Contacts of the helix formed by residues 256 - 284 (chain H) in PDB entry 4BOG
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 LYS 256 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H LEU* 3.3 41.2 + - - +
250H PRO* 5.3 0.2 - - - +
253H SER* 3.0 41.5 + - - +
254H GLY* 3.0 4.0 - - - -
255H GLU* 1.3 75.5 - - - +
257H MET* 1.3 49.4 + - - +
258H SER 3.7 1.1 - - - -
259H THR* 3.1 27.8 - - + -
260H ALA* 2.6 51.7 + - - +
263H VAL* 6.6 0.2 - - - -
244I THR* 5.7 2.0 - - - -
247I ILE* 5.2 5.2 - - - -
300I HIS* 3.9 36.9 - - + +
306I HIS* 4.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G ALA* 4.9 0.7 - - + -
251G LEU* 5.8 5.8 - - + -
254H GLY 3.5 18.4 + - - +
255H GLU* 2.7 18.5 + - - +
256H LYS* 1.3 73.7 - - - +
258H SER* 1.3 59.1 + - - +
260H ALA* 2.9 3.5 + - - +
261H ILE* 2.9 36.0 + - + +
313H HIS* 3.3 18.7 + - + +
314H PHE* 3.4 23.1 - - + -
319H THR 4.9 0.9 - - - +
320H HIS* 2.6 61.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G SER* 4.4 13.4 + - - -
251G LEU* 4.5 16.0 - - - +
254G SER* 5.9 1.7 - - - -
256H LYS 3.7 0.2 - - - -
257H MET* 1.3 79.1 - - - +
259H THR* 1.3 52.0 + - - +
261H ILE* 2.9 13.1 - - - +
262H CYS* 2.7 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H LYS* 3.1 40.1 - - + -
257H MET 3.2 1.0 - - - -
258H SER* 1.3 75.5 - - - +
260H ALA* 1.3 61.1 + - - +
262H CYS* 2.4 32.5 - - - -
263H VAL* 2.9 8.3 - - - +
244I THR* 2.2 40.2 + - - +
247I ILE* 2.8 35.5 - - + +
248I SER* 4.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H LYS* 2.6 36.9 + - + +
257H MET 2.9 0.9 + - - +
259H THR* 1.3 75.5 - - - +
261H ILE* 1.3 59.2 + - - +
263H VAL* 3.3 18.8 + - - +
264H LEU* 3.3 10.6 + - - +
267H GLN* 5.3 0.9 - - - +
309H VAL* 5.4 4.2 - - - +
313H HIS* 2.8 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G LEU* 3.1 52.0 - - + -
254G SER* 3.5 17.9 - - - +
255G ALA* 5.5 0.7 - - + +
257H MET* 2.9 24.5 + - + +
258H SER* 2.9 13.0 - - - +
260H ALA* 1.3 74.0 - - - +
262H CYS* 1.3 64.3 + - - +
264H LEU* 2.9 18.0 + - + +
265H LEU* 3.1 14.2 + - + +
309H VAL* 5.9 0.7 - - + -
310H LEU* 4.5 20.0 - - + -
313H HIS* 3.2 33.7 - - + +
314H PHE* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 262 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G SER* 5.1 4.5 - - - -
258H SER 2.7 15.9 + - - +
259H THR* 2.4 31.4 + - - +
261H ILE* 1.3 74.2 - - - +
263H VAL* 1.3 65.8 + - - +
265H LEU* 3.1 14.2 + - - +
266H ALA 2.8 18.0 + - - -
247I ILE* 3.1 26.7 - - - -
248I SER* 4.6 7.6 - - - -
251I LEU* 2.8 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H LEU* 3.2 36.1 - - + -
259H THR 2.9 20.4 - - - +
260H ALA* 3.4 11.4 - - - +
261H ILE 3.2 0.6 - - - -
262H CYS* 1.3 81.4 - - - +
264H LEU* 1.3 49.8 + - - +
267H GLN* 2.4 46.9 + - + +
247I ILE* 3.9 21.3 - - + -
251I LEU* 3.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G LEU* 3.9 26.9 - - + -
260H ALA 3.3 7.6 + - - +
261H ILE* 2.9 15.8 + - + +
263H VAL* 1.3 75.1 - - - +
265H LEU* 1.3 58.5 + - + +
267H GLN* 3.4 11.4 + - - +
268H ALA* 2.6 41.2 + - + +
306H CYS* 2.8 47.6 - - + +
309H VAL* 3.3 22.4 - - + -
