Contacts of the helix formed by residues 238 - 261 (chain A) in PDB entry 2PFV
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 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.8 2.3 - - - +
220A PHE* 3.2 35.4 + - - +
221A ALA* 3.5 8.9 + - - +
237A SER* 1.3 72.3 + - - +
239A MET* 1.3 57.7 + - - +
240A ASN 3.3 0.9 - - - -
241A SER* 3.6 11.0 + - - -
242A TYR* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 4.0 3.4 - - + +
237A SER* 3.1 15.9 + - - +
238A GLY* 1.3 77.1 - - - +
240A ASN* 1.3 60.3 + - - +
242A TYR* 3.8 10.8 - - - -
243A THR* 2.6 47.2 + - - +
283A TYR* 4.4 9.0 - - + -
286A LEU* 3.7 22.7 - - + -
287A PHE* 3.4 42.2 - - + +
290A ASN* 3.6 28.7 - - - +
304A PHE* 4.6 5.2 - - + -
308A LEU* 4.1 17.3 - - + -
311A SER* 4.1 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLY* 3.8 25.2 - - - +
237A SER* 3.7 11.7 + - - +
238A GLY 3.3 0.4 - - - -
239A MET* 1.3 84.0 - - - +
241A SER* 1.3 57.8 + - - +
243A THR* 3.6 4.8 - - - +
244A GLU* 2.9 27.0 + - - +
304A PHE* 6.0 0.4 - - - -
307A GLU* 4.0 29.5 + - - +
310A GLU* 4.6 12.3 + - - +
311A SER* 5.6 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLN* 3.4 29.7 + - - -
165A ILE* 3.6 12.8 - - - +
217A LEU* 4.3 9.0 - - - +
220A PHE* 6.1 0.2 - - - +
237A SER 4.7 0.9 + - - -
238A GLY* 3.6 15.6 + - - -
240A ASN* 1.3 76.6 - - - +
242A TYR* 1.3 57.4 + - - +
244A GLU* 3.4 12.7 - - - +
245A ALA* 2.7 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 3.4 33.2 - - + +
217A LEU* 3.7 35.9 - - + -
218A GLU* 4.2 18.1 - - + +
221A ALA* 4.1 0.4 - - + -
238A GLY 2.8 24.0 + - - +
239A MET* 3.6 10.1 - - - +
241A SER* 1.3 77.9 + - - +
243A THR* 1.3 59.0 + - - +
245A ALA* 3.0 5.5 + - - +
246A LEU* 2.9 29.8 + - + +
279A LEU 4.7 1.6 + - - -
282A ALA* 4.2 10.0 + - - +
283A TYR* 3.7 49.5 + + + +
286A LEU* 3.9 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 2.6 28.2 + - - +
240A ASN* 3.6 5.8 - - - -
242A TYR* 1.3 77.6 - - - +
244A GLU* 1.3 63.4 + - - +
246A LEU* 3.2 6.9 + - - +
247A LEU* 3.0 40.5 + - + +
283A TYR* 3.7 10.1 - - - -
311A SER* 2.7 47.8 + - - +
314A ASP* 4.4 5.2 - - + +
315A VAL* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 3.1 43.1 - - + +
171A PHE* 5.4 0.5 - - - -
240A ASN 2.9 14.9 + - - +
241A SER* 3.4 13.0 - - - +
243A THR* 1.3 76.9 - - - +
245A ALA* 1.3 62.7 + - - +
247A LEU* 3.1 14.5 + - + +
248A GLY* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PRO* 3.8 17.3 - - + -
165A ILE* 4.1 6.9 - - + +
171A PHE* 3.8 8.7 - - - -
214A MET* 4.0 8.3 - - - -
217A LEU* 3.5 23.6 - - + -
241A SER 2.7 16.6 + - - +
242A TYR 3.0 9.8 + - - +
244A GLU* 1.3 73.7 - - - +
