Contacts of the helix formed by residues 256 - 271 (chain B) in PDB entry 4Y5U
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 SER 256 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA* 1.3 78.0 - - - +
257B LEU* 1.3 74.4 + - - +
258B THR 2.9 7.1 + - - -
259B GLY* 3.0 13.2 + - - +
260B ARG* 3.4 12.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
181B MET 5.4 1.3 - - - +
184B GLN* 3.4 39.7 - - + +
187B THR* 4.2 9.6 - - + +
242B VAL* 5.8 10.5 - - + -
255B ALA* 3.6 7.4 - - + +
256B SER* 1.3 90.4 + - - +
258B THR* 1.3 58.7 + - - +
260B ARG* 2.9 57.2 + - - +
261B LEU* 3.0 16.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
239B GLN* 3.4 24.9 - - - +
242B VAL* 4.4 13.3 - - + +
255B ALA 3.4 28.3 + - - -
256B SER 2.9 0.2 - - - -
257B LEU* 1.3 77.5 - - - +
259B GLY* 1.3 64.7 + - - +
261B LEU* 4.8 1.8 - - - -
262B ASP* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B SER* 3.0 9.8 + - - +
258B THR* 1.3 79.8 - - - +
260B ARG* 1.3 57.2 + - - +
262B ASP* 3.8 3.3 - - - +
263B GLU* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN 4.9 3.6 + - - -
185B GLU* 5.9 1.0 - - - +
187B THR* 2.6 36.7 + - - -
188B GLY* 4.5 4.4 - - - +
191B GLU* 3.3 34.3 + - - +
256B SER* 3.4 9.8 + - - -
257B LEU* 2.9 41.2 + - - +
259B GLY* 1.3 77.9 - - - +
261B LEU* 1.3 59.7 + - + +
263B GLU* 3.2 9.1 + - - +
264B VAL* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B THR* 3.6 35.0 - - + +
190B LEU* 4.4 16.6 - - + -
191B GLU* 6.0 0.4 - - + +
235B TYR* 3.1 25.1 - - + -
238B LEU* 3.9 29.6 - - + +
239B GLN* 2.6 25.6 - - - +
242B VAL* 5.4 5.4 - - + -
257B LEU* 3.0 18.8 + - + +
258B THR* 4.2 0.9 - - - +
260B ARG* 1.3 77.3 - - + +
262B ASP* 1.3 60.7 + - - +
264B VAL* 2.9 23.2 + - + +
265B LEU 2.9 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR* 3.3 17.3 + - - -
239B GLN* 2.5 33.1 + - - -
258B THR* 2.9 18.8 + - - +
259B GLY* 4.0 4.3 - - - +
261B LEU* 1.3 75.6 - - - +
263B GLU* 1.3 55.5 + - - +
265B LEU* 3.5 5.1 + - + +
266B ARG* 3.2 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 5.1 1.7 + - - +
259B GLY 2.9 19.0 + - - +
260B ARG* 3.3 8.3 - - - +
262B ASP* 1.3 73.5 - - - +
264B VAL* 1.3 62.2 + - + +
265B LEU 3.2 0.2 - - - -
266B ARG* 3.0 33.5 + - - +
267B THR* 2.9 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 3.9 31.2 - - + -
191B GLU* 3.7 32.5 - - + +
194B LYS* 3.9 32.2 - - + +
231B LEU* 5.9 1.8 - - + +
235B TYR* 4.8 7.6 - - + -
260B ARG 3.0 14.3 + - - +
261B LEU* 2.9 15.7 + - + +
263B GLU* 1.3 75.7 - - + +
265B LEU* 1.3 63.6 + - - +
267B THR* 3.8 1.9 - - - -
268B LEU* 3.2 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.3 17.5 - - + -
235B TYR* 3.7 38.8 - - + +
261B LEU 2.9 11.3 + - - +
262B ASP* 3.7 9.2 - - + +
263B GLU 3.2 0.2 - - - -
264B VAL* 1.3 78.4 - - - +
266B ARG* 1.3 59.6 + - - +
268B LEU* 3.8 4.1 - - + +
269B VAL* 3.1 34.0 + - + +
297B LEU* 5.4 0.7 - - + -
301B PHE* 3.9 28.7 - - + -
394B LEU* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ASP 3.2 17.3 + - - +
263B GLU* 3.0 39.5 + - - +
265B LEU* 1.3 76.2 - - - +
267B THR* 1.3 72.8 + - - +
269B VAL* 3.5 3.4 + - - +
270B THR* 3.1 38.9 + - - +
401B ILE* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 3.6 26.1 + - + +
198B LEU* 3.8 21.5 - - + -
263B GLU* 2.9 33.9 + - - +
264B VAL 3.8 4.3 - - - -
265B LEU 3.2 0.4 - - - -
266B ARG* 1.3 84.6 + - - +
268B LEU* 1.3 63.4 + - - +
270B THR* 3.3 8.0 + - - +
271B SER* 3.3 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LYS* 4.3 12.1 - - + -
197B VAL* 4.3 8.7 - - + -
198B LEU* 4.0 23.3 - - + -
201B ILE* 5.5 0.7 - - + -
228B CYS* 4.0 38.1 - - - +
231B LEU* 4.3 22.0 - - + -
232B VAL* 4.3 12.8 - - + +
264B VAL* 3.2 20.0 + - + +
265B LEU* 3.8 7.0 - - + +
267B THR* 1.3 80.7 - - - +
269B VAL* 1.3 63.0 + - - +
271B SER* 3.5 2.3 + - - -
272B CYS* 3.1 29.1 + - - -
297B LEU* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 3.1 32.2 + - + +
266B ARG* 3.9 6.1 - - - +
267B THR 3.2 0.2 - - - -
268B LEU* 1.3 77.7 - - - +
270B THR* 1.3 60.9 + - - +
272B CYS* 3.2 18.8 + - - +
273B PHE 3.8 1.7 + - - -
295B PHE* 3.5 27.1 - - + -
297B LEU* 4.3 16.2 - - + -
301B PHE* 4.5 10.8 - - + -
392B PHE* 4.0 12.1 - - + -
394B LEU* 5.1 7.9 - - + -
401B ILE* 4.3 11.7 - - + -
403B LEU* 4.0 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 3.1 28.8 + - + +
267B THR* 3.3 11.4 + - - -
269B VAL* 1.3 76.3 - - - +
271B SER* 1.3 58.4 + - - +
272B CYS 3.1 0.9 + - - -
273B PHE* 3.7 16.1 + - - +
401B ILE* 4.0 21.8 - - + -
402B GLN 4.6 6.3 - - - +
403B LEU* 4.2 16.2 - - + -
404B GLN 5.0 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.2 36.1 + - - +
201B ILE* 3.4 35.2 - - - +
202B GLN* 5.8 0.3 + - - -
267B THR 3.3 18.0 + - - -
268B LEU 3.8 3.8 - - - -
269B VAL 3.3 0.6 - - - -
270B THR* 1.3 76.4 + - - +
272B CYS* 1.3 59.1 + - - +
273B PHE 3.4 2.4 + - - -
274B LEU* 4.1 5.9 - - - +
----------------------------------------------------------
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