Contacts of the helix formed by residues 249 - 275 (chain A) in PDB entry 4PIW
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 ALA 249 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.0 32.5 - - + -
245A ALA 3.7 1.4 + - - +
246A GLN 3.3 9.3 + - - +
248A GLU* 1.3 78.1 - - + +
250A ALA* 1.3 62.0 + - - +
251A ASP 3.4 2.2 - - - +
252A ARG* 3.9 23.6 - - + +
253A ILE* 3.1 26.7 + - + +
357A TYR* 5.7 0.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
39A TRP* 3.8 18.6 - - + -
43A ARG* 5.1 0.7 - - - +
158A MSE 3.7 20.0 - - + -
183A TYR* 3.3 19.4 + - + +
246A GLN 3.4 4.9 + - - -
247A LEU* 3.3 22.1 + - + +
248A GLU 3.3 3.6 + - - +
249A ALA* 1.3 75.5 - - - +
251A ASP* 1.3 61.6 + - - +
253A ILE* 3.9 0.3 - - - +
254A ASN* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.1 36.6 + - - -
158A MSE 3.2 8.0 - - - +
248A GLU 5.1 0.4 + - - -
249A ALA* 4.5 0.2 - - - +
250A ALA* 1.3 76.5 - - - +
252A ARG* 1.3 57.3 + - - +
254A ASN* 3.7 2.7 - - - +
255A GLN* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 6.1 4.6 - - - +
249A ALA* 3.6 24.1 + - + +
250A ALA 3.3 0.6 - - - -
251A ASP* 1.3 79.8 - - - +
253A ILE* 1.3 60.5 + - - +
255A GLN* 4.1 3.5 - - - +
256A GLN* 3.1 26.3 + - + +
357A TYR* 3.4 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.7 6.7 - - + -
10A VAL* 4.1 19.7 - - + -
182A ASN* 3.9 14.6 - - + +
183A TYR* 4.0 27.4 - - + -
246A GLN* 4.0 17.7 - - - +
249A ALA* 3.1 18.8 + - + +
250A ALA 3.9 3.1 - - - +
252A ARG* 1.3 75.0 - - - +
254A ASN* 1.3 64.7 + - - +
256A GLN* 3.3 1.6 + - - +
257A ARG* 3.0 44.1 + - - +
357A TYR* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MSE 3.5 38.7 + - + +
182A ASN* 5.0 1.6 + - - +
183A TYR* 4.1 2.6 + - - +
250A ALA 3.0 20.0 + - - +
251A ASP* 3.7 5.1 - - - +
253A ILE* 1.3 79.6 - - - +
255A GLN* 1.3 57.7 + - - +
257A ARG* 3.4 5.5 + - - +
258A LEU* 2.9 46.1 + - - +
288A GLN 5.0 1.8 + - - -
289A ASN* 3.5 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ASP 2.9 18.4 + - - +
252A ARG* 4.2 3.4 - - - +
254A ASN* 1.3 77.4 - - - +
256A GLN* 1.3 58.6 + - - +
258A LEU* 3.3 19.8 + - - +
259A ALA* 2.8 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 3.1 21.1 + - + +
253A ILE 3.7 3.1 - - - +
255A GLN* 1.3 78.0 - - - +
257A ARG* 1.3 57.6 + - - +
259A ALA* 3.2 11.6 + - - +
260A LEU* 3.0 57.4 + - + +
357A TYR* 3.9 33.3 + - + +
359A LEU 4.6 5.9 + - - -
361A PRO* 5.8 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 4.9 3.2 - - - +
8A PRO* 5.2 2.8 - - - +
180A THR 5.2 2.6 + - - -
181A LLP 4.6 4.6 + - - -
182A ASN* 3.2 39.2 + - - +
253A ILE* 3.0 35.6 + - - +
254A ASN* 3.8 3.6 - - - +
256A GLN* 1.3 74.9 - - - +
258A LEU* 1.3 58.9 + - - +
260A LEU* 3.5 9.8 + - - +
