Contacts of the helix formed by residues 243 - 273 (chain B) in PDB entry 6R7Z
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 TYR 243 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 5.5 2.8 - - + +
241B ASP* 3.4 4.4 - - - +
242B LYS* 1.3 75.4 - - - +
244B VAL* 1.3 58.9 + - - +
245B ILE 3.6 1.1 - - - -
246B PHE* 4.3 10.0 - - - +
247B ALA* 3.3 26.9 + - - +
512B SER 4.2 5.3 - - - +
513B CYS* 3.2 43.7 - - + +
516B PRO* 5.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ASP 3.6 13.3 + - - +
242B LYS* 2.9 5.9 + - + +
243B TYR* 1.3 77.8 - - - +
245B ILE* 1.3 66.8 + - - +
247B ALA* 4.4 1.2 - - - +
248B SER* 3.3 24.4 + - - -
574B ILE* 5.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ASP* 4.8 16.7 + - + +
243B TYR 3.6 0.2 - - - -
244B VAL* 1.3 79.7 - - - +
246B PHE* 1.3 58.2 + - - +
248B SER* 3.9 2.9 - - - -
249B PHE* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B MET* 6.6 0.7 - - - -
228B ILE* 5.1 15.5 - - + -
243B TYR* 4.2 9.4 + - - +
244B VAL 3.4 0.2 - - - -
245B ILE* 1.3 81.0 - - - +
247B ALA* 1.3 52.7 + - - +
249B PHE* 3.3 7.2 + - - +
250B ASN* 2.7 35.2 + - - +
512B SER* 6.1 0.2 - - - -
516B PRO* 5.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B TYR 3.3 20.9 + - - +
244B VAL* 4.4 2.0 - - - +
245B ILE 3.4 0.4 - - - -
246B PHE* 1.3 76.4 - - - +
248B SER* 1.3 60.2 + - - +
250B ASN* 3.2 7.6 + - - +
251B LEU* 2.9 29.6 + - - +
512B SER* 4.4 24.4 + - - -
513B CYS* 5.2 3.6 - - + +
570B ASN* 4.7 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL 3.3 18.6 + - - -
245B ILE* 3.9 3.8 - - - -
247B ALA* 1.3 78.1 - - - +
249B PHE* 1.3 57.0 + - - +
251B LEU* 3.5 5.3 + - - +
252B ILE* 3.0 30.1 + - - +
570B ASN* 5.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE 3.0 19.8 + - - +
246B PHE* 3.5 8.3 - - - +
247B ALA 3.2 0.2 - - - -
248B SER* 1.3 77.1 - - - +
250B ASN* 1.3 52.1 + - - +
252B ILE* 3.4 5.5 + - - +
253B TRP* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B MET* 5.6 10.1 - - + -
246B PHE 2.7 21.5 + - - +
247B ALA* 3.5 9.4 - - - +
249B PHE* 1.3 74.0 - - - +
251B LEU* 1.3 51.5 + - - +
253B TRP* 3.2 7.3 + - - +
254B SER* 2.7 35.2 + - - -
509B SER* 6.1 6.5 - - - -
512B SER* 5.5 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA 2.9 16.5 + - - +
248B SER* 4.0 5.6 - - - +
250B ASN* 1.3 72.4 - - - +
252B ILE* 1.3 61.0 + - - +
254B SER* 3.2 8.9 + - - -
255B THR* 3.0 26.5 + - - -
509B SER* 6.4 2.5 - - - -
563B SER* 5.2 9.5 - - - +
566B SER* 5.1 16.8 - - - +
567B VAL* 5.3 10.1 - - + +
570B ASN* 5.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER 3.0 19.5 + - - +
249B PHE* 3.8 5.4 - - - +
251B LEU* 1.3 76.1 - - - +
253B TRP* 1.3 58.1 + - - +
255B THR* 3.3 8.5 + - - +
256B VAL* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA* 5.5 7.9 - - + +
