Contacts of the strand formed by residues 429 - 434 (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 VAL 429 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ILE* 3.3 22.7 - - + +
380B LEU* 3.6 26.0 - - + -
417B ALA* 4.3 9.4 - - + +
420B ALA* 5.1 0.2 - - + -
421B GLN* 3.3 55.4 - - + +
424B CYS 5.0 0.4 - - - +
427B ARG 3.4 4.2 + - - +
428B ARG* 1.3 74.9 - - - +
430B ILE* 1.3 63.4 + - - +
431B VAL* 4.0 13.4 + - + -
454B HIS 5.3 0.8 + - - -
455B PRO* 3.7 3.4 - - + +
456B ILE* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 5.2 7.9 - - + -
372B PHE* 4.1 20.9 - - + -
373B ILE* 5.6 3.6 - - + -
377B ASP* 3.8 17.0 - - + +
378B ILE 2.8 11.6 + - - +
379B ILE* 3.3 16.6 - - + -
380B LEU* 2.9 28.4 + - - +
428B ARG* 3.7 40.4 - - + +
429B VAL* 1.3 77.2 - - - +
431B VAL* 1.3 63.2 + - - +
432B LEU* 4.1 27.6 - - + -
456B ILE* 3.5 8.1 - - + -
458B LEU* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 3.7 5.4 - - + +
413B THR* 4.2 28.9 - - - +
414B LEU* 4.4 11.4 - - + -
417B ALA* 3.5 25.8 - - + -
429B VAL* 4.0 10.8 - - + -
430B ILE* 1.3 75.0 - - - +
432B LEU* 1.3 61.7 + - - +
433B THR* 4.4 14.1 - - + -
448B MET* 4.8 1.8 - - + -
455B PRO* 4.5 4.9 - - + -
456B ILE 3.0 7.8 + - - +
457B ILE* 4.1 24.4 - - + +
458B LEU* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.3 9.9 - - + -
366B TRP* 3.7 26.7 - - + -
369B LEU* 3.4 27.6 - - + -
379B ILE* 3.8 24.0 - - + -
380B LEU 2.7 12.2 + - - +
381B ALA* 3.1 10.8 - - + -
382B ASP 3.1 23.6 + - - -
386B SER* 3.6 11.9 + - - +
390B ALA* 4.0 11.0 - - + -
393B LEU* 4.7 1.1 - - + -
413B THR* 4.0 1.4 + - - -
430B ILE* 4.1 15.7 - - + -
431B VAL* 1.3 71.9 - - - +
433B THR* 1.3 60.7 + - - +
458B LEU* 3.8 21.3 - - + -
460B LEU* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ASP* 4.2 5.2 + - - +
386B SER* 3.5 7.3 + - - -
413B THR* 3.9 15.8 + - - -
414B LEU* 5.1 8.6 - - + +
431B VAL* 4.4 7.4 - - + -
432B LEU* 1.3 75.0 - - - +
434B GLY* 1.3 72.9 + - - +
437B ALA* 3.7 7.4 - - - +
438B ALA* 3.6 25.9 + - + +
457B ILE* 4.4 12.6 - - + -
458B LEU 3.1 16.0 + - - +
459B VAL* 3.3 11.8 - - + -
460B LEU* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ASP* 4.7 1.6 - - - +
383B GLN 5.5 0.8 + - - -
386B SER* 3.6 7.8 + - - -
433B THR* 1.3 88.5 + - - +
435B ASP* 1.3 64.9 + - - -
436B GLY 3.3 2.5 - - - -
437B ALA* 4.3 2.2 - - - +
438B ALA* 3.1 13.5 + - - +
459B VAL* 4.3 1.9 - - - +
460B LEU* 4.0 8.5 - - - -
600B TPP 3.2 32.0 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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