Contacts of the helix formed by residues 248 - 269 (chain A) in PDB entry 1O6L
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 THR 248 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 1.3 78.5 - - - +
249A GLU* 1.3 59.9 + - - +
250A GLU* 3.7 7.1 + - - +
251A ARG* 3.1 26.0 + - + +
252A ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE 3.9 0.4 + - - -
248A THR* 1.3 72.6 - - - +
250A GLU* 1.3 57.0 + - - +
252A ALA* 3.5 1.7 + - - +
253A ARG* 2.9 38.5 + - - +
344A MET* 3.9 23.8 - - + -
372A THR 4.7 1.0 - - - +
373A LEU* 3.5 14.2 - - + +
374A SER* 2.6 50.4 + - - -
376A GLU* 4.5 2.9 - - - +
377A ALA* 3.5 13.5 - - - +
408A PHE* 3.8 12.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 3.2 7.3 - - - +
249A GLU* 1.3 77.0 - - - +
251A ARG* 1.3 63.8 + - - +
253A ARG* 3.0 43.5 + - - +
254A PHE* 3.1 21.8 + - - +
411A SER* 4.3 6.7 + - - -
412A ILE* 5.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 4.4 8.7 - - - +
244A GLU* 2.7 42.4 + - - -
247A PHE* 3.6 27.7 - - + +
248A THR* 3.1 25.1 + - - +
250A GLU* 1.3 72.8 - - - +
252A ALA* 1.3 65.3 + - - +
254A PHE* 3.3 4.7 + - - +
255A TYR* 3.0 61.9 + - + -
283A LEU* 4.9 0.4 - - - +
425A PRO* 3.9 31.0 - - + +
426A PHE* 3.5 29.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 4.4 2.4 - - + +
248A THR 3.0 16.0 + - - +
249A GLU 3.8 2.5 - - - +
251A ARG* 1.3 74.4 - - - +
253A ARG* 1.3 55.3 + - - +
255A TYR* 3.5 1.8 + - - +
256A GLY* 2.8 32.7 + - - -
340A MET* 3.5 13.5 - - + +
343A MET* 3.9 28.7 - - + -
344A MET* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU* 2.9 22.3 + - - +
250A GLU* 3.0 52.5 + - - +
252A ALA* 1.3 74.9 - - - +
254A PHE* 1.3 59.9 + - - +
257A ALA* 2.8 30.2 + - - +
376A GLU* 4.9 9.9 + - - +
408A PHE* 3.1 69.4 + - + +
409A PHE* 3.7 15.3 - - + -
411A SER* 3.8 18.2 + - - -
412A ILE* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLU 3.1 12.9 + - - +
251A ARG 3.3 8.9 + - - +
253A ARG* 1.3 76.9 - - - +
255A TYR* 1.3 74.8 + + - +
257A ALA* 3.4 5.5 + - - +
258A GLU* 3.2 62.2 + - + +
287A GLY 4.0 15.3 - - - -
288A HIS* 3.8 13.2 - + - -
412A ILE* 5.5 3.8 - - + -
422A LEU* 3.9 32.3 - - + -
423A LEU 3.8 17.0 - - - -
424A PRO* 3.7 12.6 - - + -
425A PRO* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 3.8 15.9 - - + -
247A PHE* 3.6 28.5 - + - -
251A ARG* 3.0 58.2 + - + -
252A ALA 4.0 3.8 - - - +
254A PHE* 1.3 88.9 - + - +
256A GLY* 1.3 66.3 + - - +
258A GLU* 3.2 5.4 + - - +
259A ILE* 3.0 28.9 + - + +
283A LEU* 3.6 27.5 - - + +
287A GLY 3.8 11.8 + - - -
289A ILE* 3.9 27.3 - - + +
343A MET* 4.0 15.5 - - + -
425A PRO* 4.0 6.4 - - + +
426A PHE* 3.9 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA 2.8 17.9 + - - -
253A ARG 3.7 0.4 - - - -
255A TYR* 1.3 76.9 - - - +
257A ALA* 1.3 55.1 + - - +
259A ILE* 3.2 9.8 + - - +
260A VAL* 2.9 33.1 + - - +
336A LEU* 4.3 2.5 - - - +
340A MET* 3.7 23.7 - - - -
409A PHE* 4.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG 2.8 17.9 + - - +
254A PHE* 3.7 5.8 - - - +
256A GLY* 1.3 74.6 - - - +
258A GLU* 1.3 58.5 + - - +
260A VAL 3.4 0.5 + - - -
261A SER* 3.0 26.0 + - - -
409A PHE* 3.8 6.6 - - + -
412A ILE* 4.2 12.8 - - + -
414A TRP* 3.3 34.8 - - + -
417A VAL* 3.8 19.2 - - + +
422A LEU* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 3.3 45.0 - - + +
254A PHE* 3.2 35.4 - - + +
255A TYR 3.2 7.7 + - - +
257A ALA* 1.3 74.0 - - - +
259A ILE* 1.3 64.8 + - - +
261A SER 3.4 0.5 + - - -
262A ALA* 3.1 20.8 + - - +
288A HIS* 2.7 29.1 + - - -
289A ILE* 2.8 43.8 + - + +
417A VAL* 4.1 10.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
237A LEU* 4.9 0.2 - - + -
255A TYR* 3.0 26.8 + - + +
256A GLY* 3.7 9.2 - - - +
258A GLU* 1.3 71.1 - - - +