249B PHE 2.7 23.2 + - - +
250B ASN* 3.5 9.0 - - - +
252B ILE* 1.3 71.1 - - - +
254B SER* 1.3 56.7 + - - +
256B VAL* 3.4 7.8 - - - +
257B ILE* 2.5 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN 2.7 20.6 + - - -
251B LEU* 3.2 9.6 + - - -
253B TRP* 1.3 71.6 - - - +
255B THR* 1.3 60.0 + - - +
257B ILE* 3.7 5.7 - - - +
258B LEU* 2.8 30.7 + - - +
505B PHE* 3.6 35.4 - - - -
509B SER* 6.1 0.4 - - - -
563B SER* 4.3 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU 3.0 13.5 + - - -
252B ILE* 3.6 10.8 - - - -
253B TRP 3.2 0.2 - - - -
254B SER* 1.3 76.0 - - - +
256B VAL* 1.3 61.4 + - - +
258B LEU* 3.4 6.8 + - - +
259B GLU* 3.0 22.5 + - - +
563B SER* 4.9 6.7 - - - -
606B LYS* 6.0 8.3 - - - -
609B LEU* 5.8 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ILE 2.8 17.3 + - - +
253B TRP* 3.1 9.8 + - - +
255B THR* 1.3 78.0 - - - +
257B ILE* 1.3 50.6 + - - +
259B GLU* 3.1 7.1 + - - +
260B LEU* 2.6 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA* 4.3 23.3 - - + -
253B TRP* 2.5 26.7 + - + +
254B SER* 4.0 7.0 - - - +
256B VAL* 1.3 70.5 - - - +
258B LEU* 1.3 54.5 + - - +
259B GLU 3.1 2.0 - - - -
260B LEU* 4.0 8.3 - - - +
261B TRP* 2.5 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER 2.8 19.0 + - - +
255B THR* 3.4 6.5 + - - +
256B VAL 3.3 0.2 - - - -
257B ILE* 1.3 76.5 - - - +
259B GLU* 1.3 58.9 + - - +
261B TRP* 4.0 6.8 - - - +
262B LYS* 3.7 16.6 + - - +
556B GLN 5.5 1.8 - - - +
559B PHE* 5.4 9.2 - - + -
560B GLU* 5.3 18.6 - - + +
563B SER* 5.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B THR 3.0 13.5 + - - +
256B VAL* 3.5 9.6 - - - +
258B LEU* 1.3 78.8 - - - +
260B LEU* 1.3 54.2 + - - +
261B TRP 3.2 0.2 - - - -
262B LYS* 3.0 8.4 + - - +
263B ARG* 2.6 34.9 + - - +
613B ILE* 5.4 12.1 - - + -
614B PRO 6.0 1.6 - - - +
615B ASP 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR* 6.3 0.4 - - - -
256B VAL 2.6 22.0 + - - +
257B ILE* 3.9 7.6 - - - +
259B GLU* 1.3 71.2 - - - +
261B TRP* 1.3 55.7 + - - +
263B ARG* 3.7 9.8 - - + +
264B GLY* 2.6 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 6.3 3.4 - - + -
217B TYR* 5.3 15.7 - - + -
257B ILE 2.5 23.0 + - - +
258B LEU* 4.4 7.2 - - - +
260B LEU* 1.3 72.6 - - - +
262B LYS* 1.3 54.6 + - - +
264B GLY* 3.5 0.8 - - - -
265B CYS* 2.6 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU 3.7 13.5 + - - +
259B GLU* 3.0 12.9 + - - +
261B TRP* 1.3 80.9 - - - +
263B ARG* 1.3 55.9 + - - +
265B CYS* 3.8 5.4 - - - +
266B ALA* 2.9 29.1 + - - +
615B ASP* 4.3 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU 2.6 20.1 + - - +
260B LEU* 3.7 11.0 - - - +
262B LYS* 1.3 73.8 - - - +
264B GLY* 1.3 58.7 + - - +
266B ALA* 3.3 5.2 + - - +
267B ASN* 2.8 29.5 + - - +
