Contacts of the helix formed by residues 243 - 259 (chain A) in PDB entry 2BAP
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 VAL 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.6 34.3 - - - +
205A GLN* 5.5 1.6 - - - +
206A HIS* 5.0 6.1 - - + -
240A ASP* 3.3 16.9 + - - +
241A PRO 3.3 0.2 - - - -
242A ALA* 1.3 86.3 - - + +
244A PRO* 1.4 69.4 - - - +
245A ASN* 3.2 3.1 - - + +
246A MET* 2.8 55.2 + - + +
247A MET 3.5 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASP 4.7 2.2 - - - +
241A PRO 3.4 15.3 - - - +
242A ALA 3.5 5.4 - - - +
243A VAL* 1.4 85.9 - - - +
245A ASN* 1.3 61.5 + - - +
247A MET* 3.5 4.5 + - - +
248A ILE* 2.6 36.0 + - - +
297A THR* 6.6 0.4 - - - -
298A SER* 4.1 22.0 - - - +
301A LEU* 3.9 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS* 3.4 26.0 + - + +
210A ARG* 5.3 5.7 - - - +
243A VAL* 2.8 6.3 + - + +
244A PRO* 1.3 80.4 - - - +
246A MET* 1.3 64.8 + - - +
248A ILE* 3.2 14.4 - - - +
249A ASP* 3.0 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 5.8 0.7 - - - -
190A HIS* 6.1 0.9 - - - +
202A SER 4.6 2.9 - - - +
205A GLN* 3.8 33.7 - - - +
206A HIS* 3.6 38.7 + - + -
209A ILE* 3.8 22.6 - - + +
238A ALA* 3.9 26.7 - - + +
240A ASP* 4.3 4.3 - - - +
243A VAL* 2.8 43.5 + - + +
245A ASN* 1.3 70.3 - - - +
247A MET* 1.3 54.7 + - - +
249A ASP* 3.0 5.7 + - - +
250A ALA* 2.7 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ALA 3.8 2.0 + - - -
239A MET* 3.6 31.6 - - + +
240A ASP* 3.0 49.8 + - - +
241A PRO* 4.0 3.1 - - - -
243A VAL 3.5 2.2 + - - -
244A PRO 3.5 6.5 + - - +
246A MET* 1.3 77.6 - - - +
248A ILE* 1.3 55.0 + - - +
250A ALA* 3.0 1.5 + - - -
251A ALA* 2.7 40.0 + - + +
288A PRO* 3.5 34.5 - - + +
289A LEU* 4.0 16.6 - - + +
292A GLY* 5.3 2.5 - - - +
301A LEU* 4.1 17.3 - - + -
305A CYS* 4.7 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PRO* 2.6 34.8 + - + +
245A ASN* 3.2 15.5 - - - +
247A MET* 1.3 75.1 - - - +
249A ASP* 1.3 61.8 + - - +
251A ALA* 3.9 3.3 - - - +
252A LYS* 3.1 59.7 + - + +
298A SER* 4.2 5.2 - - - +
300A ALA* 3.9 11.7 - - + +
301A LEU* 3.2 48.4 - - + +
304A GLY* 5.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS* 3.9 21.0 - - + -
209A ILE* 4.1 14.9 - - + +
210A ARG* 4.8 11.0 + - - +
213A LYS* 3.5 35.3 + - - +
245A ASN 3.0 7.1 + - - +
246A MET 3.0 8.5 + - - +
248A ILE* 1.3 82.5 - - - +
250A ALA* 1.3 57.9 + - - +
252A LYS* 4.0 10.7 - - - +
253A LEU* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 4.2 7.8 - - + +
235A LEU* 3.5 26.9 - - - +
238A ALA* 3.7 15.3 - - + -
239A MET* 3.9 14.6 - - + +
246A MET 2.7 20.0 + - - +
247A MET 3.5 3.8 - - - +
249A ASP* 1.3 71.3 - - - +
251A ALA* 1.3 65.6 + - - +
253A LEU* 3.2 8.4 - - - +
254A LEU* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 3.7 16.4 - - + +
247A MET* 2.7 23.9 + - + +
248A ILE* 3.9 4.7 - - - +
250A ALA* 1.3 70.1 - - - +
252A LYS* 1.3 59.1 + - - +
254A LEU* 2.8 9.5 + - - +
255A SER* 2.8 29.0 + - - -
289A LEU* 5.6 2.0 - - + -
304A GLY* 3.5 27.8 - - - +
308A LEU* 4.0 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 5.8 6.3 - - + +
248A ILE* 3.1 47.2 - - + +
