Contacts of the helix formed by residues 293 - 301 (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 ASP 293 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E LEU* 3.3 34.7 - - + +
267E LEU* 5.6 0.2 - - - -
270E PHE* 3.7 18.6 - - + -
291E ILE 3.9 5.9 - - - +
292E GLY* 1.3 71.4 - - - -
294E GLY* 1.3 63.1 + - - +
296E PRO* 3.9 7.7 - - - +
297E ALA* 3.9 1.2 + - - +
352E LYS* 3.1 25.6 + - - +
361E ILE* 5.2 0.5 - - - +
362E SER* 2.6 28.5 + - - -
365E CYS* 3.6 18.1 - - - +
1465E FAD 2.7 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 294 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E LEU* 5.8 1.6 - - - -
266E LEU* 5.5 0.2 - - - -
267E LEU* 5.3 6.3 - - - -
270E PHE* 3.9 6.7 - - - -
281E ILE* 5.2 11.7 - - - -
284E ASN* 3.1 15.6 + - - -
285E ILE* 5.8 0.4 - - - -
293E ASP* 1.3 76.6 - - - +
295E PRO* 1.4 71.4 - - - +
297E ALA* 3.0 20.9 + - - +
298E LEU* 3.3 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 295 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E ASN* 3.5 15.7 - - - +
285E ILE* 4.6 14.8 - - + -
289E SER 5.3 1.8 - - - +
292E GLY* 3.6 13.5 - - - +
294E GLY* 1.4 85.6 - - - +
296E PRO* 1.3 71.4 - - + +
297E ALA 3.0 0.5 + - - -
298E LEU* 3.0 2.8 + - + -
299E ILE* 2.8 32.5 + - + +
318E LEU* 3.6 11.5 - - + +
322E PHE* 3.7 27.4 - - + -
391E PRO* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 296 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E GLY 3.2 23.6 - - - +
293E ASP 3.9 4.0 - - - +
294E GLY 3.6 2.0 - - - -
295E PRO* 1.3 86.8 - - + +
297E ALA* 1.3 64.3 + - - +
299E ILE* 3.3 4.6 + - + -
300E ALA 2.9 20.4 + - - -
365E CYS* 4.5 10.5 - - - +
367E CYS* 3.5 22.3 - - + +
383E ALA* 3.5 19.6 - - + +
384E PHE 4.0 4.0 - - - +
385E GLY* 3.6 35.2 - - - +
391E PRO* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E LEU* 3.7 20.0 - - + -
266E LEU* 3.5 29.4 - - + -
293E ASP 4.1 0.4 + - - -
294E GLY 3.0 10.8 + - - +
295E PRO 3.0 0.2 + - - -
296E PRO* 1.3 81.8 - - - +
298E LEU* 1.3 64.0 + - - +
300E ALA* 3.3 4.3 + - - +
301E MET* 3.3 21.0 + - - +
348E LEU* 3.9 5.4 - - + +
350E CYS* 4.4 7.0 - - - -
367E CYS* 3.3 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E LEU* 5.6 5.4 - - + -
263E LEU* 4.4 17.5 - - + -
281E ILE* 5.1 8.5 - - + -
285E ILE* 4.2 20.2 - - + -
294E GLY* 3.3 16.1 + - - +
295E PRO 3.0 1.0 + - - -
297E ALA* 1.3 75.0 - - - +
299E ILE* 1.3 66.4 + - - +
301E MET* 2.8 32.4 + - + -
302E GLY 3.1 0.2 + - - -
303E ALA* 3.1 28.1 + - + -
318E LEU* 3.3 24.0 - - + -
339E VAL* 4.3 12.8 - - + -
341E LEU* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E PRO* 2.8 42.2 + - + +
296E PRO* 3.8 5.8 - - + +
298E LEU* 1.3 70.4 - - - +
300E ALA* 1.3 59.9 + - - +
302E GLY* 3.1 3.5 + - - -
303E ALA 4.8 2.7 - - - +
318E LEU* 3.7 15.0 - - + -
319E GLU* 3.7 41.1 - - + +
322E PHE* 4.7 2.0 - - + -
381E ARG* 2.6 31.2 + - - +
383E ALA* 4.0 10.1 - - + -
391E PRO* 3.9 26.2 - - + +
392E LYS 5.5 0.2 - - - -
393E ARG* 3.8 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E PRO 2.9 7.5 + - - +
297E ALA 3.6 3.4 - - - +
299E ILE* 1.3 75.8 - - - +
301E MET* 1.3 58.2 + - - +
302E GLY 3.2 0.2 - - - -
348E LEU* 3.6 11.2 - - + -
367E CYS* 3.5 44.4 - - + +
369E ASN* 3.1 15.6 + - + +
381E ARG* 2.9 34.3 - - - +
383E ALA* 4.0 5.3 - - + +
393E ARG* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 301 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E HIS* 3.5 35.4 - - + +
263E LEU* 4.0 24.5 - - + -
297E ALA 3.3 10.0 + - - +
298E LEU* 2.8 23.3 + - + +
300E ALA* 1.3 75.8 - - - +
302E GLY* 1.3 61.6 + - - +
303E ALA* 3.2 2.1 + - + +
341E LEU* 3.8 36.3 - - + -
342E PRO* 3.2 24.8 - - - +
345E ALA* 4.0 13.2 - - + -
348E LEU* 3.8 28.3 - - + -
369E ASN* 3.7 8.3 - - - +
381E ARG* 4.3 0.9 - - - -
----------------------------------------------------------
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