Contacts of the helix formed by residues 261 - 273 (chain B) in PDB entry 4TR8
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 ARG 261 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLY 3.4 3.8 + - - -
260B ASP* 1.3 70.1 - - - +
262B GLN* 1.3 86.5 + - - +
264B LEU* 3.7 2.1 - - - +
265B ARG* 2.9 55.8 + - - +
329B LEU* 2.9 36.3 + - + +
330B GLY* 4.2 4.2 + - - +
332B ILE* 3.3 37.1 + - + -
334B THR 3.8 12.5 + - - +
335B GLU* 2.9 23.1 + - - +
337B VAL* 4.0 16.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
260B ASP* 3.4 9.1 + - - +
261B ARG* 1.3 99.5 - - - +
263B GLN* 1.3 67.3 + - - +
265B ARG* 3.3 2.7 + - - +
266B GLU* 2.7 57.3 + - + +
335B GLU 4.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASP* 2.9 36.1 + - + +
262B GLN* 1.3 73.4 - - - +
264B LEU* 1.3 58.6 + - - +
266B GLU* 3.9 6.7 - - - +
267B ALA* 3.0 31.0 + - - +
270B ARG* 4.8 2.6 + - - +
305B GLU* 5.2 5.6 + - - +
306B GLU 4.9 3.0 + - - -
307B VAL* 3.5 40.2 - - + +
308B GLN* 4.2 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 6.1 1.8 - - + -
259B GLY* 3.9 16.2 - - - +
260B ASP 3.0 21.9 + - - +
261B ARG 3.7 3.4 - - - +
263B GLN* 1.3 73.1 - - - +
265B ARG* 1.3 60.3 + - - +
267B ALA* 3.3 3.1 + - - +
268B PHE* 2.9 47.6 + - + -
291B LEU* 3.6 31.2 - - + -
307B VAL* 4.0 23.8 - - + -
309B VAL* 4.7 4.5 - - + -
329B LEU* 3.9 11.9 - - + -
337B VAL* 3.6 25.4 - - + -
339B PHE* 4.3 14.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
261B ARG* 2.9 45.1 + - - +
262B GLN* 3.9 3.8 - - - +
264B LEU* 1.3 75.0 - - - +
266B GLU* 1.3 57.9 + - + +
268B PHE 3.4 0.2 + - - -
269B SER* 3.0 35.7 + - - -
326B LEU* 2.9 60.6 + - + +
327B ASP* 5.2 2.4 + - - +
329B LEU* 3.5 23.9 - - + +
330B GLY* 3.5 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER 5.4 3.1 - - - +
83A PRO* 5.2 9.9 - - - +
262B GLN* 2.7 54.8 + - + +
263B GLN* 3.9 5.6 - - - +
265B ARG* 1.3 72.0 - - + +
267B ALA* 1.3 60.1 + - - +
269B SER* 3.4 5.7 + - - -
270B ARG* 2.9 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLN 3.0 18.8 + - - +
264B LEU 3.7 2.2 - - - +
266B GLU* 1.3 72.9 - - - +
268B PHE* 1.4 60.3 + - - +
270B ARG* 4.0 0.8 - - - +
271B THR* 3.0 36.8 + - - +
293B ILE* 3.6 23.3 - - + -
305B GLU* 3.4 35.0 - - + +
307B VAL* 3.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 2.9 38.4 + - + +
265B ARG 3.7 3.4 - - - +
267B ALA* 1.4 70.1 - - - +
269B SER* 1.3 63.5 + - - +
271B THR* 3.1 16.5 + - - -
272B ALA* 3.1 14.9 + - - +
282B ILE* 3.5 20.9 - - + -
284B LEU* 4.4 9.4 - - + -
291B LEU* 4.2 10.1 - - + -
293B ILE* 3.7 30.1 - - + -
322B VAL* 3.5 19.3 - - + +
325B LEU* 3.7 34.5 - - + -
326B LEU* 3.9 6.1 - - + -
329B LEU* 3.7 27.8 - - + -
339B PHE* 4.5 13.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 5.8 1.3 - - - -
265B ARG* 3.0 23.7 + - - -
266B GLU* 3.8 6.7 - - - -
268B PHE* 1.3 75.8 - - - +
270B ARG* 1.4 61.2 + - - +
272B ALA* 3.3 17.9 + - - +
273B ILE* 3.6 11.2 + - - +
280B ARG* 5.3 0.9 + - - +
326B LEU* 3.9 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 2.9 53.0 + - - +
82A LEU* 3.7 18.4 - - - +
83A PRO* 4.0 22.3 - - - +
104A SER* 3.9 7.4 + - - -
106A PHE* 3.7 21.8 - - + -
263B GLN* 4.8 3.4 + - - +
266B GLU* 2.9 42.6 + - - +
267B ALA* 3.9 10.6 - - - +
269B SER* 1.4 71.1 - - - +
271B THR* 1.3 64.4 + - - +
273B ILE* 3.2 31.4 + - - +
305B GLU* 2.7 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 4.7 2.2 - - + -
267B ALA 3.0 22.1 + - - +
268B PHE* 3.1 9.2 + - - -
270B ARG* 1.3 74.6 - - + +
272B ALA* 1.4 59.6 + - - +
273B ILE 3.2 1.6 + - - -
274B LEU 3.2 11.4 + - - -
282B ILE* 3.9 5.5 - - - +
293B ILE* 3.3 34.3 - - + +
295B ALA* 3.3 21.2 - - - +
303B ALA* 3.5 24.4 - - + +
304B GLU 4.4 0.9 - - - -
305B GLU* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE 3.1 19.5 + - - +
269B SER* 3.4 9.2 - - - +
270B ARG 3.3 0.2 - - - -
271B THR* 1.4 69.8 + - - +
273B ILE* 1.4 61.7 + - - +
274B LEU 3.1 2.7 - - - -
275B SER* 2.7 32.3 + - - +
280B ARG* 2.8 35.3 + - - +
282B ILE* 4.4 3.3 - - - +
322B VAL* 3.6 21.1 - - + -
326B LEU* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 4.3 24.7 - - + +
77A ASP* 3.6 44.4 - - + +
78A ILE* 3.7 26.9 - - + +
81A SER* 3.8 12.3 - - - +
269B SER 3.6 8.5 + - - +
270B ARG* 3.3 20.6 - - + +
271B THR 3.2 0.6 + - - -
272B ALA* 1.4 77.0 - - - +
274B LEU* 1.3 69.0 + - + +
275B SER 3.7 4.5 + - - +
280B ARG* 4.7 3.6 + - - +
297B ASN* 5.3 0.5 + - - -
----------------------------------------------------------
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