246A LEU* 1.3 62.5 + - - +
248A GLY* 3.0 11.3 + - - -
249A PHE* 3.1 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 4.2 18.1 - - + +
242A TYR* 2.9 15.8 + - + +
243A THR* 3.5 9.0 - - - +
245A ALA* 1.3 76.8 - - - +
247A LEU* 1.3 57.7 + - + +
249A PHE* 3.3 3.3 + - + +
250A ILE* 2.9 55.9 + - + +
279A LEU* 3.9 34.1 - - + +
280A ILE* 4.5 8.7 - - + -
283A TYR* 3.7 42.0 - - + -
315A VAL* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.0 27.5 + - + +
244A GLU* 3.1 13.0 + - + +
246A LEU* 1.3 76.4 - - - +
248A GLY* 1.3 61.3 + - - +
250A ILE* 3.9 7.2 - - + +
251A ALA* 3.2 24.8 + - - +
314A ASP* 3.6 44.9 - - + +
315A VAL* 3.7 23.8 - - + +
318A SER* 3.7 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.8 17.3 - - - -
244A GLU 3.0 8.6 + - - -
245A ALA 3.0 8.2 + - - -
247A LEU* 1.3 76.9 - - - +
249A PHE* 1.3 58.6 + - - +
251A ALA* 4.0 2.7 - - - +
252A ASN* 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.9 18.2 - + - -
161A PRO* 3.9 11.0 - - + -
171A PHE* 3.9 19.5 - + + -
206A ARG* 5.2 3.6 - - - -
209A LEU* 6.0 0.4 - - + -
210A ILE* 3.5 44.9 - - + -
213A CYS* 3.4 35.9 - - + -
214A MET* 3.6 28.9 - - - -
245A ALA 3.1 21.3 + - - -
246A LEU* 3.8 6.5 - - - +
248A GLY* 1.3 74.3 - - - +
250A ILE* 1.3 60.6 + - - +
252A ASN* 3.7 5.4 - - + +
253A GLU* 2.8 35.6 + - - +
276A LEU* 5.0 1.3 - - - -
279A LEU* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 2.9 50.4 + - + +
247A LEU* 3.9 8.5 - - + +
249A PHE* 1.3 76.0 - - - +
251A ALA* 1.3 61.8 + - - +
253A GLU* 3.9 2.4 - - - +
254A LYS* 3.3 21.0 + - - +
276A LEU* 4.0 25.7 - - + +
279A LEU* 5.3 0.2 - - + -
280A ILE* 4.7 4.3 - - + -
315A VAL* 4.7 5.2 - - + -
318A SER* 3.4 43.5 - - - +
319A LEU* 4.2 19.7 - - + -
322A LYS* 4.0 13.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
247A LEU 3.2 16.2 + - - +
248A GLY* 4.0 3.8 - - - +
250A ILE* 1.3 81.1 - - - +
252A ASN* 1.3 66.8 + - - +
254A LYS* 3.4 8.2 + - - +
255A SER* 3.2 23.9 + - - -
318A SER* 6.5 0.9 - - - -
322A LYS* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.3 34.5 + - + +
173A TYR* 4.2 14.5 - - + -
206A ARG* 5.9 2.5 - - - +
248A GLY* 2.9 26.7 + - - +
249A PHE* 3.2 7.8 + - + +
251A ALA* 1.3 80.4 - - - +
253A GLU* 1.3 62.7 + - - +
255A SER* 3.4 8.8 + - - -
256A LEU* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 2.9 46.4 + - - +
210A ILE* 4.4 5.8 - - - +
249A PHE* 2.8 21.7 + - - +
250A ILE 3.9 2.5 - - - +
252A ASN* 1.3 72.2 - - - +
254A LYS* 1.3 61.0 + - - +
256A LEU* 3.1 12.0 + - - +
257A VAL* 2.9 34.3 + - + +
272A LEU* 3.7 19.3 - - + -
275A ILE* 3.2 50.3 - - + +
276A LEU* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE 3.3 12.1 + - - +
