Contacts of the strand formed by residues 456 - 461 (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 ILE 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372C PHE* 4.5 10.3 - - + -
428C ARG* 4.2 25.1 - - + -
429C VAL 3.0 12.8 + - - +
430C ILE* 3.5 14.5 - - + -
431C VAL 3.0 21.9 + - - -
454C HIS 4.6 3.6 - - - +
455C PRO* 1.3 75.2 - - + +
457C ILE* 1.3 59.6 - - - +
458C LEU* 3.1 33.2 - - + +
514C LEU* 4.9 2.7 - - + -
517C VAL* 4.2 14.1 - - + +
520C HIS* 4.7 7.0 - - + -
524C SER* 3.4 19.7 - - - +
526C ILE* 3.5 28.5 - - + -
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Residues in contact with ILE 457 (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* 4.3 11.7 - - + -
431C VAL* 3.7 27.8 - - + +
433C THR* 4.4 9.4 - - + -
445C LEU* 3.6 32.3 - - + -
448C MET* 3.9 15.9 - - + -
455C PRO* 4.2 8.1 - - + -
456C ILE* 1.3 73.6 - - - +
458C LEU* 1.3 63.3 + - - +
459C VAL* 4.3 10.5 - - + -
523C LEU* 4.1 13.2 - - + -
524C SER 2.9 10.0 + - - +
525C LEU* 3.3 23.2 - - + +
526C ILE* 2.8 28.9 + - - +
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Residues in contact with LEU 458 (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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365C PHE* 3.8 28.9 - - + -
369C LEU* 4.3 17.3 - - + -
372C PHE* 5.9 0.4 - - + -
430C ILE* 4.3 12.8 - - + -
431C VAL 2.8 15.9 + - - +
432C LEU* 3.8 9.9 - - + -
433C THR* 3.1 27.4 + - - +
456C ILE* 3.1 42.4 - - + +
457C ILE* 1.3 71.9 - - - +
459C VAL* 1.3 62.6 + - - +
460C LEU* 3.8 5.3 + - + +
510C LEU* 4.6 5.6 - - + -
514C LEU* 4.6 11.9 - - + -
526C ILE* 3.4 14.4 - - + +
528C VAL* 4.3 10.3 - - + -
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Residues in contact with VAL 459 (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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433C THR* 3.3 16.4 - - + +
434C GLY 4.3 1.3 - - - +
435C ASP* 3.8 30.1 - - + +
438C ALA* 5.0 1.6 - - + -
457C ILE* 4.3 3.1 - - + -
458C LEU* 1.3 71.3 - - - +
460C LEU* 1.3 62.0 + - - +
461C ASN* 3.1 5.3 + - + +
486C TRP* 3.9 40.6 - - + +
525C LEU* 3.7 24.7 - - + -
526C ILE 2.9 9.3 + - - +
527C GLU* 3.8 5.5 - - - -
528C VAL* 2.8 29.3 + - - -
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Residues in contact with LEU 460 (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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362C GLN* 4.4 2.9 - - - +
365C PHE* 3.7 30.5 - - + -
366C TRP* 4.2 14.4 - - + -
385C THR* 3.6 23.8 - - - +
386C SER* 3.7 28.5 - - - +
432C LEU* 5.4 3.8 - - + -
433C THR 2.9 13.5 + - - +
434C GLY* 4.3 4.3 - - - -
435C ASP 3.3 8.9 + - - -
458C LEU* 4.3 8.7 - - + +
459C VAL* 1.3 73.0 - - - +
461C ASN* 1.3 58.5 + - - +
462C ASN* 3.3 5.6 + - - +
528C VAL* 3.7 13.7 - - + -
530C LEU* 4.0 20.2 - - + -
601C MG 3.3 20.8 - - - -
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Residues in contact with ASN 461 (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* 3.4 13.1 - - + +
459C VAL* 3.1 3.9 + - + +
460C LEU* 1.3 68.3 - - - +
462C ASN* 1.3 55.4 + - - +
463C GLU* 3.1 27.2 + - - +
483C LEU* 5.4 2.4 - - - +
484C TRP 4.9 3.0 + - - -
486C TRP* 3.8 15.5 - - + +
527C GLU* 2.8 33.5 + - + -
528C VAL 2.8 13.7 + - - +
529C MET* 3.5 25.7 - - - +
530C LEU 2.8 30.0 + - - +
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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