Contacts of the strand formed by residues 456 - 461 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372D PHE* 4.5 12.6 - - + -
428D ARG* 4.1 25.6 - - + -
429D VAL 3.0 14.2 + - - +
430D ILE* 3.5 15.0 - - + -
431D VAL 3.0 22.9 + - - -
454D HIS 4.7 2.9 - - - +
455D PRO* 1.3 73.1 - - + +
457D ILE* 1.3 60.3 + - - +
458D LEU* 3.2 31.1 - - + +
514D LEU* 4.6 3.8 - - + -
517D VAL* 4.4 13.5 - - + +
520D HIS* 4.8 5.8 - - + -
524D SER* 3.3 17.5 - - - +
526D ILE* 3.4 29.2 - - + -
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Residues in contact with ILE 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D LEU* 4.1 11.9 - - + -
431D VAL* 3.7 27.8 - - + +
433D THR* 4.4 9.9 - - + -
445D LEU* 3.6 32.3 - - + -
448D MET* 3.9 15.0 - - - -
455D PRO* 4.3 7.0 - - + -
456D ILE* 1.3 75.4 - - - +
458D LEU* 1.3 59.3 + - - +
459D VAL* 4.2 10.1 - - + -
523D LEU* 3.9 10.1 - - + -
524D SER 2.8 12.5 + - - +
525D LEU* 3.3 24.8 - - + +
526D ILE* 2.8 33.1 + - - +
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Residues in contact with LEU 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D PHE* 3.9 29.2 - - + -
369D LEU* 4.3 16.6 - - + -
372D PHE* 5.9 0.2 - - + -
430D ILE* 4.2 13.0 - - + -
431D VAL 2.8 15.4 + - - +
432D LEU* 3.9 9.3 - - + -
433D THR* 3.1 26.7 + - - +
456D ILE* 3.2 40.8 - - + +
457D ILE* 1.3 74.5 - - - +
459D VAL* 1.3 62.0 + - - +
460D LEU* 3.7 6.2 + - + +
510D LEU* 4.6 11.7 - - + -
514D LEU* 4.7 6.5 - - + -
526D ILE* 3.4 13.0 - - + +
528D VAL* 4.4 10.8 - - + -
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Residues in contact with VAL 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D THR* 3.3 12.1 - - + +
434D GLY 4.4 1.3 - - - +
435D ASP* 3.9 29.2 - - + +
438D ALA* 5.0 1.6 - - + -
457D ILE* 4.2 7.9 - - + -
458D LEU* 1.3 72.8 - - - +
460D LEU* 1.3 60.7 + - - +
461D ASN* 3.0 7.5 + - + +
486D TRP* 3.9 40.8 - - + +
525D LEU* 3.5 26.2 - - + -
526D ILE 2.9 10.4 + - - +
527D GLU* 3.8 6.4 - - - -
528D VAL 2.9 25.7 + - - -
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Residues in contact with LEU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D GLN* 4.4 3.8 - - - +
365D PHE* 3.8 27.4 - - + -
366D TRP* 4.2 14.4 - - + -
385D THR* 3.7 21.3 - - - +
386D SER* 3.7 31.2 - - - +
432D LEU* 5.5 2.2 - - + -
433D THR 2.9 14.4 + - - +
434D GLY* 4.4 3.8 - - - -
435D ASP 3.3 18.0 + - - -
458D LEU* 4.2 9.2 - - + +
459D VAL* 1.3 72.3 - - - +
461D ASN* 1.3 59.6 + - - +
462D ASN* 3.3 8.6 + - - +
528D VAL* 3.6 16.6 - - + -
530D LEU* 4.0 20.6 - - + -
600D TPP 4.7 0.7 - - - +
601D MG 3.5 6.6 - - - -
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Residues in contact with ASN 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D ASP* 3.3 13.8 - - + +
459D VAL* 3.0 4.1 + - + +
460D LEU* 1.3 68.6 - - - +
462D ASN* 1.3 59.7 + - - +
463D GLU* 3.1 26.3 + - - +
483D LEU* 5.4 2.5 - - - +
484D TRP 4.9 3.0 + - - -
486D TRP* 3.9 14.8 - - + +
527D GLU* 2.8 32.3 + - + -
528D VAL 2.8 13.9 + - - +
529D MET* 3.5 28.5 - - - +
530D LEU* 2.8 26.0 + - - +
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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