261A TRP* 3.0 21.8 + - - +
289A ASN 4.2 1.6 - - - +
290A ALA* 3.1 31.5 + - + +
291A HIS* 2.9 34.8 + - - +
355A LEU* 3.7 20.5 + - + +
356A PHE* 3.4 29.9 - - - +
357A TYR* 3.7 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN* 2.9 46.0 + - - +
255A GLN* 3.6 24.5 - - - +
256A GLN 3.2 0.2 - - - -
257A ARG* 1.3 76.7 - - - +
259A ALA* 1.3 63.2 + - - +
261A TRP* 3.4 3.4 + - - +
262A GLN* 3.2 23.0 + - - +
287A VAL* 5.8 4.3 - - + -
288A GLN* 4.0 31.2 - - + +
290A ALA* 3.7 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 2.8 18.2 + - + +
256A GLN* 3.2 19.7 + - - +
258A LEU* 1.3 75.4 - - - +
260A LEU* 1.3 64.6 + - + +
262A GLN* 3.2 13.8 + - - +
263A ASN* 2.8 23.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
256A GLN* 3.0 43.0 + - + +
257A ARG* 3.5 3.3 + - - +
259A ALA* 1.3 76.0 - - + +
261A TRP* 1.3 61.0 + - - +
263A ASN* 3.4 9.1 + - - +
264A TYR* 3.4 10.0 + - - -
355A LEU* 3.6 22.4 - - + -
356A PHE 3.3 26.2 - - - +
357A TYR 5.0 0.2 - - - +
359A LEU* 3.9 27.1 - - + +
361A PRO* 5.6 5.6 - - + -
364A GLN* 2.8 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ARG 3.0 19.1 + - - +
258A LEU* 3.6 7.2 - - - +
259A ALA 3.2 0.2 - - - -
260A LEU* 1.3 77.0 - - - +
262A GLN* 1.3 77.7 + - - +
264A TYR* 3.3 10.4 + - - +
265A TYR* 3.3 47.6 + + + -
280A PRO* 3.9 24.7 - - + +
282A ILE* 3.9 18.4 - - + -
288A GLN* 3.1 33.1 + - - +
290A ALA* 3.7 20.4 - - + -
292A MSE 3.3 26.5 + - - -
293A PHE* 3.3 29.7 - + + +
355A LEU* 4.2 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU 3.2 13.4 + - - +
259A ALA* 3.6 10.5 - - - +
261A TRP* 1.3 89.6 - - - +
263A ASN* 1.3 62.9 + - - +
265A TYR* 3.4 9.8 + - - +
266A ASP* 2.9 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 2.8 20.1 + - - +
260A LEU* 3.4 7.6 - - - +
261A TRP 3.2 0.4 - - - -
262A GLN* 1.3 79.6 - - - +
264A TYR* 1.3 61.0 + - - +
266A ASP* 4.2 7.2 + - - +
267A ALA* 3.4 23.2 + - - +
364A GLN* 3.4 33.0 - - - +
368A ILE* 3.9 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 3.4 12.0 + - - -
261A TRP* 3.3 10.7 + - - +
262A GLN 3.2 0.4 - - - -
263A ASN* 1.3 77.7 - - - +
265A TYR* 1.3 59.0 + - - +
267A ALA* 3.3 1.3 + - - -
268A LEU* 2.9 39.6 + - + +
293A PHE* 3.6 41.5 - + + -
353A LEU* 3.9 26.2 - - + -
354A PRO* 2.8 32.2 + - - +
355A LEU* 4.6 8.7 - - + -
359A LEU* 4.5 2.2 - - + +
364A GLN* 4.3 17.7 - - + +
367A VAL* 3.9 25.2 - - + +
368A ILE* 3.6 32.8 - - + -
371A LEU* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TRP* 3.3 36.2 + + + +
262A GLN* 3.4 11.2 + - - +
264A TYR* 1.3 79.0 - - - +
266A ASP* 1.3 65.1 + - - +
269A ALA* 3.0 41.0 + - + +
273A LYS* 4.6 16.0 + - - -
279A LEU* 3.6 36.7 - - + +
280A PRO* 4.2 12.6 - - + -
