Contacts of the helix formed by residues 243 - 273 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU* 5.6 2.4 - - + +
241A ASP* 3.4 4.8 - - - +
242A LYS* 1.3 74.8 - - - +
244A VAL* 1.3 58.4 + - - +
245A ILE 3.6 1.3 - - - -
246A PHE* 4.3 10.1 - - - +
247A ALA* 3.3 26.9 + - - +
512A SER 4.2 4.4 - - - +
513A CYS* 3.2 43.7 - - + +
516A PRO* 5.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP 3.6 13.1 + - - +
242A LYS* 2.9 6.0 + - + +
243A TYR* 1.3 78.1 - - - +
245A ILE* 1.3 67.0 + - - +
247A ALA* 4.4 1.5 - - - +
248A SER* 3.3 24.9 + - - -
574A ILE* 5.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP* 4.8 16.4 + - + +
243A TYR* 4.7 0.2 - - - +
244A VAL* 1.3 79.2 - - - +
246A PHE* 1.3 57.7 + - - +
248A SER* 3.9 3.1 - - - -
249A PHE* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 6.6 0.4 - - - -
228A ILE* 5.1 15.5 - - + -
243A TYR* 4.2 9.0 + - - +
244A VAL 3.4 0.4 - - - -
245A ILE* 1.3 80.3 - - - +
247A ALA* 1.3 52.2 + - - +
249A PHE* 3.3 7.2 + - - +
250A ASN* 2.7 35.3 + - - +
516A PRO* 5.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR 3.3 20.9 + - - +
244A VAL* 4.4 2.2 - - - +
245A ILE 3.4 0.2 - - - -
246A PHE* 1.3 75.9 - - - +
248A SER* 1.3 59.9 + - - +
250A ASN* 3.5 8.0 - - - +
251A LEU* 2.9 29.5 + - - +
512A SER* 4.4 24.4 + - - +
513A CYS* 5.2 3.1 - - + +
570A ASN* 4.7 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL 3.3 18.8 + - - -
245A ILE* 3.9 3.6 - - - -
247A ALA* 1.3 78.3 - - - +
249A PHE* 1.3 57.2 + - - +
251A LEU* 3.5 4.9 + - - +
252A ILE* 3.0 30.0 + - - +
570A ASN* 5.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE 3.0 20.6 + - - +
246A PHE* 3.5 8.3 - - - +
248A SER* 1.3 76.1 - - - +
250A ASN* 1.3 52.6 + - - +
252A ILE* 3.4 5.9 + - - +
253A TRP* 2.7 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 5.6 9.4 - - + -
246A PHE 2.7 20.8 + - - +
247A ALA* 3.2 9.6 + - - +
249A PHE* 1.3 74.0 - - - +
251A LEU* 1.3 51.7 + - - +
253A TRP* 3.2 7.1 + - - +
254A SER* 2.7 34.7 + - - -
509A SER* 6.1 6.7 - - - -
512A SER* 5.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA 2.9 16.5 + - - +
248A SER* 4.0 5.4 - - - +
250A ASN* 1.3 73.0 - - - +
252A ILE* 1.3 62.1 + - - +
254A SER* 3.2 8.7 + - - -
255A THR* 3.0 26.3 + - - -
509A SER* 6.4 2.7 - - - -
563A SER* 5.2 8.8 - - - +
566A SER* 5.1 16.8 - - - +
567A VAL* 5.3 10.5 - - + +
570A ASN* 5.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A SER 3.0 17.5 + - - +
249A PHE* 3.8 5.2 - - - +
251A LEU* 1.3 76.8 - - - +
253A TRP* 1.3 57.0 + - - +
255A THR* 3.3 8.6 + - - +
256A VAL* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 5.5 7.6 - - + +
249A PHE 2.7 23.0 + - - +
250A ASN* 3.5 9.0 - - - +
252A ILE* 1.3 70.2 - - - +
254A SER* 1.3 55.8 + - - +
256A VAL* 3.4 8.2 - - - +
