Contacts of the strand formed by residues 429 - 434 (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 VAL 429 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378D ILE* 3.3 21.5 - - + +
380D LEU* 3.5 27.8 - - + -
417D ALA* 4.3 8.3 - - + +
420D ALA* 5.0 0.4 - - + -
421D GLN* 3.2 56.1 - - + +
424D CYS 4.9 0.7 - - - +
427D ARG 3.4 6.7 + - - +
428D ARG* 1.3 74.7 - - - +
430D ILE* 1.3 62.4 + - - +
431D VAL* 4.1 12.6 - - + -
454D HIS 5.3 0.6 + - - -
455D PRO* 3.5 4.1 - - + +
456D ILE* 3.0 28.9 + - - +
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Residues in contact with ILE 430 (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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369D LEU* 5.2 8.1 - - + -
372D PHE* 4.0 20.6 - - + -
373D ILE* 5.7 4.0 - - + -
377D ASP* 3.8 15.0 - - + +
378D ILE 2.7 12.6 + - - +
379D ILE* 3.3 16.1 - - + +
380D LEU* 2.9 28.2 + - - +
428D ARG* 3.7 41.1 - - + +
429D VAL* 1.3 76.6 - - - +
431D VAL* 1.3 61.7 + - - +
432D LEU* 4.1 27.1 - - + -
456D ILE* 3.5 8.1 - - + -
458D LEU* 4.2 12.3 - - + -
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Residues in contact with VAL 431 (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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380D LEU* 3.7 5.6 - - + +
413D THR* 4.2 19.1 - - - +
414D LEU* 4.4 12.3 - - + -
417D ALA* 3.5 33.2 - - + -
429D VAL* 4.1 11.2 - - + +
430D ILE* 1.3 76.5 - - - +
432D LEU* 1.3 61.1 + - - +
433D THR* 4.5 12.1 - - + -
448D MET* 4.7 1.6 - - + -
455D PRO* 4.5 4.5 - - + -
456D ILE 3.0 9.7 + - - +
457D ILE* 4.1 26.9 - - + +
458D LEU* 2.8 33.6 + - - +
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Residues in contact with LEU 432 (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* 4.4 4.5 - - + -
366D TRP* 3.5 31.6 - - + -
369D LEU* 3.6 26.0 - - + -
379D ILE* 3.9 22.4 - - + -
380D LEU 2.7 14.6 + - - +
381D ALA* 3.2 9.2 - - + -
382D ASP 3.0 24.4 + - - -
386D SER* 3.3 12.2 + - - +
390D ALA* 4.0 12.1 - - + -
393D LEU* 4.5 1.6 - - + -
413D THR* 4.1 1.0 + - - -
430D ILE* 4.1 16.2 - - + -
431D VAL* 1.3 74.6 - - - +
433D THR* 1.3 59.6 + - - +
458D LEU* 3.9 20.6 - - + -
460D LEU* 5.5 2.5 - - + -
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Residues in contact with THR 433 (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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382D ASP* 4.3 4.5 + - - +
386D SER* 3.5 7.3 + - - -
413D THR* 3.9 16.2 + - - -
414D LEU* 5.2 7.1 - - + +
431D VAL* 4.5 7.4 - - + -
432D LEU* 1.3 75.5 - - - +
434D GLY* 1.3 74.0 + - - +
437D ALA* 3.6 6.9 - - - +
438D ALA* 3.5 26.2 + - + +
457D ILE* 4.4 12.8 - - + -
458D LEU 3.1 12.6 + - - +
459D VAL* 3.3 12.2 - - + -
460D LEU 2.9 23.4 + - - -
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Residues in contact with GLY 434 (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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382D ASP* 4.7 1.8 - - - +
383D GLN 5.4 1.0 + - - -
386D SER* 3.6 7.5 + - - -
433D THR* 1.3 90.2 + - - +
435D ASP* 1.3 65.1 + - - -
436D GLY 3.3 2.5 - - - -
437D ALA* 4.2 2.2 - - - +
438D ALA* 3.1 13.2 + - - +
459D VAL* 4.4 0.9 - - - -
460D LEU* 4.0 8.1 - - - -
600D TPP 3.2 33.0 + - - -
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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