310H LEU* 3.3 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G LEU* 5.3 12.1 - - + -
254G SER* 2.3 55.9 - - - +
255G ALA* 3.7 13.9 - - + +
257G LEU* 5.0 1.8 - - + -
258G ALA* 2.6 32.8 - - + +
262G PHE* 3.2 9.6 - - + -
261H ILE* 3.1 9.6 + - + +
262H CYS* 3.1 11.3 + - - +
264H LEU* 1.3 81.3 - - + +
266H ALA* 1.5 54.9 + - - +
268H ALA* 4.1 3.1 - - - -
269H VAL* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H CYS 2.8 7.9 + - - -
265H LEU* 1.5 57.3 - - - +
267H GLN* 1.3 52.1 + - - +
268H ALA 3.0 4.3 - - - -
269H VAL* 3.2 5.8 - - - +
270H PHE* 2.1 66.5 - - + -
251I LEU* 3.1 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H ILE* 4.9 18.9 - - + +
242H LEU* 4.5 20.2 - - + +
243H ALA* 4.7 16.8 - - - +
246H ALA* 5.5 2.6 - - - +
260H ALA 5.3 0.5 - - - +
263H VAL* 2.4 58.9 + - + +
264H LEU* 3.4 25.9 + - - +
266H ALA* 1.3 69.0 - - - +
268H ALA* 1.3 59.2 + - - +
270H PHE* 3.6 14.3 - - + +
271H LEU* 3.3 22.9 + - - +
302H VAL* 5.6 1.4 - - - +
306H CYS* 3.8 27.1 - - - +
309H VAL* 4.7 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G LEU* 4.9 11.0 - - + -
262G PHE* 3.4 18.2 - - + -
264H LEU* 2.6 29.1 + - + +
265H LEU* 3.2 5.6 - - - +
267H GLN* 1.3 70.9 - - - +
269H VAL* 1.3 64.6 + - - +
270H PHE 3.0 1.3 - - - -
271H LEU* 3.0 19.6 + - + +
272H LEU* 2.8 26.7 + - + +
303H VAL* 6.5 0.2 - - + -
306H CYS* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G VAL* 4.9 5.4 - - + -
262G PHE* 3.4 18.9 - - + -
265G LEU* 4.7 11.0 - - + -
265H LEU 2.7 17.7 + - - +
266H ALA* 3.2 7.4 - - - +
268H ALA* 1.3 72.2 - - - +
270H PHE* 1.3 89.2 + - + +
272H LEU* 3.2 27.1 - - + +
273H LEU* 3.5 17.5 + - + +
255I VAL* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H ILE* 4.4 20.2 - - + -
242H LEU* 6.5 1.1 - - + -
266H ALA* 2.1 52.0 - - + +
267H GLN* 3.6 12.1 - - + +
269H VAL* 1.3 93.8 - - + +
271H LEU* 1.3 56.1 + - - +
273H LEU* 4.9 0.2 - - - +
274H THR* 3.1 30.6 + - - -
277H ARG* 4.1 6.5 + - - +
251I LEU* 3.5 20.2 - - + -
254I THR* 3.3 24.2 - - + -
255I VAL* 3.3 26.5 - - + -
258I LEU* 4.6 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H GLN 3.3 12.1 + - - +
268H ALA* 3.0 15.0 + - + +
270H PHE* 1.3 77.8 - - - +
272H LEU* 1.3 77.8 + - + +
274H THR* 3.3 9.6 - - - +
275H SER* 3.1 22.9 + - - +
296H MET* 5.7 1.6 - - + -
299H VAL* 3.8 25.1 - - + +
302H VAL* 6.0 0.7 - - + -
303H VAL* 2.8 52.9 - - + +
306H CYS* 5.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G ILE* 5.6 5.4 - - + -
262G PHE* 3.6 32.8 - - + +
265G LEU* 3.5 32.5 - - + -
268H ALA* 2.8 29.4 - - + +
269H VAL* 3.2 23.3 - - - +
271H LEU* 1.3 83.7 - - + +
273H LEU* 1.3 56.1 + - - +
275H SER* 2.2 34.8 + - - -
276H GLN* 2.7 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G LEU* 4.6 32.1 - - + -
269H VAL* 3.5 16.4 + - + +
270H PHE 4.9 0.2 - - - +
272H LEU* 1.3 75.6 - - - +
274H THR* 1.3 65.9 + - - +
276H GLN* 2.9 48.5 + - + +
277H ARG* 2.9 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 4.4 17.8 - - + -
235H PRO* 5.8 4.2 - - - +
270H PHE 3.1 20.8 + - - -
271H LEU* 3.3 12.3 - - - +
272H LEU 3.1 1.0 - - - -
273H LEU* 1.3 77.8 - - - +
275H SER* 1.4 70.1 + - - +
277H ARG* 3.1 32.6 + - - +
