Contacts of the helix formed by residues 241 - 259 (chain E) in PDB entry 3KC3
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 ASP 241 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E ALA* 4.0 13.7 - - + +
185E ARG* 4.4 19.2 + - - +
212E LYS* 5.1 8.9 - - + +
213E GLU 4.9 7.4 - - - +
214E THR* 4.9 13.1 - - - +
238E GLU* 4.7 4.2 - - - +
239E LYS* 3.2 30.8 + - - +
240E TYR* 1.3 71.1 - - - +
242E LYS* 1.3 67.0 + - - +
243E SER 3.2 2.3 + - - -
244E CYS* 3.3 25.7 - - - -
245E ASP* 4.3 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E HIS* 3.0 82.3 + - + +
181E ASN* 3.8 9.9 - - - +
183E ALA* 4.0 9.3 - - + +
214E THR* 2.8 38.5 + - + +
238E GLU* 2.8 26.5 + - - +
239E LYS 5.3 0.9 + - - +
240E TYR* 3.5 1.1 - - - -
241E ASP* 1.3 82.0 + - - +
243E SER* 1.3 56.8 + - - +
245E ASP* 3.1 16.3 + - - +
246E MET* 3.8 0.3 - - - +
316E ILE* 5.3 0.9 - - + -
280J ARG* 6.0 1.7 - - - +
281J MET* 4.6 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E TYR* 3.0 22.7 + - - +
241E ASP 3.2 0.4 - - - -
242E LYS* 1.3 76.0 - - - +
244E CYS* 1.3 62.7 + - - +
245E ASP 3.2 0.4 - - - -
246E MET* 3.3 12.4 + - - +
247E TRP 3.3 12.3 + - - -
310E PRO* 3.4 34.0 + - - +
313E ARG* 3.1 24.4 + - - -
314E MET 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 4.1 12.3 - - + +
233B GLU* 3.7 16.4 + - - +
234B VAL* 4.8 14.4 - - + -
185E ARG* 4.1 30.1 - - - -
240E TYR 4.5 1.3 + - - +
241E ASP* 3.3 20.5 + - - +
242E LYS 3.2 1.6 - - - -
243E SER* 1.3 77.1 + - - +
245E ASP* 1.3 66.2 + - - +
246E MET 3.2 0.4 - - - -
247E TRP* 3.3 4.6 + - - +
248E SER* 2.9 26.2 + - - -
313E ARG* 4.0 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E ILE* 4.3 13.6 - - + +
177E LEU* 5.0 0.2 - - - +
178E HIS* 2.6 31.4 + - + +
183E ALA* 3.5 4.9 - - - -
184E HIS* 2.9 28.7 + - - +
185E ARG* 2.7 31.7 + - - +
187E VAL* 4.0 8.6 + - - +
241E ASP 5.0 0.2 - - - -
242E LYS 3.1 11.7 + - - +
244E CYS* 1.3 78.5 - - - +
246E MET* 1.3 59.7 + - + +
248E SER* 3.1 10.9 + - - -
249E LEU* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E ILE* 4.3 2.9 - - - -
178E HIS* 3.2 32.1 - - + -
242E LYS 3.8 3.8 - - - +
243E SER* 3.3 15.6 + - - +
244E CYS 3.2 0.4 - - - -
245E ASP* 1.3 78.1 - - + +
247E TRP* 1.3 66.6 + - - +
249E LEU* 3.3 15.9 + - + +
250E GLY 3.1 13.9 + - - -
305E LEU* 3.6 32.2 - - + +
313E ARG* 4.5 5.8 - - - -
314E MET 3.1 24.9 - - - +
315E THR* 4.1 1.8 - - - -
316E ILE* 3.3 43.7 - - + +
319E PHE* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR 5.6 0.4 + - - -
229B TYR 3.5 19.8 + - - -