293A PHE* 3.5 14.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLN* 2.9 47.7 + - - +
263A ASN* 4.2 8.2 + - - +
264A TYR 3.3 0.2 - - - -
265A TYR* 1.3 83.5 - - - +
267A ALA* 1.3 58.4 + - + +
269A ALA* 4.1 5.0 - - - +
270A PRO* 4.0 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN 3.4 16.4 + - - +
264A TYR 3.3 3.2 + - - +
266A ASP* 1.3 78.3 - - + +
268A LEU* 1.3 64.7 + - + +
269A ALA 3.4 0.7 - - - -
270A PRO* 3.5 13.0 - - - +
271A LEU* 5.2 1.0 + - - +
368A ILE* 3.8 29.8 - - + -
372A LEU* 4.0 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 2.9 19.4 + - + +
267A ALA* 1.3 89.1 - - + +
269A ALA* 1.3 64.1 + - - +
270A PRO 3.5 1.6 - - - -
271A LEU* 3.5 13.9 + - + +
272A ALA* 3.2 16.5 + - - +
277A ILE* 4.0 12.8 - - + +
279A LEU* 3.5 20.2 - - + +
293A PHE* 3.7 14.4 - - + -
295A ILE* 3.7 30.7 - - + -
353A LEU* 3.9 12.6 - - + -
368A ILE* 4.5 6.7 - - + -
371A LEU* 4.1 21.8 - - + -
372A LEU* 4.5 14.4 - - + -
375A PHE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.0 28.1 + - + +
266A ASP* 4.1 7.2 - - - +
268A LEU* 1.3 76.5 - - - +
270A PRO* 1.4 67.3 - - + +
272A ALA* 3.0 3.4 + - - +
273A LYS* 2.8 43.1 + - + +
279A LEU* 3.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP 4.0 6.1 - - - +
267A ALA 3.5 19.1 - - - +
268A LEU 3.6 0.2 - - - -
269A ALA* 1.4 92.9 - - + +
271A LEU* 1.3 58.2 + - + +
273A LYS* 3.4 8.1 + - + +
274A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA 5.4 0.4 - - - +
268A LEU* 3.5 17.0 + - + +
269A ALA 3.2 0.6 - - - -
270A PRO* 1.3 79.8 - - + +
272A ALA* 1.3 58.5 + - - +
274A ALA* 3.3 6.2 + - + +
275A GLY 3.1 6.9 + - - -
276A ARG* 3.0 41.7 + - + -
277A ILE* 3.5 21.4 + - + -
372A LEU* 3.9 26.9 - - + -
375A PHE* 3.6 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU 3.2 13.8 + - - +
269A ALA* 3.0 8.8 + - - +
271A LEU* 1.3 76.7 - - - +
273A LYS* 1.3 71.3 + - + +
275A GLY* 3.5 10.7 + - - -
277A ILE* 3.6 18.8 - - + +
278A GLU* 4.8 0.4 - - - -
279A LEU* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 4.6 14.9 + - - -
269A ALA* 2.8 29.4 + - + +
270A PRO* 3.9 7.0 - - + +
272A ALA* 1.3 82.8 - - - +
274A ALA* 1.3 62.8 + - - +
275A GLY* 3.3 0.8 - - - -
279A LEU* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PRO 2.9 17.2 + - - +
271A LEU* 3.6 12.3 - - + +
272A ALA 3.3 0.2 - - - -
273A LYS* 1.3 80.2 - - - +
275A GLY* 1.3 57.5 + - - +
276A ARG* 3.4 6.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU 3.1 3.8 + - - -
272A ALA 3.5 8.7 + - - -
273A LYS 3.3 3.2 - - - -
274A ALA* 1.3 78.9 - - - +
276A ARG* 1.3 64.5 + - - +
277A ILE 3.4 7.8 + - - +
278A GLU* 5.8 0.9 - - - +
298A ARG* 5.7 2.9 - - - +
----------------------------------------------------------
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