Contacts of the helix formed by residues 352 - 359 (chain C) 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 MSE 352 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C PHE* 4.2 2.7 - - + -
326C GLY* 5.3 0.2 - - - -
329C LEU* 3.9 18.8 - - + -
341C ALA* 3.3 40.4 - - + -
342C ILE 4.1 5.4 - - - +
343C THR* 4.0 16.4 - - - -
347C ARG* 2.8 26.4 + - + +
350C SER* 3.8 13.7 - - - +
351C GLY* 1.3 76.0 - - - +
353C VAL* 1.3 65.1 + - - +
354C GLU 3.5 1.8 - - - -
355C PHE* 3.4 10.5 + - + -
356C SER* 2.9 24.4 + - - -
363C TYR* 3.7 22.2 - - + -
390C ALA* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ARG* 4.0 26.9 - - - +
348C GLU* 4.0 32.3 - - + +
351C GLY* 3.6 2.6 - - - -
352C MSE 1.3 75.0 - - - +
354C GLU* 1.3 66.0 + - - +
356C SER* 2.8 23.5 + - - -
357C ARG* 3.2 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LYS* 5.4 5.9 + - - -
326C GLY 6.4 0.9 - - - -
327C ASP* 4.6 13.8 - - - +
330C CYS* 3.8 15.7 - - - +
351C GLY 5.2 1.9 + - - +
352C MSE 4.6 0.2 - - - +
353C VAL* 1.3 80.7 - - - +
355C PHE* 1.3 63.1 + - - +
357C ARG* 3.3 11.0 + - - +
358C LYS* 2.7 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C GLY 4.7 2.0 - - - +
329C LEU* 3.8 29.2 - - + -
330C CYS* 3.6 16.2 - - - -
333C ALA* 3.9 14.4 - - + -
339C LEU* 3.8 12.8 - - + -
341C ALA* 3.4 25.8 - - + -
351C GLY 5.4 0.8 + - - +
352C MSE 3.4 23.8 + - + +
353C VAL 3.1 0.8 - - - -
354C GLU* 1.3 80.0 - - - +
356C SER* 1.3 59.6 + - - +
358C LYS 4.6 0.2 - - - +
359C PHE* 2.8 56.8 + + + +
362C ARG* 3.6 22.4 - - + -
363C TYR* 3.5 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ARG* 2.9 36.0 + - - -
352C MSE 2.9 13.3 + - - -
353C VAL 2.8 16.6 + - - -
355C PHE* 1.3 77.3 - - - +
357C ARG* 1.3 58.0 + - - +
360C PRO* 3.2 28.3 - - - +
363C TYR* 3.6 36.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ARG* 4.5 8.8 - - - +
353C VAL* 3.2 40.4 + - - +
354C GLU* 3.7 10.9 - - - +
355C PHE 3.1 0.6 - - - -
356C SER* 1.3 85.1 + - - +
358C LYS* 1.3 65.0 + - + +
360C PRO* 3.3 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C CYS* 4.5 13.6 - - + +
354C GLU* 2.7 51.4 + - + +
357C ARG* 1.3 78.3 - - + +
359C PHE* 1.3 88.7 + - + +
360C PRO* 3.2 8.1 - - - +
361C ASP* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C CYS* 3.5 26.5 - - + -
333C ALA* 3.8 20.0 - - + -
334C ALA* 3.5 28.0 - - + -
355C PHE* 2.8 43.5 + + + +
358C LYS* 1.3 104.1 - - + +
360C PRO* 1.3 52.5 - - - +
361C ASP* 3.0 11.7 - - - -
362C ARG* 2.8 47.2 + - + -
363C TYR* 3.2 12.5 + - - +
----------------------------------------------------------
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