Contacts of the helix formed by residues 253 - 276 (chain A) in PDB entry 3KMR
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 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR 4.0 0.4 + - - -
252A LEU* 1.3 75.5 - - - +
254A ILE* 1.3 64.9 + - - +
255A ALA* 4.1 2.2 - - - -
256A ASP* 3.1 23.5 + - - +
257A GLN* 2.9 20.8 + - - +
343A GLU* 2.8 27.5 + - - +
344A GLN* 3.8 27.4 + - + +
347A ARG* 4.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU 3.5 0.2 + - - -
253A THR* 1.3 71.9 - - - +
255A ALA* 1.3 64.7 + - - +
257A GLN* 3.2 30.1 + - - +
258A ILE* 3.0 28.1 + - + +
633C HIS* 3.5 37.9 - - + +
636C LEU* 4.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.2 1.3 - - - -
254A ILE* 1.3 79.0 - - - +
256A ASP* 1.3 59.1 + - - +
258A ILE* 3.4 9.5 + - - +
259A THR* 3.0 31.7 + - - +
343A GLU* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.5 11.2 - - + +
253A THR* 3.1 26.0 + - - +
255A ALA* 1.3 74.7 - - - +
257A GLN* 1.3 65.8 + - - +
259A THR* 3.8 1.2 + - - -
260A LEU* 2.9 31.8 + - - +
341A ASP 4.4 1.6 - - - +
342A LEU* 3.6 21.4 - - + +
343A GLU* 2.8 30.8 + - - +
344A GLN* 2.9 37.8 + - - +
348A VAL* 4.7 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 3.5 52.3 - - + +
250A THR* 3.5 25.1 + - - +
252A LEU* 2.9 25.8 + - + +
253A THR 2.9 12.6 + - - +
254A ILE* 3.4 33.9 - - - +
256A ASP* 1.3 74.4 - - - +
258A ILE* 1.3 57.6 + - - +
260A LEU* 3.8 1.2 - - - +
261A LEU* 3.0 35.7 + - - +
636C LEU* 3.7 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 3.0 25.6 + - + +
255A ALA* 3.7 7.4 - - - +
257A GLN* 1.3 73.2 - - - +
259A THR* 1.3 67.3 + - - +
261A LEU* 3.3 2.0 + - - +
262A LYS* 3.0 45.0 + - + +
629C HIS* 4.0 26.2 - - + +
632C LEU* 3.9 21.5 - - + +
633C HIS* 3.5 40.8 - - + +
636C LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 3.0 19.6 + - - +
256A ASP* 3.3 5.0 + - - -
258A ILE* 1.3 77.0 - - - +
260A LEU* 1.3 62.8 + - - +
262A LYS* 3.6 6.9 + - - +
263A ALA* 3.1 24.3 + - + +
339A ARG* 4.5 6.5 - - + -
340A GLN 3.4 25.4 - - - +
341A ASP* 4.3 12.8 + - + +
342A LEU* 3.8 24.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
249A PHE* 4.0 12.6 - - + -
252A LEU* 3.7 30.1 - - + -
256A ASP 2.9 18.5 + - - +
257A GLN 3.8 3.4 - - - +
259A THR* 1.3 77.2 - - - +
261A LEU* 1.3 63.1 + - - +
263A ALA* 3.3 4.7 + - - +
264A ALA* 3.0 27.2 + - - +
334A LEU* 3.4 30.0 - - + +
335A ILE* 4.4 4.5 - - - -
336A CYS 3.4 27.4 - - - +
339A ARG* 3.9 8.7 + - + -
342A LEU* 3.8 20.9 - - + -
348A VAL* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A THR* 4.4 14.6 - - + +
240A VAL* 4.4 19.7 - - + -
243A ALA* 3.9 22.2 - - + -
249A PHE* 3.8 18.4 - - + -
257A GLN 3.0 23.4 + - - +
258A ILE* 3.3 4.7 + - - +
260A LEU* 1.3 76.5 - - - +
262A LYS* 1.3 57.3 + - - +
264A ALA 3.5 0.7 + - - -
265A CYS* 3.0 31.4 + - - +
268A ILE* 5.8 0.2 - - + -
334A LEU* 3.9 11.7 - - + -
