Contacts of the helix formed by residues 264 - 275 (chain B) in PDB entry 1TF4
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 264 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ASP* 3.6 14.0 - - - +
243B LEU* 4.0 17.6 - - - +
244B SER* 5.1 6.4 + - - -
253B SER* 5.4 2.9 - - - -
262B ASP* 2.5 28.6 + - - -
263B LYS* 1.3 75.9 - - - +
265B TYR* 1.3 67.3 + - - +
267B THR* 2.6 26.6 + - - -
268B TYR* 3.0 34.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLU* 4.5 0.7 + - - -
253B SER* 3.2 43.6 - - - -
254B TYR* 3.7 8.5 + - - -
255B ARG 4.0 0.5 + - - -
256B TRP* 3.3 30.7 + - + +
257B THR 3.5 26.7 - - - -
258B ILE* 3.7 7.9 - - + +
262B ASP* 3.6 29.6 + - + -
264B SER* 1.3 77.0 - - - +
266B GLY* 1.3 62.1 - - - +
268B TYR* 3.4 28.2 - + - +
269B VAL* 3.6 3.3 + - - +
287B TRP* 3.4 62.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 4.4 9.1 - - - -
218B TRP* 4.2 5.8 - - - -
258B ILE* 3.9 21.7 - - - +
263B LYS 2.9 9.7 + - - -
265B TYR* 1.3 78.2 - - - +
267B THR* 1.3 58.2 + - - +
269B VAL* 3.3 5.4 + - - +
270B LEU* 2.9 36.3 + - - +
325B VAL* 5.0 5.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
214B ASP 4.6 1.3 - - - +
217B VAL* 3.7 29.8 - - + +
218B TRP* 3.8 31.0 - - + +
221B TYR* 5.8 2.7 - - + -
240B TYR* 3.9 5.5 - - - -
243B LEU* 3.8 17.0 - - - +
263B LYS 3.6 11.9 - - - +
264B SER* 2.6 20.6 + - - -
266B GLY* 1.3 73.5 - - - +
268B TYR* 1.3 65.5 + - - +
270B LEU* 4.2 8.5 - - + -
271B LEU* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TYR* 3.2 29.4 - + - +
243B LEU* 4.1 15.4 - - + +
244B SER 4.7 0.9 + - - -
252B ARG* 3.5 23.2 - - + +
253B SER* 2.7 34.9 + - - -
254B TYR* 5.5 0.2 - - + -
264B SER* 3.0 31.3 - - - -
265B TYR* 3.4 29.2 - + + +
267B THR* 1.3 81.7 + - - +
269B VAL* 1.3 59.1 + - + +
272B ALA* 3.1 25.1 + - - +
280B TYR* 3.4 7.9 - - - +
283B ASP* 3.9 26.2 - - + -
284B ALA* 3.9 21.3 - - - +
286B ARG* 6.2 0.2 - - - -
287B TRP* 4.5 5.8 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
75B TRP* 5.0 4.0 - - + -
265B TYR 3.6 0.6 + - - +
266B GLY 3.3 7.5 + - - +
267B THR 3.2 0.4 - - - -
268B TYR* 1.3 78.5 - - - +
270B LEU* 1.3 61.4 + - - +
272B ALA* 3.3 5.9 + - - +
273B LYS* 2.8 31.3 + - + +
284B ALA* 4.0 19.1 - - + -
287B TRP* 4.1 13.0 - - + -
288B LEU* 4.9 0.7 - - + -
325B VAL* 3.5 29.8 - - + -
328B VAL* 4.2 21.1 - - + -
329B TYR* 4.0 33.0 - - + -
332B VAL* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 3.5 33.4 - - + +
79B GLU* 4.9 0.9 - - - +
218B TRP* 3.6 33.2 - - + -
221B TYR* 3.6 56.0 + - + +
222B TRP* 3.9 9.6 - - + +
266B GLY 2.9 20.4 + - - +
267B THR* 3.3 7.2 + - + +
269B VAL* 1.3 73.9 - - + +
271B LEU* 1.3 58.6 + - + +
273B LYS* 3.4 16.3 + - + +
274B GLU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 4.3 14.4 - - + -
221B TYR* 4.0 24.7 - - + -
233B LEU* 4.1 21.3 - - + -
236B ALA* 4.6 10.3 - - + +
237B GLU* 4.7 8.3 - - + -
240B TYR* 3.5 36.3 - - + -
267B THR* 2.9 18.4 + - - +
270B LEU* 1.3 73.5 - - + +
272B ALA* 1.3 59.4 + - - +
274B GLU* 4.2 2.5 - - + -
275B THR* 2.7 39.1 + - + -
280B TYR* 3.6 30.3 - - + +
----------------------------------------------------------
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 TYR 3.1 20.5 + - - +
269B VAL* 3.6 8.3 - - - +
271B LEU* 1.3 75.4 - - - +
273B LYS* 1.3 59.4 + - - +
276B GLY* 3.0 30.9 + - - +
277B LYS 4.9 0.2 - - - -
280B TYR* 3.5 20.8 - - + +
281B ILE* 4.0 22.5 - - + +
329B TYR* 4.3 14.4 - - + -
332B VAL* 5.1 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 3.5 34.8 + - - +
221B TYR* 5.2 4.9 - - - +
269B VAL* 2.8 18.7 + - + +
270B LEU* 3.5 15.5 - - + +
272B ALA* 1.3 79.7 - - - +
274B GLU* 1.3 63.0 + - - +
276B GLY* 4.8 0.7 + - - -
328B VAL* 4.1 13.5 - - + -
331B LYS* 6.5 0.4 - - - -
332B VAL* 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR* 3.5 22.3 + - + -
224B TYR* 3.5 34.7 + - + -
225B LYS* 3.2 28.0 + - - -
233B LEU* 4.4 11.7 - - + -
270B LEU 2.9 17.0 + - - +
271B LEU* 3.7 6.1 - - + +
273B LYS* 1.3 83.4 - - - +
275B THR* 1.3 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 4.6 15.0 - - + -
237B GLU* 3.7 28.9 - - + +
271B LEU* 2.7 24.3 + - + +
273B LYS 5.1 0.2 - - - -
274B GLU* 1.3 82.2 - - + +
276B GLY* 1.3 61.5 + - - +
277B LYS* 3.2 25.0 + - - +
280B TYR* 3.1 20.0 - - + -
----------------------------------------------------------
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