Contacts of the strand formed by residues 415 - 419 (chain D) in PDB entry 2O1S
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 LEU 415 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D PHE* 6.0 0.4 - - + -
328D TRP* 3.8 27.8 - - + -
387D PRO 3.3 13.1 + - - +
388D ILE* 3.4 19.5 - - + +
389D VAL* 2.8 27.7 + - - -
413D PRO 3.7 1.5 + - - +
414D VAL* 1.3 77.3 - - - +
416D PHE* 1.3 76.2 + - - +
417D ALA* 3.9 0.8 + - - +
461D LEU* 3.8 10.1 - - + +
464D GLY* 4.1 13.7 - - - +
465D TYR* 3.8 22.9 - - + +
472D SER* 3.4 24.5 - - - +
474D VAL* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D VAL* 4.1 19.1 - - + -
389D VAL* 3.5 27.6 - - + +
391D ILE* 4.8 2.2 - - + -
396D LEU* 4.3 18.2 - - + -
403D VAL* 3.8 37.9 - - + -
407D VAL* 4.3 5.4 - - + -
414D VAL* 3.8 27.8 - - + -
415D LEU* 1.3 78.7 - - - +
417D ALA* 1.3 59.4 + - - +
418D ILE* 3.4 13.3 + - + +
440D LEU* 6.6 0.2 - - + -
446D MSE 4.8 3.4 - - + -
471D PRO* 4.2 14.1 - - + -
472D SER 2.9 23.6 + - - +
473D ALA* 3.4 12.7 - - + -
474D VAL 2.9 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D PHE* 3.5 37.9 - - + -
388D ILE* 4.5 5.2 - - + -
389D VAL 2.9 13.7 + - - +
390D ALA* 3.5 2.7 - - - +
391D ILE* 3.0 25.2 + - - +
415D LEU* 3.9 2.7 + - + -
416D PHE* 1.3 69.0 - - - +
418D ILE* 1.3 61.2 + - - +
419D ASP* 3.5 3.7 + - - +
461D LEU* 4.9 5.2 - - + -
474D VAL* 3.7 7.2 - - - +
476D TYR* 3.6 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D ILE* 3.1 7.9 - - + +
392D TYR 4.1 0.2 - - - -
393D SER* 3.3 42.8 - - - +
396D LEU* 3.8 17.9 - - + -
416D PHE* 3.9 16.6 - - + +
417D ALA* 1.3 71.2 - - - +
419D ASP* 1.3 58.7 + - - +
421D ALA* 4.0 0.9 - - + +
436D ASP* 4.4 10.3 - - + +
440D LEU* 3.7 29.8 - - + -
448D ILE* 6.5 0.2 - - + -
473D ALA* 4.0 13.7 - - + -
474D VAL 2.9 12.8 + - - +
475D ARG* 3.2 13.6 - - + +
476D TYR* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D SER* 2.7 27.3 + - - -
349D GLY 3.4 6.9 - - - +
350D SER* 4.1 9.4 - - - +
391D ILE 3.2 6.5 + - - +
392D TYR* 3.2 17.1 - - + -
393D SER 3.0 21.7 + - - -
417D ALA 3.5 3.3 + - - +
418D ILE* 1.3 70.3 - - - +
420D ARG* 1.3 107.6 + - - +
421D ALA 3.1 3.4 + - - -
476D TYR* 3.3 32.5 + - + +
477D PRO 3.7 9.0 - - - +
----------------------------------------------------------
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