413A MET* 3.5 15.7 - - + +
632C LEU* 4.4 13.0 - - + -
636C LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 3.0 39.7 + - + +
259A THR* 3.9 5.4 - - - +
261A LEU* 1.3 76.7 - - - +
263A ALA* 1.3 63.2 + - - +
264A ALA 3.5 0.3 + - - -
265A CYS* 3.6 11.4 + - - +
266A LEU 5.0 0.3 + - - -
412A GLU 3.1 22.2 + - - +
413A MET* 3.1 40.6 + - + +
414A LEU* 4.6 5.0 - - - +
415A GLU 2.9 28.2 + - - +
629C HIS* 4.1 15.7 + - + +
632C LEU* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A THR* 3.1 19.1 + - + +
260A LEU 3.8 2.2 - - - +
262A LYS* 1.3 77.9 - - - +
264A ALA* 1.3 58.5 + - - +
265A CYS 3.8 0.2 + - - -
266A LEU 5.1 0.9 + - - -
267A ASP* 3.3 14.0 - - - +
339A ARG* 3.4 46.1 + - + +
388A SER* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 3.0 16.6 + - - +
261A LEU 4.4 0.9 - - - +
263A ALA* 1.3 75.7 - - - +
265A CYS* 1.3 64.9 + - - +
266A LEU 3.4 2.0 - - - -
267A ASP* 3.2 9.1 + - + +
268A ILE* 2.9 34.2 + - + +
333A CYS 4.0 2.2 - - - +
334A LEU* 3.8 33.7 - - + +
339A ARG* 3.6 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.9 25.8 - - - -
239A THR* 5.6 6.1 + - - +
261A LEU 3.0 17.6 + - - +
262A LYS 3.7 9.6 - - - +
263A ALA 3.4 1.8 - - - -
264A ALA* 1.3 78.6 - - - +
266A LEU* 1.3 60.2 + - - +
268A ILE* 3.4 4.0 + - - +
269A LEU* 3.0 40.3 + - - +
413A MET* 3.9 29.6 - - + -
414A LEU* 4.0 16.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
1A EQN 3.9 51.6 - - + -
262A LYS 5.0 0.2 + - - -
263A ALA 5.1 0.8 + - - -
264A ALA 3.4 0.2 - - - -
265A CYS* 1.3 77.0 - - - +
267A ASP* 1.3 60.6 + - - +
269A LEU* 4.3 8.1 - - + -
270A ILE* 2.8 42.3 + - + +
388A SER* 3.9 18.8 - - - +
391A GLY* 3.7 35.7 - - - -
392A ALA* 3.9 6.3 - - + +
395A VAL* 4.5 7.2 - - + -
414A LEU* 4.0 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ALA 3.3 22.3 - - - +
264A ALA* 3.4 9.9 - - - +
266A LEU* 1.3 77.8 + - - +
268A ILE* 1.3 58.5 + - - +
270A ILE* 4.9 0.2 - - - -
271A LEU* 3.0 28.8 + - - +
333A CYS* 4.8 15.4 - - + -
339A ARG* 4.1 10.4 + - - -
381A ILE 4.8 0.3 - - - +
384A LEU* 3.2 45.3 - - + +
385A ARG* 3.4 7.5 + - - +
388A SER* 2.9 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A THR* 3.7 40.4 - - + +
242A PHE* 4.9 5.8 - - + -
261A LEU* 5.8 0.2 - - + -
264A ALA* 2.9 33.6 + - + +
265A CYS 4.0 2.2 - - - +
267A ASP* 1.3 73.9 - - - +
269A LEU* 1.3 65.3 + - - +
271A LEU* 3.3 6.7 + - - +
272A ARG* 2.9 42.1 + - + +
330A SER* 4.1 39.9 - - - +
333A CYS* 4.9 5.2 - - + -
334A LEU* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.3 64.1 - - + +
232A SER* 4.4 3.4 - - - +
235A CYS* 3.2 44.6 - - + -
236A ILE* 4.1 12.8 - - + +
239A THR* 4.3 6.5 - - - +
265A CYS* 3.0 35.4 + - - +
266A LEU* 3.9 8.1 - - + +
268A ILE* 1.3 76.8 - - - +
270A ILE* 1.3 63.5 + - - +
272A ARG* 3.2 5.0 + - - +
273A ILE 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.9 31.0 - - + +
266A LEU* 2.8 36.2 + - + +