249A ASP* 4.0 12.3 - - - +
251A ALA* 1.3 75.7 - - - +
253A LEU* 1.3 63.2 + - - +
255A SER* 3.7 11.7 - - - -
256A ALA* 3.2 24.8 + - - +
300A ALA* 4.5 9.5 + - - +
303A VAL* 5.7 2.2 - - - +
304A GLY* 4.5 11.1 - - - +
307A GLN* 3.5 28.9 + - - +
1186C LEU* 3.6 28.5 - - + +
1189C LEU* 4.4 0.6 - - + +
1190C GLN* 5.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 3.7 39.7 - - + +
213A LYS* 3.8 20.2 - - + +
216A MET* 3.6 29.2 - - + +
235A LEU* 3.8 23.1 - - + -
249A ASP 3.0 17.7 + - - +
250A ALA* 3.2 7.4 + - - +
251A ALA 2.9 0.4 + - - -
252A LYS* 1.3 80.9 - - - +
254A LEU* 1.3 61.2 + - - +
256A ALA* 3.9 6.2 + - - +
257A LEU* 3.8 16.5 + - - +
1182C MET* 3.7 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 4.0 15.9 - - + +
235A LEU* 3.8 31.6 - - + -
236A VAL* 3.6 22.4 - - + -
239A MET* 2.7 35.7 - - + -
250A ALA 3.0 8.0 + - - +
251A ALA 2.8 7.6 + - - +
253A LEU* 1.3 73.9 - - - +
255A SER* 1.3 56.2 + - - +
256A ALA 3.1 1.8 - - - -
257A LEU* 2.6 45.0 + - + +
258A CYS* 3.2 8.1 + - - -
270A VAL* 4.2 25.2 - - + +
274A MET* 4.8 1.6 - - + -
308A LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA 2.8 22.1 + - - -
252A LYS* 3.7 8.7 - - - -
254A LEU* 1.3 71.5 - - - +
256A ALA* 1.3 60.9 - - - +
257A LEU 3.3 1.0 + - - -
258A CYS* 3.3 19.8 + - - +
259A ILE* 3.4 13.3 + - - +
304A GLY 5.0 0.2 + - - -
307A GLN* 4.0 2.0 + - - -
308A LEU* 3.2 32.7 + - - +
311A ALA* 3.7 17.7 - - - +
1189C LEU* 3.7 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LYS 3.2 13.8 + - - +
253A LEU 4.2 0.9 - - - +
254A LEU 3.0 1.0 + - - -
255A SER* 1.3 78.2 - - - +
257A LEU* 1.3 63.0 + - - +
259A ILE* 4.0 11.1 - - - +
260A LEU* 3.8 10.4 + - - +
1182C MET* 3.7 37.7 - - + +
1185C LEU* 3.5 35.7 - - + +
1186C LEU* 5.0 1.8 - - + -
1189C LEU* 4.7 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A MET* 5.2 7.4 - - - -
222A ILE* 4.3 25.1 - - + +
225A MET* 6.1 1.3 - - + -
226A LEU* 3.9 28.9 - - + -
232A ILE* 3.8 28.5 - - + -
235A LEU* 4.3 8.7 - - + -
253A LEU 3.8 16.8 - - - +
254A LEU* 2.6 28.3 + - + +
256A ALA* 1.3 71.1 - - - +
258A CYS* 1.3 67.4 + - - +
260A LEU* 2.8 29.3 + - + +
266A MET* 3.3 19.3 - - + +
270A VAL* 4.8 3.4 - - + -
1182C MET* 6.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 3.2 10.4 + - - -
255A SER* 3.4 10.1 - - - +
257A LEU* 1.3 78.0 - - - +
259A ILE* 1.3 55.3 + - - +
260A LEU 2.7 19.6 + - - +
266A MET* 3.9 15.1 + - - +
267A ASN* 4.2 9.0 + - + +
270A VAL* 4.0 17.5 - - - -
308A LEU* 4.7 1.3 - - - -
311A ALA* 3.2 38.8 - - + +
312A LEU* 3.6 26.9 - - - -
315A PRO* 4.5 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER 3.5 12.6 - - - +
256A ALA* 4.0 11.0 - - - +
257A LEU 3.3 0.2 - - - -
258A CYS* 1.3 77.5 - - + +
260A LEU* 1.3 60.2 + - - +
261A PRO* 3.5 9.7 - - - +
311A ALA* 4.3 21.3 - - + +
314A THR* 5.7 1.3 - - + -
315A PRO* 5.0 11.4 - - + -
1185C LEU* 3.9 31.6 - - + +
1188C ALA 4.4 1.1 - - - +
1189C LEU* 3.9 17.9 - - + -
1194C ALA* 3.8 42.8 - - + +
1195C PHE* 4.4 12.8 - - + -
----------------------------------------------------------
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