260A VAL* 1.3 60.3 + - - +
262A ALA* 3.3 6.5 + - - +
263A LEU* 2.9 44.1 + - + +
276A ILE* 4.1 19.3 - - + -
281A LEU* 3.8 35.2 - - + -
289A ILE* 4.1 17.5 - - + -
291A ILE* 4.4 5.6 - - + -
336A LEU* 3.9 22.7 - - + -
339A VAL* 4.4 6.7 - - + -
343A MET* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLY 2.9 22.8 + - - +
257A ALA 3.7 5.8 - - - +
259A ILE* 1.3 77.4 - - - +
261A SER* 1.3 55.1 + - - +
263A LEU* 3.3 1.6 + - - +
264A GLU* 2.9 29.8 + - - +
333A TRP* 4.2 20.0 - - + -
336A LEU* 3.6 26.7 - - + -
400A ALA* 4.6 2.7 - - + +
403A VAL* 3.9 16.6 - - + -
404A MET* 3.8 31.0 - - + -
409A PHE* 4.3 9.0 - - + -
414A TRP* 3.9 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A HIS* 3.3 26.9 + - - -
211A PHE* 4.0 8.2 - - - -
257A ALA 3.0 17.0 + - - -
258A GLU 3.5 6.3 - - - -
259A ILE 3.3 0.2 - - - -
260A VAL* 1.3 78.4 - - - +
262A ALA* 1.3 59.3 + - - +
264A GLU* 3.4 9.6 + - - +
265A TYR 3.1 17.5 + - - -
404A MET* 6.2 0.9 - - - -
414A TRP* 4.4 8.6 + - - -
417A VAL* 4.0 10.5 - - - -
418A VAL* 3.8 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A HIS* 3.7 12.3 + - + -
211A PHE* 4.1 15.0 - - + -
212A LEU* 3.9 13.8 - - + +
258A GLU 3.1 13.7 + - - +
259A ILE 3.6 7.2 - - - +
261A SER* 1.3 77.9 - - - +
263A LEU* 1.3 56.5 + - - +
265A TYR* 3.3 4.5 + - - +
266A LEU* 3.0 33.9 + - - +
291A ILE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 2.9 34.3 + - + +
260A VAL* 3.9 0.4 - - - +
262A ALA* 1.3 73.0 - - - +
264A GLU* 1.3 59.8 + - - +
266A LEU* 4.4 9.6 - - + +
267A HIS* 2.9 38.8 + - + +
273A TYR* 4.1 11.4 - - + -
276A ILE* 3.9 22.9 - - + -
291A ILE* 5.0 3.1 - - + -
332A ASP* 3.9 45.5 - - + +
333A TRP* 3.7 34.5 - - + -
336A LEU* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A HIS* 5.9 0.9 - - - -
260A VAL 2.9 18.7 + - - +
261A SER* 3.5 9.8 + - - +
263A LEU* 1.3 75.4 - - - +
265A TYR* 1.3 63.8 + - - +
267A HIS* 3.4 5.4 + - - +
268A SER* 3.0 41.5 + - - -
333A TRP* 4.4 0.4 - - - -
399A ASP* 5.2 0.2 - - - -
400A ALA* 3.7 29.2 - - + -
404A MET* 4.0 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
206A ASN 4.0 0.9 + - - -
207A THR* 3.6 17.0 - - + -
208A ARG* 3.0 44.8 + - - +
209A HIS* 3.4 35.9 - + + +
212A LEU* 3.7 19.1 - - + -
261A SER 3.1 6.8 + - - +
262A ALA 3.5 6.7 - - - +
264A GLU* 1.3 84.7 + - - +
266A LEU* 1.3 64.1 + - - +
268A SER* 2.7 26.1 + - - -
269A ARG* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 4.5 6.5 - - + -
207A THR* 4.0 18.6 - - + -
212A LEU* 3.9 35.7 - - + -
262A ALA 3.0 20.7 + - - +
263A LEU* 3.8 13.9 - - + +
265A TYR* 1.3 75.2 - - + +
267A HIS* 1.3 60.0 + - + +
269A ARG* 3.0 14.6 + - - -
270A ASP 3.3 0.2 + - - -
271A VAL* 2.9 53.5 + - + +
273A TYR* 4.1 34.5 - - + -
291A ILE* 5.2 2.7 - - + -
294A PHE* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 2.9 22.2 + - + +
264A GLU 3.9 3.4 - - - +
266A LEU* 1.3 77.9 - - + +
268A SER* 1.3 57.2 + - - +
270A ASP* 3.1 21.7 + - - +
271A VAL 3.2 21.8 - - - +
272A VAL* 4.4 2.4 - - + -
301A ILE 4.6 3.1 - - - +
302A SER* 5.6 0.2 - - - -
329A ARG* 3.5 50.6 + - + +
332A ASP* 2.7 29.2 + - + +
333A TRP* 3.7 26.6 - + - -
399A ASP* 2.7 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 3.0 26.3 + - - -
265A TYR* 2.7 27.4 + - - -
267A HIS* 1.3 76.1 - - - +
269A ARG* 1.3 62.9 + - - +
270A ASP* 3.2 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN* 2.8 45.3 + - - +
207A THR* 5.2 4.2 - - + +
265A TYR* 3.1 45.3 + - + +
266A LEU* 3.0 10.8 + - - +
268A SER* 1.3 80.7 - - - +
270A ASP* 1.3 70.0 + - - +
271A VAL* 3.3 16.2 + - + +
300A GLY 5.3 0.3 + - - -
----------------------------------------------------------
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