278H LEU* 3.5 9.7 + - - +
295H ILE* 6.5 0.2 - - + -
296H MET* 5.0 9.2 - - + -
299H VAL* 5.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G TYR* 5.3 9.7 + - - -
271H LEU* 3.1 10.5 + - - +
272H LEU* 2.2 19.8 + - - -
274H THR* 1.4 86.1 - - - +
276H GLN* 1.2 72.9 + - - +
278H LEU* 3.0 11.9 - - - +
279H PRO* 2.6 31.9 - - - +
296H MET* 3.4 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G TYR* 4.1 26.0 + - - -
266G LEU* 4.5 18.0 - - - +
269G LYS* 4.8 13.3 - - + +
272H LEU* 2.8 20.7 - - + +
273H LEU* 2.9 43.3 + - + +
275H SER* 1.2 110.6 + - - +
277H ARG* 1.3 54.5 + - - +
278H LEU 3.0 0.2 - - - -
279H PRO* 2.6 27.2 - - - +
280H GLU* 3.6 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 4.7 14.6 - - + -
270H PHE* 4.1 6.3 + - - +
273H LEU* 2.9 44.5 + - + +
274H THR* 3.1 40.1 + - - +
276H GLN* 1.3 75.7 - - + +
278H LEU* 1.3 61.1 + - - +
280H GLU* 3.4 23.2 - - + +
281H THR* 3.4 15.9 + - + +
258I LEU* 6.0 5.9 - - - +
259I VAL* 5.3 0.2 - - - +
262I GLU* 2.5 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 278 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 4.8 16.8 - - + -
274H THR 3.5 7.0 + - - +
275H SER* 3.0 20.4 - - - +
277H ARG* 1.3 79.4 - - - +
279H PRO* 1.3 60.4 - - + +
281H THR* 3.0 8.3 + - - +
282H ALA* 2.9 24.4 + - + -
287H LEU* 4.1 6.5 - - + -
292H LEU* 3.4 25.1 - - + -
295H ILE* 3.7 42.4 - - + -
296H MET* 4.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 279 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G TYR* 2.8 44.2 + - + +
223G TYR* 4.1 12.3 - - + +
275H SER 2.6 28.0 - - - +
276H GLN* 2.6 22.0 - - - +
278H LEU* 1.3 73.6 - - + +
280H GLU* 1.3 62.6 + - - +
282H ALA* 2.6 13.7 + - + +
283H LEU* 2.4 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H GLN 3.7 9.6 - - - +
277H ARG* 3.4 19.1 - - + +
279H PRO* 1.3 83.4 - - - +
281H THR* 1.3 74.0 + - + +
283H LEU* 3.6 8.1 + - - +
284H ALA* 3.5 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H PHE* 6.1 2.3 - - + -
277H ARG* 3.4 13.4 + - + +
278H LEU* 3.0 14.0 + - - +
280H GLU* 1.3 88.6 - - + +
282H ALA* 1.3 71.8 + - - +
284H ALA* 3.4 7.8 + - - +
285H VAL* 3.0 29.9 + - - +
287H LEU* 5.0 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G TYR* 3.8 7.0 - - + +
278H LEU* 2.9 11.6 + - + +
279H PRO* 2.6 30.9 + - + +
281H THR* 1.3 77.4 - - - +
283H LEU* 1.3 52.9 + - - +
285H VAL 2.1 45.1 + - - +
287H LEU* 3.6 25.6 - - + -
292H LEU* 5.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G GLN* 4.4 19.3 - - - +
219G PHE* 6.5 0.2 - - + -
220G TYR* 3.1 35.9 + - + +
273G THR* 6.2 4.0 - - + -
46H LYS* 5.6 0.2 - - - -
48H THR* 2.9 31.8 + - + +
279H PRO 2.4 24.7 + - - +
280H GLU* 4.1 6.3 - - - +
282H ALA* 1.3 66.7 - - - +
284H ALA* 1.3 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H LYS* 4.0 33.3 + - - +
47H GLU* 4.9 2.9 + - - +
48H THR* 3.0 13.6 + - - -
223H ARG* 5.5 0.7 + - - -
280H GLU* 3.5 11.3 + - - +
281H THR* 3.4 12.5 + - - +
282H ALA 2.9 0.8 + - - -
283H LEU* 1.3 72.8 - - - +
285H VAL* 1.3 64.4 + - + +
----------------------------------------------------------
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