230B VAL 3.6 11.9 + - - -
231B ALA* 3.5 18.8 - - + -
232B PRO* 3.5 36.1 - - + -
243E SER 3.3 6.9 + - - -
244E CYS 3.3 8.5 + - - +
246E MET* 1.3 72.6 - - - +
248E SER* 1.3 57.2 + - - +
250E GLY* 2.7 24.4 + - - -
251E VAL* 2.9 25.9 + - + +
263E PHE* 3.5 35.3 - + - -
279E ILE* 4.1 13.2 - - + +
282E GLY* 5.3 0.2 - - - -
305E LEU 3.8 9.4 - - - -
306E LEU* 3.0 43.4 - - + +
307E LYS 3.4 23.3 - - - -
308E THR* 3.9 2.9 - - + -
313E ARG* 3.6 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TYR* 4.3 12.0 + - - -
185E ARG 5.6 1.7 + - - -
187E VAL* 3.2 41.3 + - - +
244E CYS* 2.9 13.1 + - - -
245E ASP* 3.2 9.3 - - - -
247E TRP* 1.3 83.0 - - - +
249E LEU* 1.3 63.3 + - - +
251E VAL* 3.2 7.2 + - - +
252E ILE* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E MET* 4.4 5.6 - - - +
170E ILE* 3.6 36.1 - - + -
171E GLY* 4.8 1.6 - - - -
174E ILE* 4.1 15.5 - - + -
187E VAL* 5.0 3.4 - - + -
245E ASP 2.9 13.7 + - - +
246E MET* 3.4 26.2 - - + +
247E TRP 3.2 0.2 - - - -
248E SER* 1.3 74.9 - - - +
250E GLY* 1.3 55.0 + - - +
252E ILE* 3.2 5.9 + - + +
253E MET* 2.7 37.3 + - - +
305E LEU* 4.8 3.4 - - + -
316E ILE* 4.8 5.2 - - + -
319E PHE* 3.5 52.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E MET 3.1 3.6 + - - -
247E TRP 2.7 14.2 + - - -
249E LEU* 1.3 76.3 - - - +
251E VAL* 1.3 63.3 + - - -
253E MET* 3.1 3.9 + - - +
254E TYR* 2.9 23.0 + - - +
302E ILE* 4.7 5.6 - - - +
305E LEU* 3.7 25.5 - - - +
306E LEU* 3.8 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 4.5 9.9 - - + +
229B TYR* 4.1 31.4 - - + +
189E PRO* 6.4 0.4 - - + -
247E TRP* 2.9 43.2 + - + +
248E SER* 3.8 4.9 - - - +
250E GLY* 1.3 74.6 - - - +
252E ILE* 1.3 66.9 + - + +
254E TYR* 3.0 4.5 + - - +
255E ILE* 3.0 31.9 + - + +
262E PRO* 3.7 30.2 - - + +
263E PHE* 5.1 0.9 - - + -
306E LEU* 3.6 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E LEU* 4.7 2.0 - - + -
147E PHE* 4.5 13.0 - - + -
167E MET* 3.0 27.6 - - + -
170E ILE* 3.9 11.0 - - + -
187E VAL* 3.8 36.3 - - + +
188E LYS* 4.1 6.1 - - - -
189E PRO* 4.6 17.0 - - + -
192E LEU* 4.0 18.8 - - + -
248E SER 3.0 21.5 + - - +
249E LEU* 3.5 8.3 - - + +
251E VAL* 1.3 77.0 - - + +
253E MET* 1.3 62.1 + - - +
255E ILE* 2.8 18.9 + - - +
256E LEU 2.8 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E MET* 3.7 31.4 - - + +
249E LEU 2.7 18.3 + - - +
250E GLY* 3.6 4.0 - - - +
252E ILE* 1.3 73.3 - - - +
254E TYR* 1.3 63.2 + - - +
256E LEU* 3.3 3.5 + - + +
257E LEU* 3.0 33.5 + - + +
298E VAL* 5.1 1.6 - - - +
301E LEU* 3.7 23.3 - - + -