251A ALA* 3.6 10.3 - - - +
252A ASN 3.3 0.2 - - - -
253A GLU* 1.3 80.0 - - - +
255A SER* 1.3 57.6 + - - +
257A VAL* 3.4 3.0 + - + +
258A ASP* 2.9 66.4 + - - +
268A LYS* 4.7 7.9 - - - +
272A LEU* 3.7 23.8 - - + +
322A LYS* 3.8 26.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
173A TYR* 3.5 10.8 - - - -
251A ALA 3.2 11.9 + - - -
252A ASN* 3.6 12.2 + - - -
253A GLU 3.2 0.4 - - - -
254A LYS* 1.3 79.6 - - - +
256A LEU* 1.3 57.7 + - - +
258A ASP* 3.4 7.5 + - - +
259A ASP* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 5.7 0.2 - - + -
173A TYR* 3.2 16.1 + - + +
174A TYR* 4.0 18.6 - - + -
179A LEU* 3.7 27.8 - - + -
182A LEU* 5.3 0.2 - - + -
202A LEU* 5.2 2.7 - - + -
206A ARG* 3.7 40.8 - - + +
252A ASN 3.0 14.0 + - - +
253A GLU* 3.1 18.8 + - - +
255A SER* 1.3 77.2 - - - +
257A VAL* 1.3 61.4 + - + +
259A ASP* 3.1 1.9 + - - +
260A LEU* 2.9 49.5 + - + +
275A ILE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 6.2 0.7 - - + -
253A GLU* 2.9 19.6 + - + +
254A LYS* 3.9 5.4 - - + +
256A LEU* 1.3 77.2 - - + +
258A ASP* 1.3 68.9 + - - +
260A LEU* 3.3 4.7 + - + +
261A TYR* 3.2 34.9 + - + -
268A LYS* 3.7 44.0 - - + +
271A VAL* 4.3 19.5 - - + -
272A LEU* 4.0 22.9 - - + -
275A ILE* 4.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LYS* 2.9 61.7 + - - +
255A SER* 3.8 7.5 - - - +
257A VAL* 1.3 78.7 - - - +
259A ASP* 1.3 63.0 + - - +
261A TYR 3.4 15.1 - - - +
263A GLN* 5.5 4.9 - - - +
268A LYS* 3.2 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 2.5 34.1 + - - +
179A LEU* 4.3 22.7 - - + +
183A SER* 3.9 5.0 + - - -
255A SER* 2.9 20.6 + - - +
256A LEU* 3.5 4.7 - - - +
257A VAL 3.1 0.2 - - - -
258A ASP* 1.3 82.1 - - - +
260A LEU* 1.3 61.5 + - - +
261A TYR 3.7 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 6.3 0.4 - - + -
179A LEU* 3.9 14.1 - - + +
182A LEU* 3.5 39.7 - - + -
183A SER* 2.7 35.9 + - - +
186A LEU* 4.1 8.9 - - + +
187A ASP* 6.1 0.3 - - - -
202A LEU* 4.2 32.8 - - + -
256A LEU* 2.9 41.7 + - + +
257A VAL* 3.3 6.0 + - + +
259A ASP* 1.3 78.4 - - - +
261A TYR* 1.3 73.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.5 32.2 - - + +
187A ASP* 6.0 1.8 - - - -
190A HIS* 4.1 19.9 + + - -
199A GLN* 4.3 6.1 - - - +
202A LEU* 3.5 22.6 - - + +
257A VAL* 3.2 32.9 + - + -
258A ASP 3.4 16.3 - - - +
259A ASP 4.4 2.5 - - - +
260A LEU* 1.3 87.0 - - + +
262A SER* 1.3 67.8 + - - +
263A GLN* 3.6 1.0 + - - -
265A THR* 3.3 29.8 - - + +
267A SER* 4.9 2.7 - - - -
268A LYS* 3.8 15.2 - - + +
271A VAL* 3.9 28.1 - - + +
----------------------------------------------------------
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