Contacts of the helix formed by residues 242 - 253 (chain E) in PDB entry 1CSE
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 SER 242 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E LEU* 5.7 0.2 - - - -
240E ASN 3.6 2.0 + - - -
241E LEU* 1.3 78.3 - - - +
243E ALA* 1.3 65.9 + - - +
244E SER* 3.6 8.4 + - - -
245E GLN* 3.1 35.4 + - - +
246E VAL* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E TYR* 4.0 17.7 - - + +
146E GLY* 3.7 38.5 + - - +
147E VAL 3.8 17.0 - - - +
148E VAL* 3.9 15.2 - - + +
242E SER* 1.3 75.8 - - - +
244E SER* 1.3 57.8 + - - +
246E VAL* 3.4 3.6 + - - +
247E ARG* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E TYR* 3.6 23.6 + - - -
242E SER* 3.1 8.4 + - - -
243E ALA* 1.3 77.1 - - - +
245E GLN* 1.3 60.8 + - - +
247E ARG* 3.3 1.1 + - - +
248E ASN* 2.7 50.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E ASN 4.7 0.9 - - - +
241E LEU* 3.7 24.3 - - + +
242E SER* 3.1 35.4 + - - +
244E SER* 1.3 76.6 - - - +
246E VAL* 1.3 61.3 + - - +
248E ASN* 3.4 5.1 + - - +
249E ARG* 2.9 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E VAL* 4.0 9.9 - - + -
231E ALA* 3.7 39.0 - - + +
234E ILE* 4.3 13.1 - - + +
235E LEU* 3.6 32.8 - - + -
241E LEU* 3.8 10.1 - - + -
242E SER 3.0 16.1 + - - +
243E ALA* 3.6 8.1 - - - +
245E GLN* 1.3 75.4 - - - +
247E ARG* 1.3 65.6 + - - +
249E ARG* 3.2 11.4 + - - +
250E LEU* 3.1 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E TYR* 3.3 38.3 + - + -
148E VAL* 5.0 3.6 - - + -
172E ASP* 2.9 29.9 + - - +
173E SER 3.7 9.3 - - - -
174E VAL 3.4 13.8 + - - -
175E ILE* 3.7 29.2 - - + +
197E GLU* 2.7 41.6 + - - +
243E ALA 2.9 17.7 + - - +
244E SER 3.6 4.5 - - - +
245E GLN 3.2 0.2 - - - -
246E VAL* 1.3 81.0 - - - +
248E ASN* 1.3 69.0 + - - +
250E LEU* 3.1 14.0 + - - +
251E SER* 3.2 15.7 + - - +
401E CA 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E TYR* 5.1 0.8 + - - -
244E SER* 2.7 43.1 + - - +
245E GLN* 4.1 4.5 - - - +
247E ARG* 1.3 81.6 - - - +
249E ARG* 1.3 55.4 + - - +
251E SER* 3.6 9.7 + - - -
252E SER* 2.8 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ILE* 4.1 9.6 - - + -
238E HIS* 3.7 22.7 + - - -
241E LEU* 3.7 36.1 - - - +
245E GLN* 2.9 29.1 + - + +
246E VAL 3.7 4.5 - - - +
247E ARG 3.2 0.2 - - - -
248E ASN* 1.3 75.9 - - - +
250E LEU* 1.3 64.5 + - - +
252E SER* 3.9 4.9 - - - -
253E THR* 2.7 32.9 + - + +
273E ALA* 2.8 36.0 + - + +
275E GLN* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ILE* 4.7 11.9 - - + -
198E VAL* 4.4 4.0 - - + -
227E VAL* 4.0 22.2 - - + +
230E ALA* 3.8 22.0 - - + -
231E ALA* 4.1 30.1 - - + +
234E ILE* 3.8 15.0 - - + -
246E VAL* 3.1 15.8 + - + +
247E ARG* 3.1 9.9 + - - +
249E ARG* 1.3 80.8 - - - +
251E SER* 1.3 61.8 + - - +
253E THR* 3.9 1.7 + - - -
254E ALA* 3.6 19.1 + - - +
268E ILE* 4.0 33.8 - - + +
269E ASN 5.2 0.7 + - - +
270E VAL* 5.2 2.9 - - + -
273E ALA* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E GLU* 4.3 17.0 + - - -
198E VAL* 3.7 22.7 - - - -
247E ARG* 3.2 13.6 + - - +
248E ASN* 3.6 13.3 + - - -
250E LEU* 1.3 80.9 - - - +
252E SER* 1.4 68.5 + - - +
253E THR 3.4 0.3 + - - -
254E ALA* 3.4 6.1 + - - -
265E LYS* 3.1 43.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E ASN* 2.8 26.6 + - - -
249E ARG* 3.7 3.6 + - - -
251E SER* 1.4 82.2 + - - +
253E THR* 1.3 71.2 + - - +
254E ALA 3.4 2.4 + - - +
265E LYS* 5.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ARG* 2.7 25.4 + - + +
250E LEU 3.9 2.5 + - - -
251E SER 3.3 0.2 - - - -
252E SER* 1.3 85.3 - - - +
254E ALA* 1.3 65.6 + - - +
255E THR* 3.7 1.0 + - - -
269E ASN* 3.8 18.7 + - - +
272E ALA* 3.7 22.0 - - - +
273E ALA* 3.4 17.6 + - - +
275E GLN* 3.7 26.5 - - - +
----------------------------------------------------------
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