Contacts of the helix formed by residues 235 - 250 (chain B) 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 GLY 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLN* 3.5 14.1 + - - +
181B ALA* 5.4 0.5 - - - +
194B CYS* 6.4 0.7 - - - -
195B SER 5.3 3.1 - - - -
196B SER* 5.2 9.2 - - - -
202B ILE* 3.9 12.4 - - - +
230B GLY 4.9 0.4 + - - -
231B LYS* 4.9 4.8 + - - +
233B SER 2.9 3.2 + - - +
234B GLN* 1.3 78.4 - - - +
236B ASN* 1.3 65.0 + - - +
237B HIS 3.4 0.2 - - - -
238B LEU* 3.4 9.9 + - - +
239B ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 3.1 34.5 - - + +
198B HIS* 6.3 0.4 - - - +
201B GLU* 3.8 19.4 - - - +
202B ILE* 3.6 23.8 - - - +
205B LYS* 3.1 28.3 - - - +
232B GLU 5.5 0.2 + - - -
233B SER* 2.8 26.6 + - - +
234B GLN 3.2 0.2 - - - -
235B GLY* 1.3 76.5 - - - +
237B HIS* 1.3 63.2 - - - +
239B ALA* 3.4 1.7 + - - +
240B ILE* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.8 9.7 - - + -
76B ALA* 3.4 25.6 - - + +
83B GLU* 3.7 23.9 + - - +
84B PRO 4.1 8.8 + - - -
85B VAL* 3.8 40.8 - - + +
97B PRO* 5.1 11.4 - - + -
233B SER 5.4 0.7 - - - -
234B GLN* 4.1 22.7 + - - +
235B GLY 3.4 0.4 - - - -
236B ASN* 1.3 76.2 - - + +
238B LEU* 1.3 57.9 + - - +
241B ALA* 3.0 28.9 + - - +
257B TYR* 3.8 18.4 - - - +
265B ILE* 5.7 5.4 - - + +
299B TRP* 5.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLN* 3.7 21.1 - - + +
180B ALA* 3.5 20.2 - - - +
181B ALA* 4.1 13.0 - - + +
234B GLN 3.4 24.0 - - - +
235B GLY* 3.7 7.0 - - - +
236B ASN 3.3 0.2 - - - -
237B HIS* 1.3 75.1 - - - +
239B ALA* 1.3 61.1 + - - +
241B ALA* 3.2 4.0 + - - +
242B CYS* 2.9 33.3 + - - -
255B MET* 3.3 44.1 - - + +
257B TYR* 3.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ALA* 4.1 12.3 - - + +
192B ILE* 4.3 12.7 - - + +
194B CYS* 5.3 0.4 - - + -
202B ILE* 3.7 23.3 - - + -
206B VAL* 3.7 21.1 - - + +
235B GLY 3.2 13.9 + - - +
236B ASN* 4.0 2.7 - - - +
238B LEU* 1.3 75.1 - - - +
240B ILE* 1.3 66.1 + - - +
242B CYS* 3.1 4.9 + - - +
243B ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.4 6.5 - - + -
73B ASP 5.6 1.1 - - - +
74B ASN* 6.3 0.2 - - - -
75B ASP 3.8 17.7 - - - +
76B ALA* 3.9 8.1 - - + -
85B VAL* 3.8 35.0 - - + -
205B LYS* 4.0 35.4 - - + +
206B VAL* 3.9 6.0 - - + +
209B ALA* 3.7 20.4 - - + -
236B ASN 3.0 21.9 + - - +
237B HIS 4.1 3.1 - - - +
239B ALA* 1.3 76.3 - - - +
241B ALA* 1.3 59.7 + - - +
243B ALA* 3.1 2.2 + - - -
244B VAL* 2.8 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.3 8.2 - - + +
37B PHE* 4.1 7.9 - - + -
85B VAL* 5.0 2.0 - - + +
100B LEU* 3.7 19.9 - - + +
237B HIS 3.0 20.5 + - - +
238B LEU 3.2 5.4 + - - +
240B ILE* 1.3 75.7 - - - +
242B CYS* 1.3 62.5 + - - +
244B VAL* 4.9 1.8 - - - -
245B ALA* 3.1 27.5 + - - +
255B MET* 3.7 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.8 6.7 - - - -
181B ALA* 3.6 26.7 - - + -
182B LEU 4.6 0.9 - - - +
