Contacts of the strand formed by residues 415 - 419 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B TRP* 4.0 20.4 - - + -
387B PRO 3.1 14.4 + - - +
388B ILE* 3.2 21.5 - - + +
389B VAL 2.8 27.0 + - - -
413B PRO 3.7 1.7 + - - +
414B VAL* 1.3 76.1 - - - +
416B PHE* 1.3 76.1 + - - +
417B ALA 4.8 0.2 - - - +
461B LEU* 3.7 27.6 - - + +
464B GLY* 4.0 15.0 - - - +
465B TYR* 3.9 11.2 - - + +
472B SER* 3.3 28.7 - - - +
474B VAL* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 3.9 27.4 - - + -
389B VAL* 3.5 24.7 - - + +
391B ILE* 4.8 0.9 - - + -
396B LEU* 4.4 14.4 - - + -
403B VAL* 3.8 36.6 - - + -
407B VAL* 4.2 15.5 - - + -
414B VAL* 3.8 26.0 - - + -
415B LEU* 1.3 78.5 - - - +
417B ALA* 1.3 60.7 + - - +
418B ILE* 3.5 13.0 + - + -
440B LEU* 6.4 0.2 - - + -
446B MSE 4.9 4.0 - - - -
471B PRO* 4.2 6.5 - - + -
472B SER 2.9 23.9 + - - +
473B ALA* 3.4 12.9 - - + +
474B VAL* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PHE* 3.4 39.9 - - + -
388B ILE* 4.4 5.8 - - + +
389B VAL 2.9 12.0 + - - +
390B ALA* 3.5 2.6 - - - -
391B ILE 3.1 23.7 + - - +
415B LEU* 4.0 2.0 + - + -
416B PHE* 1.3 70.1 - - - +
418B ILE* 1.3 58.8 + - - +
419B ASP* 3.4 3.9 + - - +
461B LEU* 4.8 5.6 - - + -
474B VAL* 3.7 7.4 - - - -
476B TYR* 3.6 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 3.2 7.6 - - + +
392B TYR 4.3 0.2 - - - -
393B SER* 3.5 40.4 - - - +
396B LEU* 3.5 28.9 - - + -
416B PHE* 4.0 13.9 - - + +
417B ALA* 1.3 70.5 - - - +
419B ASP* 1.3 57.8 + - - +
421B ALA* 4.1 1.6 - - + +
436B ASP* 3.5 24.7 - - - +
440B LEU* 3.7 13.7 - - + -
448B ILE* 6.4 0.2 - - + -
473B ALA* 4.0 15.3 - - + -
474B VAL 2.9 12.1 + - - +
475B ARG* 3.9 8.5 - - + -
476B TYR* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B SER* 2.6 26.6 + - - -
349B GLY 3.8 4.9 - - - +
350B SER* 3.8 13.5 - - - +
391B ILE 3.0 8.1 + - - +
392B TYR* 3.4 17.4 - - + -
393B SER 3.1 18.9 + - - -
417B ALA 3.4 2.7 + - - +
418B ILE* 1.3 71.3 - - - +
420B ARG* 1.3 112.4 + - - +
421B ALA 3.1 3.6 + - - -
476B TYR* 3.4 30.8 + - + +
477B PRO 4.0 6.1 - - - +
----------------------------------------------------------
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