302E ILE* 3.7 25.8 - - + -
305E LEU* 3.7 14.6 - - + -
319E PHE* 3.2 39.3 - - + -
324E TRP* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E GLY 2.9 12.1 + - - +
251E VAL* 3.2 10.5 - - - +
253E MET* 1.3 76.9 - - - +
255E ILE* 1.3 64.4 + - - +
257E LEU* 3.0 11.8 + - - -
258E CYS* 3.4 19.6 + - - -
260E TYR* 3.2 33.8 - + - -
261E PRO 3.4 11.6 + - - -
262E PRO* 3.5 37.4 + - + +
284E TYR* 4.2 5.2 - + - -
285E GLU 2.5 30.7 + - - -
286E PHE* 3.8 15.9 - + - -
287E PRO* 4.1 2.3 - - - +
291E TRP* 3.4 34.7 + + - -
302E ILE* 4.2 14.8 - - + +
306E LEU* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 4.3 23.6 - - + +
147E PHE* 3.4 37.5 - - + -
189E PRO* 4.7 3.6 - - + -
251E VAL* 3.0 17.5 + - + +
252E ILE* 2.8 12.8 + - - +
254E TYR* 1.3 71.6 - - - +
256E LEU* 1.3 58.9 + - - +
257E LEU 3.1 0.2 + - - -
259E GLY* 2.7 46.5 + - - -
260E TYR* 3.6 7.2 - - - +
261E PRO* 3.6 36.6 - - + -
338E THR* 3.8 1.2 - - - +
342E LEU* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E LEU* 4.5 2.9 - - + -
147E PHE* 3.1 29.6 - - + -
150E ILE* 3.2 24.5 - - + -
158E PHE* 3.5 14.7 - - + -
163E ALA* 3.6 29.2 - - + +
166E ILE* 3.6 31.6 - - + -
167E MET* 3.8 16.8 - - + -
252E ILE 2.8 8.1 + - - +
253E MET* 3.5 12.1 - - - +
255E ILE* 1.3 77.4 - - - +
257E LEU* 1.3 54.7 + - + +
336E LEU* 4.5 0.3 - - - +
338E THR* 2.6 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E GLU* 4.4 12.3 - - + -
163E ALA* 4.1 14.6 - - + -
253E MET* 3.0 24.5 + - + +
254E TYR 3.0 2.8 + - - -
256E LEU* 1.3 78.4 - - + +
258E CYS* 1.3 59.5 + - - +
290E GLU* 4.8 4.2 - - - +
291E TRP* 3.6 28.5 - - + -
294E VAL* 4.6 10.1 - - + +
298E VAL* 3.3 33.4 - - + -
302E ILE* 4.0 6.3 - - + -
324E TRP* 4.5 6.7 - - + -
336E LEU* 3.6 48.5 - - + +
337E HIS 4.7 1.2 + - - -
338E THR* 3.5 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 258 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E TYR* 3.4 16.4 + - - -
255E ILE 3.1 1.8 + - - -
256E LEU 3.3 0.2 - - - -
257E LEU* 1.3 77.7 - - - +
259E GLY* 1.3 60.5 + - - +
260E TYR* 3.3 55.7 - - + -
290E GLU* 3.7 19.6 - - + +
291E TRP* 3.5 22.7 - - + +
337E HIS* 5.3 0.2 - - - -
338E THR* 3.8 13.2 + - - +
341E VAL* 3.5 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E ILE* 2.7 24.1 + - - -
258E CYS* 1.3 72.5 - - - +
260E TYR* 1.3 58.9 + - - +
338E THR* 3.7 16.9 - - - +
341E VAL* 3.3 18.9 - - - +
342E LEU* 3.4 28.6 + - - +
----------------------------------------------------------
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