Contacts of the strand formed by residues 373 - 379 (chain B) in PDB entry 3OVS
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 ARG 373 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B MET* 3.5 45.1 - - - +
346B GLY 2.9 18.8 + - - -
347B PRO* 3.4 13.1 - - - +
348B GLN* 3.5 39.9 - - + +
369B ILE* 3.7 3.1 - - - -
370B GLU 2.5 39.3 + - - +
371B ASN 4.6 4.5 - - - +
372B GLY* 1.3 77.6 - - - +
374B TRP* 1.3 66.7 + - - +
375B TRP* 3.1 19.9 - - + +
703B EDO 4.5 8.1 + - - -
15D C 4.3 5.5 - - - +
16D A 5.9 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 3.9 30.6 - + - +
346B GLY* 2.7 32.6 + - - -
347B PRO* 3.1 29.6 - - + +
349B PHE* 3.9 18.4 + - + +
355B VAL* 3.5 39.1 - - + +
358B PHE* 4.2 4.9 - + + -
359B LEU* 3.7 27.4 - - + -
366B ARG* 3.8 22.7 - - - -
367B PRO* 3.9 8.1 - - + -
368B PHE* 3.3 51.2 + - - -
369B ILE* 3.4 30.9 - - + +
373B ARG* 1.3 70.9 + - - +
375B TRP* 1.3 56.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG* 3.4 42.6 - - + -
344B ARG 3.2 11.0 - - - +
345B MET* 3.5 50.5 - - + -
346B GLY 4.1 0.4 - - - +
358B PHE* 3.9 3.6 - - - -
367B PRO* 3.4 5.7 - - - +
368B PHE* 2.8 53.7 + + + -
370B GLU* 3.3 35.5 + - + +
371B ASN* 6.0 2.0 - - - -
373B ARG* 3.1 35.7 + - + +
374B TRP* 1.3 75.1 - - - +
376B ALA* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG* 3.4 3.8 - - - -
344B ARG* 2.7 41.0 + - + +
358B PHE* 3.6 11.8 - - + -
363B ARG* 3.5 45.8 - - - +
367B PRO* 4.4 8.5 - - + -
368B PHE* 4.7 2.7 - - - -
375B TRP* 1.3 74.4 - - - +
377B PHE* 1.3 63.2 + - - +
378B GLU* 3.7 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 3.2 38.6 - - - +
316A LEU* 4.1 28.7 - - + -
317A ARG* 3.8 9.4 - - + -
332A GLU* 4.7 2.0 - - - -
432A MET 3.6 25.1 - - - -
433A MET 3.6 11.0 - - - -
434A GLY 4.4 0.9 - - - -
341B VAL* 4.6 8.1 - - + -
342B PHE 3.4 11.0 - - - +
343B ARG* 5.0 2.9 - - + -
363B ARG* 3.8 17.0 - - - +
364B ALA 5.2 0.7 + - - -
365B PHE* 4.1 26.7 + - + +
366B ARG 4.3 5.6 - - - -
367B PRO* 5.2 0.8 - - - +
368B PHE* 3.5 36.1 - + - -
376B ALA* 1.3 72.4 - - - +
378B GLU* 1.3 67.6 + - - +
379B MET* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 3.1 8.9 - - - +
342B PHE* 3.0 53.8 + - + +
344B ARG* 3.2 43.5 + - + +
361B ARG* 5.7 2.1 + - - -
363B ARG* 2.8 42.8 + - - +
376B ALA 3.7 0.2 + - - -
377B PHE* 1.3 82.9 - - - +
379B MET* 1.3 68.2 + - - +
14D U 5.7 0.5 - - - +
15D C 4.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU* 3.7 41.7 - - + +
340B ARG* 3.5 30.1 - - + -
341B VAL* 3.3 32.3 - - + -
342B PHE* 3.9 7.5 - - - -
364B ALA* 5.0 14.4 - - + +
365B PHE* 4.1 13.5 - - + -
377B PHE 5.9 0.2 - - - +
378B GLU* 1.3 79.6 - - - +
380B ARG* 1.3 65.6 + - - +
381B LYS* 4.1 11.1 + - - -
----------------------------------------------------------
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