Contacts of the strand formed by residues 456 - 461 (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 ILE 456 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372B PHE* 4.5 16.4 - - + -
428B ARG* 4.2 24.7 - - + -
429B VAL 2.9 17.1 + - - +
430B ILE* 3.5 9.4 - - + -
431B VAL 3.0 21.6 + - - -
454B HIS 4.7 4.0 - - - +
455B PRO* 1.3 75.9 - - - +
457B ILE* 1.3 59.1 + - - +
458B LEU* 3.3 25.7 - - + +
514B LEU* 4.2 4.0 - - + -
517B VAL* 4.1 14.8 - - + +
520B HIS* 4.7 6.7 - - + -
524B SER* 3.4 17.3 - - - +
526B ILE* 3.4 28.9 - - + -
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Residues in contact with ILE 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 4.6 10.3 - - + -
431B VAL* 3.7 22.2 - - + +
433B THR* 4.4 9.2 - - + -
445B LEU* 3.7 30.5 - - + -
448B MET* 4.1 10.5 - - + -
455B PRO* 3.7 13.9 - - + -
456B ILE* 1.3 71.8 - - - +
458B LEU* 1.3 64.3 + - - +
459B VAL* 4.3 10.3 - - + -
523B LEU* 3.9 24.7 - - + -
524B SER 2.8 10.4 + - - +
525B LEU* 3.4 23.7 - - + +
526B ILE* 2.8 29.3 + - - +
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Residues in contact with LEU 458 (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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365B PHE* 3.8 30.1 - - + -
369B LEU* 4.2 16.8 - - + -
372B PHE* 5.9 0.2 - - + -
430B ILE* 4.2 13.9 - - + -
431B VAL 2.8 15.0 + - - +
432B LEU* 3.8 9.7 - - + -
433B THR* 3.1 28.6 + - - +
456B ILE* 3.3 39.3 - - + +
457B ILE* 1.3 74.7 - - - +
459B VAL* 1.3 61.0 + - - +
460B LEU* 3.8 5.9 + - + +
510B LEU* 4.5 13.0 - - + -
514B LEU* 4.8 4.3 - - + -
526B ILE* 3.4 12.1 - - + +
528B VAL* 4.4 9.9 - - + -
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B THR* 3.3 15.5 - - + -
434B GLY 4.3 2.7 - - - +
435B ASP* 3.8 29.2 - - + +
438B ALA* 5.0 1.3 - - + -
457B ILE* 4.3 2.9 - - + -
458B LEU* 1.3 72.9 - - - +
460B LEU* 1.3 64.6 + - - +
461B ASN* 3.1 5.1 + - + +
486B TRP* 3.9 41.3 - - + +
525B LEU* 3.6 26.2 - - + -
526B ILE 2.9 9.0 + - - +
527B GLU* 3.8 6.3 - - - -
528B VAL* 2.8 28.8 + - - -
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Residues in contact with LEU 460 (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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362B GLN* 4.4 4.0 - - - +
365B PHE* 3.7 30.5 - - + -
366B TRP* 4.3 14.1 - - + -
385B THR* 3.7 23.6 - - - +
386B SER* 3.8 22.4 - - - +
432B LEU* 5.5 2.5 - - + -
433B THR 2.9 20.0 + - - +
434B GLY* 4.4 3.8 - - - -
435B ASP* 3.2 21.2 + - - -
458B LEU* 4.4 9.0 - - + +
459B VAL* 1.3 73.0 - - - +
461B ASN* 1.3 59.1 + - - +
462B ASN* 3.4 10.6 + - - +
528B VAL* 3.7 13.2 - - + -
530B LEU* 4.1 20.9 - - + -
601B MG 3.6 4.5 - - - -
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Residues in contact with ASN 461 (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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435B ASP* 3.4 13.0 - - + +
459B VAL* 3.1 4.1 + - + +
460B LEU* 1.3 67.9 - - - +
462B ASN* 1.3 58.5 + - - +
463B GLU* 3.1 26.7 + - - +
483B LEU* 5.4 3.2 - - - +
484B TRP 4.9 2.8 + - - -
486B TRP* 3.8 14.5 - - + +
527B GLU* 2.8 33.8 + - + -
528B VAL 2.8 14.7 + - - +
529B MET* 3.5 26.3 - - - +
530B LEU 2.8 25.5 + - - +
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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