615B ASP 4.3 10.5 + - - +
617B PRO* 5.3 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU 2.6 22.2 + - - -
261B TRP* 3.5 1.3 - - - -
263B ARG* 1.3 73.4 - - - +
265B CYS* 1.3 56.7 + - - +
267B ASN* 3.7 7.7 - - - +
268B MET* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TRP 2.6 23.4 + - - +
262B LYS* 3.9 5.4 - - - +
264B GLY* 1.3 70.0 - - - +
266B ALA* 1.3 57.3 + - - +
268B MET* 3.9 4.6 - - - +
269B THR* 2.7 39.5 + - - -
550B ALA 4.6 14.4 - - - +
551B ASN* 5.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LYS 2.9 19.2 + - - +
263B ARG* 3.5 7.6 - - - +
265B CYS* 1.3 77.2 - - - +
267B ASN* 1.3 56.3 + - - +
269B THR* 4.9 2.5 - - - -
270B TYR* 2.9 33.0 + - - +
275B LEU* 4.8 6.4 - - + +
615B ASP 5.5 0.4 - - - -
616B LYS* 4.6 11.7 - - + -
617B PRO* 4.4 18.8 - - + -
620B ILE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ARG 2.8 21.0 + - - +
264B GLY* 3.7 8.5 - - - +
266B ALA* 1.3 74.4 - - - +
268B MET* 1.3 57.1 + - - +
270B TYR* 4.0 3.2 - - - +
271B ARG* 3.0 28.6 + - - +
617B PRO* 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLY 2.9 18.3 + - - +
265B CYS* 3.9 4.9 - - - +
267B ASN* 1.3 77.4 - - - +
269B THR* 1.3 51.6 + - - +
271B ARG* 3.0 6.8 + - - +
272B TRP* 2.7 73.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B CYS 2.7 23.8 + - - -
268B MET* 1.3 70.3 - - - +
270B TYR* 1.3 59.4 + - - +
272B TRP* 4.2 8.3 - - - +
273B GLY 2.9 16.4 + - - +
274B THR* 3.8 14.6 - - - +
275B LEU* 2.8 44.6 + - - +
549B SER 5.3 1.1 - - - -
550B ALA* 4.5 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 4.5 11.8 - - - +
266B ALA 2.9 20.0 + - - +
267B ASN* 4.1 3.4 - - - +
269B THR* 1.3 75.7 - - - +
271B ARG* 1.3 65.7 + - - +
272B TRP 3.1 1.0 + - - -
273B GLY* 3.6 8.7 + - - -
275B LEU* 4.0 8.7 - - + +
620B ILE* 5.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 5.2 0.7 + - - -
267B ASN 3.0 18.4 + - - +
268B MET* 3.0 7.9 + - - +
270B TYR* 1.3 77.3 - - - +
272B TRP* 1.3 71.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL 3.6 11.4 - - - +
197B ILE* 4.0 18.2 - - + -
198B ASP* 4.1 19.8 - - + +
201B ARG* 3.3 80.0 + - + +
206B GLU* 4.7 15.0 - - + -
209B ALA* 4.2 20.4 - - + -
210B LEU* 5.3 2.9 - - + -
213B GLY* 6.6 0.2 - - - -
268B MET* 2.7 47.6 + - + +
269B THR* 4.4 7.4 - - - -
270B TYR 4.3 0.2 - - - -
271B ARG* 1.3 88.0 - - + +
273B GLY* 1.3 56.0 + - - +
274B THR* 3.6 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 3.5 29.2 - - - +
97B MET* 4.6 10.8 - - - -
269B THR 2.9 8.2 + - - -
270B TYR* 3.6 8.6 + - - -
272B TRP* 1.3 77.8 - - - +
274B THR* 1.3 56.2 + - - +
275B LEU 3.2 5.8 - - - -
276B LEU* 3.1 18.2 + - - +
277B MET* 3.5 7.8 + - - +
----------------------------------------------------------
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