Contacts of the helix formed by residues 250 - 266 (chain B) in PDB entry 6BFN
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 250 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP* 1.3 87.6 - - - +
251B ALA* 1.3 57.9 + - - +
253B LYS* 3.4 20.1 + - - +
254B GLN* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP* 3.1 30.0 - - + +
250B THR* 1.3 79.3 - - - +
252B VAL* 1.3 57.2 + - + +
254B GLN* 3.4 12.1 + - - +
255B SER* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.1 22.9 - - + +
242B LYS 3.8 21.1 - - - +
243B GLU* 4.5 13.9 - - + +
249B TRP* 3.7 24.4 + - + +
250B THR 3.3 0.4 - - - -
251B ALA* 1.3 76.3 - - + +
253B LYS* 1.3 64.6 + - - +
255B SER* 3.1 7.6 + - - -
256B PHE* 2.9 21.5 + - - +
284B TYR* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TRP 3.8 8.4 + - - +
250B THR* 3.4 23.4 + - - +
251B ALA 3.4 0.2 - - - -
252B VAL* 1.3 80.3 - - - +
254B GLN* 1.3 59.0 + - - +
256B PHE* 3.2 3.8 + - + +
257B LEU* 3.0 48.4 + - + +
284B TYR* 3.7 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B THR* 2.9 41.3 + - + +
251B ALA* 3.6 9.8 - - - +
253B LYS* 1.3 79.9 - - + +
255B SER* 1.3 53.0 + - - +
257B LEU* 4.0 7.0 - - + +
258B THR* 2.6 40.8 + - - +
360B GLY 4.8 0.2 - - - -
363B ARG* 4.4 18.1 + - - +
385B ARG* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.9 8.1 - - - -
251B ALA* 3.0 15.3 + - - +
252B VAL* 3.1 10.2 + - - -
254B GLN* 1.3 73.8 - - - +
256B PHE* 1.3 60.7 + - - +
259B GLU* 2.9 27.7 + - - +
360B GLY* 3.3 34.5 + - - -
361B LEU* 3.9 15.2 - - - +
363B ARG* 5.9 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.0 11.4 - - + +
252B VAL 2.9 13.0 + - - +
253B LYS* 3.4 7.6 - - + +
255B SER* 1.3 76.6 - - - +
257B LEU* 1.3 84.3 + - + +
259B GLU* 3.2 6.4 + - - +
260B VAL* 3.0 30.5 + - + +
277B TYR* 3.7 32.5 - + + -
278B CYS 4.0 9.9 - - - -
279B ALA* 3.9 18.4 - - + -
284B TYR* 3.5 34.5 - + + -
285B CYS 3.4 30.5 - - - -
286B LEU* 3.5 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LYS* 3.0 41.2 + - + +
254B GLN* 4.0 5.8 - - + +
256B PHE* 1.3 95.8 - - + +
258B THR* 1.3 64.0 + - - +
260B VAL* 3.2 8.1 + - + +
261B GLU* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLN* 2.6 25.2 + - - +
255B SER 3.7 0.2 - - - -
257B LEU* 1.3 77.2 - - - +
259B GLU* 1.3 57.0 + - - +
261B GLU* 3.8 7.5 - - - +
262B GLN* 2.9 41.7 + - + +
359B PHE 3.6 15.0 - - - +
360B GLY 3.5 14.4 - - - +
362B ALA 3.4 26.7 - - - +
363B ARG* 3.6 13.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
239B LYS* 3.0 23.1 + - - -
241B LEU* 5.5 1.2 - - - +
255B SER 2.9 18.4 + - - +
256B PHE 3.2 3.3 + - - +
258B THR* 1.3 76.7 - - - +
260B VAL* 1.3 64.0 + - - +
263B LEU* 3.0 47.9 + - + +
286B LEU* 3.2 17.3 - - + +
288B TYR* 2.6 28.5 + - - +
358B ASP 3.6 6.4 + - - -
359B PHE* 3.4 32.2 + - + -
360B GLY* 3.8 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PRO* 3.8 28.9 - - + -
256B PHE* 3.0 23.7 + - + +
257B LEU* 3.2 10.5 + - + +
259B GLU* 1.3 76.7 - - - +
261B GLU* 1.3 62.3 + - - +
263B LEU* 3.9 1.0 - - - +
264B SER* 2.8 28.6 + - - -
274B PHE* 3.9 20.3 - - + -
277B TYR* 3.8 23.1 - - + -
286B LEU* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PRO* 4.4 23.8 - - + +
196A PHE* 4.4 10.1 - - + -
257B LEU 2.9 16.9 + - - +
258B THR* 3.8 7.5 - - - +
260B VAL* 1.3 75.9 - - - +
262B GLN* 1.3 80.8 + - - +
264B SER* 3.1 9.0 + - - -
265B ARG* 2.9 26.5 + - + +
364B PHE* 4.9 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B THR* 2.9 35.2 + - + +
259B GLU 4.5 0.9 - - - +
261B GLU* 1.3 95.2 + - - +
263B LEU* 1.3 59.6 + - - +
265B ARG* 4.3 5.5 - - - +
266B PHE* 2.8 54.9 + - - +
336B LEU* 3.9 16.6 - - + +
359B PHE* 4.1 20.6 - - + -
362B ALA* 4.2 13.1 + - + -
363B ARG* 5.6 0.6 - - - +
364B PHE* 3.5 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 2.8 22.0 + - - -
259B GLU* 3.0 41.0 + - + +
262B GLN* 1.3 77.4 - - - +
264B SER* 1.3 60.1 + - - +
266B PHE 3.5 13.9 - - - +
271B ILE* 3.9 21.3 - - + -
272B VAL* 4.2 11.2 - - + +
274B PHE* 3.7 28.9 - - + -
288B TYR* 3.5 31.4 - - + -
359B PHE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.6 40.1 - - - +
198A PHE 5.7 0.7 + - - -
267A ARG* 4.1 6.7 + - - +
197B PRO* 3.7 24.3 - - - +
260B VAL 2.8 19.5 + - - -
261B GLU* 3.1 9.8 + - - -
263B LEU* 1.3 79.1 - - - +
265B ARG* 1.3 61.3 + - - +
267B ARG* 4.3 14.6 + - - +
274B PHE* 4.3 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG 4.1 6.9 + - - -
195A PRO* 2.8 50.6 + - + +
196A PHE* 3.9 8.9 - - + +
198A PHE* 3.7 50.6 + - + +
199A CYS 4.9 4.0 + - - +
261B GLU* 2.9 12.4 + - + +
262B GLN* 3.7 10.3 - - - +
264B SER* 1.3 80.4 - - - +
266B PHE* 1.3 81.9 + - + +
267B ARG* 3.7 4.9 + - - +
332B ASP* 2.7 38.4 + - - -
333B SER 5.9 0.4 + - - -
364B PHE* 4.2 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 4.1 13.2 - + - -
267A ARG* 4.9 1.4 + - - -
262B GLN* 2.8 36.7 + - + +
263B LEU* 3.5 13.7 - - - +
265B ARG* 1.3 86.6 - - + +
267B ARG* 1.3 62.4 + - - +
268B HIS 4.1 0.4 - - - -
271B ILE* 4.0 24.9 - - + +
272B VAL 5.4 0.3 - - - +
328B PHE* 3.8 19.7 - + + -
329B LEU* 3.7 28.0 - - + -
332B ASP* 3.5 37.5 - - + -
336B LEU* 3.5 40.8 - - + -
359B PHE* 4.9 3.8 - + + -
364B PHE* 4.2 3.4 - + - -
----------------------------------------------------------
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