267A ASP* 4.0 2.2 - - - +
269A LEU* 1.3 71.7 - - - +
271A LEU* 1.3 66.7 + - - +
273A ILE* 3.5 2.9 - - - +
274A CYS* 3.1 37.6 + - - -
302A PHE* 5.0 3.8 - - + -
305A LEU* 5.5 5.2 - - + -
309A VAL* 4.3 18.6 - - + -
312A PHE* 4.8 2.7 - - + -
384A LEU* 3.8 17.7 - - + -
387A ILE* 3.9 26.9 - - + +
388A SER* 4.6 9.4 - - - +
391A GLY* 5.6 0.4 - - - -
----------------------------------------------------------
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 ASP 3.0 18.6 + - - +
268A ILE* 3.7 6.3 - - - +
270A ILE* 1.3 77.0 - - - +
272A ARG* 1.3 61.3 + - + +
274A CYS* 3.3 1.0 + - - +
275A THR* 2.8 35.3 + - - +
312A PHE* 4.2 17.5 - - + -
316A LEU* 3.8 31.0 - - + -
321A MET* 6.0 1.3 - - + -
326A THR* 4.1 20.4 - - + +
329A LEU* 4.2 19.7 - - + -
330A SER* 3.4 34.1 - - - +
333A CYS* 5.5 0.4 - - - -
384A LEU* 4.0 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 4.4 11.7 - - + +
195A HIS* 4.1 20.1 + - + -
198A THR* 2.8 49.1 + - - -
199A PHE* 3.5 41.3 - - + +
235A CYS* 3.8 21.1 - - - -
238A LYS* 3.9 14.9 + - - +
239A THR* 4.5 6.9 - - - +
242A PHE* 3.9 21.2 - - - +
268A ILE* 2.9 36.5 + - + +
269A LEU 3.2 4.2 + - - +
271A LEU* 1.3 79.1 - - + +
273A ILE* 1.3 62.6 + - - +
275A THR* 3.3 19.1 + - - -
276A ARG* 3.7 4.5 + - - +
326A THR* 6.0 1.1 - - + -
330A SER* 5.3 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.6 34.5 - - + +
269A LEU 3.0 7.0 + - - +
270A ILE* 3.5 13.0 - - - +
272A ARG* 1.3 76.5 - - - +
274A CYS* 1.3 63.1 + - - +
276A ARG* 3.0 24.0 + - - +
284A MET* 3.8 30.6 - - + +
285A THR 3.3 34.8 - - - +
286A PHE* 3.6 28.9 - - + +
297A MET* 3.9 11.2 - - + -
302A PHE* 4.6 9.6 - - + -
309A VAL* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 3.1 23.6 + - - +
271A LEU 3.8 3.4 - - - +
273A ILE* 1.3 71.8 - - - +
275A THR* 1.3 62.7 + - - +
276A ARG 3.1 2.5 + - - -
277A TYR* 3.3 19.9 - - - +
284A MET* 4.0 8.7 - - - -
309A VAL* 3.5 44.9 - - - -
312A PHE* 3.8 20.6 - - + -
313A ALA* 3.8 19.5 - - + +
316A LEU* 4.1 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 5.7 0.2 - - - +
199A PHE* 3.7 25.6 - - + -
202A LEU* 5.2 4.2 - - - +
271A LEU* 2.8 30.3 + - - +
272A ARG* 3.3 12.7 - - - -
273A ILE 3.2 0.2 - - - -
274A CYS* 1.3 78.2 - - - +
276A ARG* 1.3 56.9 + - + +
277A TYR 3.4 4.0 + - - +
316A LEU* 4.1 8.4 - - - +
326A THR* 4.2 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EQN 3.0 20.6 + - - -
199A PHE* 3.3 34.8 - - + -
200A PRO* 2.8 38.2 + - - +
202A LEU* 3.9 32.4 - - + +
205A LEU* 3.7 16.8 - - - +
272A ARG 3.7 4.1 + - - +
273A ILE* 3.0 11.8 + - - +
275A THR* 1.3 82.1 - - + +
277A TYR* 1.3 58.5 + - - +
278A THR* 3.8 1.2 + - - -
283A THR 3.8 0.3 - - - +
284A MET* 3.4 2.3 - - - -
285A THR* 3.0 59.8 + - - +
287A SER* 3.0 34.4 + - - +
----------------------------------------------------------
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