact with VAL 459 (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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433A THR* 3.3 11.2 - - + +
434A GLY 4.3 1.3 - - - +
435A ASP* 3.8 27.1 - - + +
438A ALA* 5.0 1.1 - - + -
457A ILE* 4.3 7.6 - - + -
458A LEU* 1.3 73.4 - - - +
460A LEU* 1.3 63.3 + - - +
461A ASN* 3.1 5.3 + - + +
486A TRP* 3.8 44.6 - - + +
525A LEU* 3.5 26.7 - - + -
526A ILE 2.9 8.2 + - - +
527A GLU* 3.7 5.9 - - - -
528A VAL 2.8 28.8 + - - -
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Residues in contact with LEU 460 (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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362A GLN* 4.4 2.9 - - - +
365A PHE* 3.7 31.9 - - + -
366A TRP* 4.3 13.0 - - + -
385A THR* 3.5 24.0 - - - +
386A SER* 3.5 29.6 - - - +
432A LEU* 5.5 2.9 - - + -
433A THR 2.9 13.1 + - - +
434A GLY* 4.4 4.0 - - - -
435A ASP* 3.3 20.0 + - - -
458A LEU* 4.4 9.0 - - + +
459A VAL* 1.3 73.2 - - - +
461A ASN* 1.3 58.9 - - - +
462A ASN* 3.4 8.4 + - - +
528A VAL* 3.6 12.6 - - + -
530A LEU* 4.0 20.9 - - + -
600A TPP 4.8 1.3 - - - +
601A MG 3.7 5.0 - - - -
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Residues in contact with ASN 461 (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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435A ASP* 3.4 11.9 - - + +
459A VAL* 3.1 3.5 + - + +
460A LEU* 1.3 68.9 - - - +
462A ASN* 1.3 57.8 + - - +
463A GLU* 3.1 25.9 + - - +
483A LEU* 5.5 2.6 - - - +
484A TRP 4.8 2.6 + - - -
486A TRP* 3.6 17.6 - - + +
527A GLU* 2.8 33.9 + - + -
528A VAL 2.7 14.3 + - - +
529A MET* 3.5 26.5 - - - +
530A LEU* 2.9 24.9 + - - +
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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