257A ILE* 2.5 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASN 2.7 20.3 + - - -
251A LEU* 3.2 10.5 + - - -
253A TRP* 1.3 71.3 - - - +
255A THR* 1.3 60.4 + - - +
257A ILE* 4.0 6.1 - - - +
258A LEU* 2.8 31.2 + - - +
505A PHE* 3.6 35.9 - - - -
509A SER* 6.1 0.4 - - - -
563A SER* 4.3 12.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU 3.0 13.3 + - - -
252A ILE* 3.6 10.5 - - - -
254A SER* 1.3 75.3 - - - +
256A VAL* 1.3 64.2 + - - +
258A LEU* 3.4 6.5 + - - +
259A GLU* 3.0 23.0 + - - +
563A SER* 4.9 7.5 - - - -
606A LYS* 6.0 8.5 - - - -
609A LEU* 5.8 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE 2.8 19.1 + - - +
253A TRP* 3.4 9.4 - - - +
255A THR* 1.3 77.1 - - - +
257A ILE* 1.3 50.8 + - - +
259A GLU* 3.1 6.6 + - - +
260A LEU* 2.6 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 6.6 0.2 - - + -
221A ALA* 4.3 23.1 - - + -
253A TRP 2.5 27.2 + - - +
254A SER* 4.0 6.1 - - - +
256A VAL* 1.3 68.9 - - - +
258A LEU* 1.3 57.1 + - - +
259A GLU 3.1 1.6 - - - -
260A LEU* 4.0 8.1 - - + +
261A TRP* 2.5 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER 2.8 19.1 + - - +
255A THR* 3.8 7.2 - - - +
256A VAL 3.3 0.2 - - - -
257A ILE* 1.3 75.7 - - - +
259A GLU* 1.3 58.1 + - - +
261A TRP* 4.0 6.4 - - - +
262A LYS* 3.7 16.3 + - - +
556A GLN 5.5 2.5 - - - +
559A PHE* 5.4 8.7 - - + +
560A GLU* 5.3 18.6 - - + +
563A SER* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A THR 3.0 13.3 + - - +
256A VAL* 3.5 8.3 - - - +
257A ILE 3.1 0.2 - - - -
258A LEU* 1.3 79.8 - - - +
260A LEU* 1.3 52.9 + - - +
261A TRP 3.2 0.4 - - - -
262A LYS* 3.0 7.7 + - - +
263A ARG* 2.6 35.2 + - - +
613A ILE* 5.4 12.3 - - + -
614A PRO 6.0 1.6 - - - +
615A ASP 4.9 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
217A TYR* 6.3 0.4 - - - -
256A VAL 2.6 21.6 + - - +
257A ILE* 3.9 7.9 - - - +
259A GLU* 1.3 70.6 - - - +
261A TRP* 1.3 55.5 + - - +
263A ARG* 3.6 10.2 - - + +
264A GLY* 2.6 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 6.3 3.4 - - + -
217A TYR* 5.3 15.7 - - + +
257A ILE 2.5 23.3 + - - +
258A LEU* 4.4 6.5 - - - +
260A LEU* 1.3 71.8 - - - +
262A LYS* 1.3 54.1 + - - +
264A GLY* 3.5 1.2 - - - -
265A CYS* 2.6 37.9 + - - +
----------------------------------------------------------
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 LEU 3.7 12.6 + - - +
259A GLU* 3.0 12.3 + - - +
261A TRP* 1.3 80.0 - - - +
263A ARG* 1.3 55.2 + - - +
265A CYS* 3.9 4.7 - - - +
266A ALA* 2.9 29.8 + - - +
615A ASP* 4.3 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU 2.6 20.2 + - - +
260A LEU* 3.7 11.0 - - + +
262A LYS* 1.3 73.0 - - - +
264A GLY* 1.3 57.6 + - - +
266A ALA* 3.3 5.0 + - - +
267A ASN* 2.8 29.3 + - - +
615A ASP 4.3 11.1 + - - +
