Contacts of the helix formed by residues 264 - 275 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP* 3.7 14.6 - - - +
243A LEU* 4.0 16.3 - - - +
244A SER* 5.2 6.1 + - - -
253A SER* 5.4 3.5 - - - -
262A ASP* 2.5 28.5 + - - -
263A LYS* 1.3 74.3 - - - +
265A TYR* 1.3 65.9 + - - +
267A THR* 2.6 27.1 + - - -
268A TYR* 3.0 33.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 4.6 0.3 + - - -
253A SER* 3.2 43.7 - - - -
254A TYR* 3.7 8.9 + - - -
255A ARG 4.0 0.5 + - - -
256A TRP* 3.3 30.2 + - + +
257A THR 3.5 26.7 - - - -
258A ILE* 3.7 8.3 - - + +
262A ASP* 3.6 28.9 + - + -
263A LYS 3.1 0.2 + - - -
264A SER* 1.3 77.3 - - - +
266A GLY* 1.3 62.2 + - - +
268A TYR* 3.4 29.7 - + - +
269A VAL* 3.6 3.6 + - - +
287A TRP* 3.4 61.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 4.4 9.1 - - - -
218A TRP* 4.3 5.6 - - - -
258A ILE* 3.9 21.9 - - - +
263A LYS 2.9 9.7 + - - -
265A TYR* 1.3 78.3 - - - +
267A THR* 1.3 57.4 + - - +
269A VAL* 3.3 5.5 + - - +
270A LEU* 2.9 36.9 + - - +
325A VAL* 5.0 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP* 4.6 2.0 - - - +
217A VAL* 3.8 30.5 - - + +
218A TRP* 3.9 30.3 - - + +
221A TYR* 5.9 2.9 - - + -
240A TYR* 3.8 15.2 - - - -
243A LEU* 3.8 6.4 - - - +
263A LYS 3.6 13.0 - - - +
264A SER* 2.6 22.5 + - - -
266A GLY* 1.3 74.8 - - - +
268A TYR* 1.3 64.7 + - - +
270A LEU* 4.2 8.3 - - + -
271A LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TYR* 3.2 31.0 - + - +
243A LEU* 4.3 12.4 - - + +
244A SER 4.8 0.9 + - - -
252A ARG* 3.5 23.8 - - + +
253A SER* 2.7 34.7 + - - -
264A SER* 3.0 36.7 - - - -
265A TYR* 3.4 29.2 - + + +
266A GLY 3.3 0.2 - - - -
267A THR* 1.3 80.5 + - - +
269A VAL* 1.3 57.6 + - - +
272A ALA* 3.1 25.5 + - - +
280A TYR* 3.5 8.0 - - - +
283A ASP* 3.9 25.8 - - + -
284A ALA* 3.9 22.4 - - + +
287A TRP* 4.5 6.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 5.1 3.6 - - + -
265A TYR 3.6 0.6 + - - +
266A GLY 3.3 7.0 + - - +
267A THR 3.2 0.2 - - - -
268A TYR* 1.3 79.0 - - - +
270A LEU* 1.3 61.4 + - - +
272A ALA* 3.3 6.8 + - - +
273A LYS* 2.8 31.3 + - + +
284A ALA* 4.0 18.6 - - + -
287A TRP* 4.1 12.8 - - + -
288A LEU* 4.9 0.4 - - + -
325A VAL* 3.5 32.5 - - + -
328A VAL* 4.2 20.9 - - + -
329A TYR* 4.0 33.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.5 34.1 - - + +
79A GLU* 5.0 1.1 - - - +
218A TRP* 3.6 34.8 - - + -
221A TYR* 3.6 55.9 + - + +
222A TRP* 4.0 9.9 - - + -
266A GLY 2.9 19.7 + - - +
267A THR* 4.0 6.3 - - + +
269A VAL* 1.3 73.7 - - + +
271A LEU* 1.3 59.3 + - + +
273A LYS* 3.4 15.5 + - + +
274A GLU* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 4.3 14.1 - - + -
221A TYR* 4.0 24.0 - - + -
233A LEU* 4.2 20.2 - - + -
236A ALA* 4.6 12.3 - - + +
237A GLU* 4.7 7.0 - - + -
240A TYR* 3.4 37.2 - - + -
267A THR* 2.9 16.4 + - - +
270A LEU* 1.3 73.5 - - + +
272A ALA* 1.3 59.3 + - - +
274A GLU* 4.2 2.5 - - + -
275A THR* 2.8 38.3 + - + -
280A TYR* 3.6 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR 3.1 20.3 + - - +
269A VAL 3.6 5.2 - - - +
271A LEU* 1.3 76.2 - - - +
273A LYS* 1.3 58.9 + - - +
276A GLY* 3.0 31.2 + - - +
280A TYR* 3.5 20.1 - - + +
281A ILE* 4.0 23.1 - - + +
329A TYR* 4.2 16.8 - - + -
332A VAL* 5.1 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.5 33.7 + - - +
221A TYR* 5.2 4.7 - - - +
269A VAL* 2.8 18.4 + - + +
270A LEU* 3.5 16.2 - - + +
272A ALA* 1.3 80.9 - - - +
274A GLU* 1.3 63.1 + - - +
276A GLY* 4.8 0.9 + - - -
328A VAL* 4.1 15.0 - - + -
331A LYS* 6.5 0.2 - - - -
332A VAL* 3.6 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.5 22.0 + - + -
224A TYR* 3.5 36.4 + - + +
225A LYS* 3.3 26.6 + - - -
233A LEU* 4.3 11.9 - - + -
270A LEU 3.0 16.0 + - - +
271A LEU* 3.1 6.3 + - + +
273A LYS* 1.3 83.1 - - - +
275A THR* 1.3 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.6 14.1 - - + -
237A GLU* 3.6 29.6 - - + +
271A LEU* 2.8 24.3 + - + +
273A LYS 5.1 0.2 - - - -
274A GLU* 1.3 82.2 - - + +
276A GLY* 1.3 60.9 + - - +
277A LYS* 3.2 24.2 + - - +
280A TYR* 3.1 19.2 - - + -
----------------------------------------------------------
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