183B ALA* 3.5 19.5 - - + +
192B ILE* 5.5 0.7 - - + -
238B LEU 2.9 19.9 + - - +
239B ALA* 3.6 8.5 - - - +
241B ALA* 1.3 71.9 - - - +
243B ALA* 1.3 53.3 + - - +
245B ALA 3.6 0.5 - - - -
246B ALA* 2.8 36.6 + - - +
253B CYS* 3.3 24.9 - - - +
254B LYS 4.0 1.3 - - - -
255B MET* 3.7 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ALA* 3.8 9.1 - - - +
190B VAL* 5.0 2.7 - - + -
192B ILE* 4.3 5.8 - - + -
206B VAL* 3.6 30.3 - - + +
209B ALA* 5.6 0.4 - - + -
210B LEU* 3.8 19.6 - - + +
239B ALA 2.9 16.6 + - - +
240B ILE* 3.6 4.0 - - - +
242B CYS* 1.3 75.3 - - - +
244B VAL* 1.3 66.0 + - + +
246B ALA* 2.9 4.6 + - - +
247B ARG* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.7 15.0 - - + -
69B ASP 4.7 0.9 - - - +
70B LEU* 3.5 31.6 - - + -
71B PRO* 3.7 23.4 - - + +
73B ASP 5.9 0.7 - - - +
100B LEU* 5.7 2.9 - - + -
209B ALA* 4.1 17.9 - - + +
210B LEU* 4.2 9.2 - - + -
240B ILE* 2.8 39.5 + - + +
241B ALA* 4.2 4.0 - - - +
243B ALA* 1.3 72.0 - - - +
245B ALA* 1.3 62.8 + - - +
247B ARG* 3.3 4.8 + - - +
248B ALA* 3.1 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.9 16.8 - - + -
65B PHE* 3.9 28.3 - - + -
100B LEU* 4.2 3.8 - - + +
102B ALA* 4.8 1.8 - - + -
241B ALA 3.1 20.6 + - - +
242B CYS 3.8 0.7 - - - +
244B VAL* 1.3 76.5 - - - +
246B ALA* 1.3 50.5 + - - +
249B THR* 2.6 42.3 + - - +
253B CYS* 3.6 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ALA* 4.3 11.0 - - + +
185B PRO* 4.0 26.1 - - + +
190B VAL* 5.5 2.5 - - + -
242B CYS 2.8 22.8 + - - +
243B ALA* 2.9 5.1 + - - +
245B ALA* 1.3 70.6 - - - +
247B ARG* 1.3 60.8 + - - +
249B THR* 3.4 0.2 + - - -
250B GLY* 2.9 33.8 + - - -
251B ARG 3.5 19.5 - - - +
253B CYS* 3.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO* 3.1 39.2 - - - +
72B HIS* 4.5 9.5 - - - -
185B PRO* 5.8 1.1 - - - +
210B LEU* 3.4 37.6 + - + -
243B ALA 2.9 10.0 + - - +
244B VAL 3.4 9.8 + - - +
246B ALA* 1.3 77.5 - - - +
248B ALA* 1.3 63.4 + - - +
250B GLY* 4.2 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.7 34.8 - - + -
244B VAL* 3.1 10.2 + - + +
246B ALA 3.1 0.6 - - - -
247B ARG* 1.3 84.5 - - + +
249B THR* 1.3 65.6 + - + +
250B GLY 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.3 31.2 - - + -
62B ILE* 4.7 6.7 - - + -
63B ALA* 4.3 22.9 - - + -
65B PHE* 4.7 2.5 - - + -
102B ALA* 4.5 5.2 - - + -
245B ALA 2.6 27.9 + - - +
246B ALA* 3.4 0.5 + - - -
248B ALA* 1.3 74.0 - - + +
250B GLY* 1.3 58.6 + - - +
251B ARG* 3.1 33.8 + - - +
253B CYS* 3.7 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 5.3 1.3 + - - -
185B PRO* 3.8 15.3 - - - +
246B ALA 2.9 14.7 + - - -
247B ARG 4.2 3.1 + - - -
248B ALA 3.2 4.5 + - - -
249B THR* 1.3 75.7 - - - +
251B ARG* 1.3 59.0 + - - +
252B PRO* 4.6 0.5 - - - +
----------------------------------------------------------
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