617A PRO* 5.3 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 2.6 22.3 + - - -
261A TRP* 3.5 1.8 - - - -
263A ARG* 1.3 73.6 - - - +
265A CYS* 1.3 56.8 + - - +
267A ASN* 3.4 6.8 + - - +
268A MET* 2.9 30.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
261A TRP 2.6 22.4 + - - +
262A LYS* 3.9 6.7 - - - +
264A GLY* 1.3 69.0 - - - +
266A ALA* 1.3 56.9 + - - +
268A MET* 3.9 4.4 - - - +
269A THR* 2.7 39.1 + - - -
550A ALA 4.6 14.8 - - - +
551A ASN* 5.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS 2.9 19.6 + - - +
263A ARG* 3.5 7.4 - - - +
265A CYS* 1.3 77.4 - - - +
267A ASN* 1.3 56.4 + - - +
269A THR* 4.9 2.2 - - - -
270A TYR* 2.9 32.3 + - - +
275A LEU* 4.8 6.8 - - + +
615A ASP 4.9 0.4 - - - +
616A LYS* 4.6 11.4 - - + -
617A PRO* 4.4 18.6 - - + -
620A ILE* 5.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ARG 2.8 19.7 + - - +
264A GLY* 3.7 9.0 - - - +
265A CYS 3.3 0.2 - - - -
266A ALA* 1.3 74.4 - - - +
268A MET* 1.3 57.9 + - - +
270A TYR* 4.0 2.9 - - - +
271A ARG* 3.0 28.2 + - - +
617A PRO* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLY 2.9 18.0 + - - +
265A CYS* 3.9 4.9 - - - +
267A ASN* 1.3 77.2 - - - +
269A THR* 1.3 51.9 + - - +
271A ARG* 3.0 6.9 + - - +
272A TRP* 2.7 72.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A CYS* 2.7 23.6 + - - -
266A ALA* 4.9 0.4 - - - -
268A MET* 1.3 70.2 - - - +
270A TYR* 1.3 60.0 + - - +
272A TRP* 4.2 8.7 - - - +
273A GLY 2.9 16.5 + - - -
274A THR* 3.8 13.5 - - - +
275A LEU* 2.8 43.9 + - - +
549A SER 5.3 1.1 - - - -
550A ALA* 4.5 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 4.5 11.8 - - - +
266A ALA 2.9 21.5 + - - +
267A ASN* 4.1 3.1 - - - +
269A THR* 1.3 74.9 - - - +
271A ARG* 1.3 65.8 + - - +
272A TRP 3.1 0.7 + - - -
273A GLY* 3.6 9.1 + - - +
275A LEU* 4.0 9.5 - - + +
620A ILE* 5.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ARG* 5.2 0.7 + - - -
267A ASN 3.0 18.7 + - - +
268A MET* 3.0 8.3 + - - +
270A TYR* 1.3 76.9 - - - +
272A TRP* 1.3 72.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL 3.6 11.3 - - - +
197A ILE* 4.0 18.6 - - + -
198A ASP* 4.1 19.1 - - + +
201A ARG* 3.3 77.9 + - + +
206A GLU* 4.8 15.3 - - + -
209A ALA* 4.2 21.8 - - + -
210A LEU* 5.3 2.7 - - + -
268A MET* 2.7 46.1 + - + +
269A THR* 4.4 7.0 - - - -
270A TYR 4.3 0.2 - - - -
271A ARG* 1.3 89.0 - - + +
273A GLY* 1.3 57.2 + - - +
274A THR* 3.6 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.5 29.3 - - - +
97A MET* 4.6 10.5 - - - -
269A THR 2.9 8.4 + - - -
270A TYR* 3.6 8.6 + - - -
272A TRP* 1.3 77.5 - - - +
274A THR* 1.3 55.6 + - - +
275A LEU 3.2 5.4 - - - -
276A LEU* 3.1 17.8 + - - +
277A MET* 3.5 8.4 + - - +
----------------------------------------------------------
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