Contacts of the strand formed by residues 360 - 365 (chain V) in PDB entry 5OA1
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 TRP 360 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303V VAL* 4.4 7.8 - - - -
318V ILE* 4.0 18.4 - - - +
319V ASP 3.0 21.1 + - - +
320V ILE* 5.4 0.5 - - - -
322V GLY* 3.7 10.4 - - - -
358V SER 3.4 3.1 + - - -
359V SER* 1.4 70.8 - - - +
361V LYS* 1.3 60.1 + - - +
362V ARG 3.7 1.3 - - - -
375V PHE 3.6 9.9 - - - -
376V ASP* 4.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 361 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303V VAL* 4.2 20.5 - - - +
304V ASP* 4.5 1.8 + - - -
318V ILE* 6.3 0.4 - - - -
359V SER 3.5 5.2 + - - -
360V TRP* 1.3 72.8 - - - +
362V ARG* 1.4 54.3 + - - +
375V PHE 2.9 11.4 + - - -
376V ASP* 3.9 1.6 - - - +
402V ILE 4.6 9.4 - - - -
403V ARG* 4.1 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 362 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304V ASP* 5.3 5.8 - - - +
318V ILE* 6.6 0.7 - - - -
360V TRP* 3.7 1.7 - - - -
361V LYS* 1.4 78.3 - - - +
363V ILE* 1.4 57.5 + - - +
374V VAL* 3.3 3.8 - - - -
375V PHE* 3.0 29.9 + - - +
402V ILE 5.2 0.6 + - - -
403V ARG 4.6 6.4 + - - -
404V ASP* 5.2 7.0 - - - +
405V TYR* 5.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304V ASP* 5.8 3.2 - - - +
305V PHE 5.1 9.2 + - - +
306V ALA* 6.1 2.9 - - - -
362V ARG* 1.4 75.0 - - - +
364V GLU* 1.3 57.5 + - - +
373V LEU 3.2 12.1 - - - -
374V VAL* 4.2 1.1 - - - +
405V TYR* 4.6 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363V ILE* 1.3 73.1 - - - +
365V TRP* 1.3 59.0 + - - +
372V ILE* 3.7 2.1 - - - -
373V LEU* 2.9 31.3 + - - +
405V TYR 5.7 1.8 - - - -
406V LYS* 5.8 2.0 - - - +
407V ARG* 5.5 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 365 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364V GLU* 1.3 74.7 - - - +
366V PHE* 1.3 67.6 + - - +
367V SER* 3.9 0.7 + - - -
369V PHE* 5.8 1.6 - - - +
371V LYS 3.8 6.7 - - - -
372V ILE* 4.5 1.8 - - - +
407V ARG* 4.9 13.4 + - - +
----------------------------------------------------------
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