Contacts of the helix formed by residues 260 - 268 (chain E) in PDB entry 2W3S
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 HIS 260 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E TYR* 4.5 6.3 - + - -
255E PHE* 5.4 3.8 - + - -
256E ALA* 2.7 26.9 + - + +
259E PRO* 1.3 97.2 + - + +
261E PRO* 1.4 67.8 - - - +
262E ALA 3.2 3.1 - - - -
263E LEU* 2.9 26.2 + - + +
264E ALA 3.3 5.0 + - - -
301E MET* 3.5 32.3 - - + +
341E LEU* 4.6 11.3 - - + +
342E PRO* 2.8 30.0 + - + -
343E LYS 3.6 4.6 + - - -
344E SER 4.1 1.1 - - - -
345E ALA* 3.8 31.4 + - + +
348E LEU* 4.9 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 261 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E ALA 3.3 3.6 - - - +
257E GLU* 3.9 9.2 - - + +
258E GLY 3.2 17.3 - - - +
259E PRO 3.5 3.1 - - - +
260E HIS* 1.4 86.8 - - - +
262E ALA* 1.3 54.3 + - - +
264E ALA* 3.0 8.5 + - + +
265E GLY* 2.7 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E HIS 2.9 3.4 + - - -
261E PRO* 1.3 77.4 - - - +
263E LEU* 1.3 57.5 + - - +
265E GLY* 3.5 1.8 + - - -
266E LEU* 2.9 28.2 + - - +
348E LEU* 3.5 47.3 - - + +
349E ARG* 4.3 6.5 - - - +
350E CYS* 3.8 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E LEU* 3.9 27.6 - - + -
256E ALA* 3.9 16.8 - - + -
260E HIS* 2.9 11.7 + - + +
262E ALA* 1.3 75.8 - - - +
264E ALA* 1.3 56.4 + - - +
266E LEU* 2.9 10.4 + - + +
267E LEU* 2.7 54.5 + - + +
294E GLY* 5.4 2.2 - - - +
297E ALA* 3.7 28.3 - - + -
298E LEU* 4.4 13.5 - - + -
301E MET* 4.0 26.9 - - + -
341E LEU* 4.5 5.6 - - + -
348E LEU* 4.4 3.5 - - + +
350E CYS* 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E ARG* 3.3 31.0 + - - +
256E ALA* 3.7 7.3 - - + +
257E GLU* 3.6 50.9 - - + +
260E HIS 3.3 2.2 + - - +
261E PRO* 3.0 8.2 + - + +
263E LEU* 1.3 77.7 - - - +
265E GLY* 1.3 63.0 + - - +
268E ARG 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E PRO 2.7 19.0 + - - -
262E ALA* 3.8 2.2 - - - -
264E ALA* 1.3 70.8 - - - +
266E LEU* 1.3 63.4 + - - +
268E ARG* 3.3 24.3 + - - +
269E ARG* 4.0 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ALA 2.9 14.1 + - - +
263E LEU* 2.9 14.8 + - + +
265E GLY* 1.3 71.2 - - - +
267E LEU* 1.3 57.3 + - + +
268E ARG 2.8 4.7 + - - -
269E ARG* 2.8 33.8 + - + +
270E PHE* 4.4 1.0 - - + +
293E ASP* 3.3 40.8 - - + +
297E ALA* 3.5 24.0 - - + -
350E CYS* 3.6 24.4 - - + +
352E LYS* 4.2 28.3 - - + +
365E CYS* 4.6 8.3 - - - -
367E CYS* 4.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ILE* 3.7 36.1 - - + +
252E LEU* 3.6 36.8 - - + -
253E ARG* 3.8 18.8 - - + +
263E LEU* 2.7 40.6 + - + +
264E ALA 3.8 4.5 - - - +
266E LEU* 1.3 75.7 - - + +
268E ARG* 1.3 60.0 + - - +
269E ARG 3.2 0.4 - - - -
270E PHE* 3.2 30.5 - - + +
276E ARG* 3.1 26.0 + - - -
281E ILE* 6.0 0.2 - - + -
294E GLY* 5.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASP* 6.0 0.6 - - - +
127E ASP* 2.7 48.4 + - + +
253E ARG* 3.2 37.5 - - - +
264E ALA 3.1 5.4 + - - +
265E GLY* 3.3 18.0 + - - +
266E LEU 2.8 0.8 + - - -
267E LEU* 1.3 78.3 - - - +
269E ARG* 1.3 76.2 + - - +
270E PHE 3.3 0.4 - - - -
271E ALA 4.7 0.2 - - - +
276E ARG* 2.9 25.8 + - - +
358E ASP* 4.2 15.4 + - - +
458E LEU* 3.7 28.3 - - - +
----------------------------------------------------------
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