Contacts of the helix formed by residues 247 - 261 (chain D) in PDB entry 3HTM
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 GLU 247 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D VAL* 1.3 74.9 - - - +
248D PRO* 1.3 68.4 - - + -
249D GLU* 4.9 8.8 - - - +
250D VAL* 2.8 25.3 + - + +
251D PHE* 2.7 32.0 + - - -
272D ASP* 5.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D VAL* 4.1 22.0 - - + +
207D ALA* 4.2 12.8 - - + -
209D GLN* 3.6 32.3 - - - +
211D PHE* 4.9 7.2 - - + -
246D VAL 3.7 4.6 - - - +
247D GLU* 1.3 90.5 - - + +
249D GLU* 1.3 63.5 + - - +
251D PHE* 3.1 9.6 + - + +
252D LYS* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D GLU* 3.4 10.1 - - - +
248D PRO* 1.3 78.7 - - - +
250D VAL* 1.3 63.8 + - + +
252D LYS* 3.5 16.5 + - + +
253D GLU* 3.3 16.3 + - - +
265D ASN* 5.7 3.1 + - - +
268D LYS* 3.0 33.4 + - - -
269D MSE 3.5 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D VAL* 3.9 14.4 - - + -
247D GLU* 2.8 28.3 + - + +
249D GLU* 1.3 76.5 - - + +
251D PHE* 1.3 66.1 + - - +
253D GLU* 3.0 5.2 + - - +
254D MSE 3.0 19.9 + - - +
269D MSE 4.1 20.2 - - + -
272D ASP* 3.9 31.0 - - + +
273D LEU* 3.8 32.9 - - + +
276D ALA* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 3.4 30.1 - - + -
206D VAL* 3.7 25.8 - - + -
211D PHE* 3.9 32.5 - + + -
243D ILE* 3.2 33.4 - - + -
246D VAL* 3.5 13.4 - - + +
247D GLU 2.7 15.9 + - - +
248D PRO* 3.3 14.4 - - + +
250D VAL* 1.3 73.5 - - - +
252D LYS* 1.3 61.4 + - + +
254D MSE 3.1 18.2 + - + +
255D MSE 2.9 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TRP* 4.9 9.4 + - + +
209D GLN* 4.9 7.3 + - - -
211D PHE* 3.7 37.5 - - + -
248D PRO* 2.9 24.8 + - - +
249D GLU* 3.6 14.2 - - + +
250D VAL 3.2 0.2 - - - -
251D PHE* 1.3 80.3 - - + +
253D GLU* 1.3 57.5 + - - +
255D MSE 3.3 7.9 + - - +
256D CYS* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLU 3.3 5.9 + - - +
250D VAL 3.0 9.9 + - - +
252D LYS* 1.3 79.8 - - - +
254D MSE 1.3 58.1 + - - +
256D CYS* 3.2 8.7 + - - +
257D PHE* 2.9 27.4 + - - +
262D LYS 4.4 0.9 - - - +
263D ALA* 2.9 24.2 - - + +
264D PRO* 3.0 5.6 - - - +
265D ASN* 2.8 52.0 + - - +
266D LEU 4.5 1.3 - - - +
269D MSE 3.6 21.7 - - - +
273D LEU* 3.7 27.4 - - + -
285D LEU* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D PHE* 4.1 8.7 - - + -
246D VAL* 5.2 2.2 - - + -
250D VAL 3.0 12.1 + - - +
251D PHE* 3.2 30.5 - - + +
253D GLU* 1.3 77.6 - - - +
255D MSE 1.3 84.0 + - + +
257D PHE* 3.1 5.7 + - - +
258D ILE* 2.9 28.9 + - + +
273D LEU* 4.1 6.4 - - + +
276D ALA* 4.0 22.4 - - + +
280D TYR* 3.5 46.4 - - + -
282D LEU* 3.4 22.2 - - + -
285D LEU* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TRP* 3.6 36.3 - - + -
204D LEU* 4.0 7.6 - - + -
213D ALA* 4.9 0.9 - - - -
218D LEU* 3.8 22.2 - - + -
225D PHE* 3.9 6.3 - - + -
251D PHE* 2.9 48.5 + - + +
252D LYS 3.5 7.4 - - - +
253D GLU 3.3 0.2 - - - -
254D MSE 1.3 107.2 - - + +
256D CYS* 1.3 67.1 + - - +
258D ILE* 3.1 24.4 + - + +
259D TYR* 2.9 34.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TRP* 4.7 13.8 - - + +
252D LYS 2.8 14.9 + - - +
253D GLU* 3.4 15.5 - - - +
255D MSE 1.3 75.9 - - - +
257D PHE* 1.3 58.0 + - - +
259D TYR* 3.4 1.3 + - - -
260D THR* 2.8 48.2 + - - +
262D LYS* 3.4 14.4 - - - -
264D PRO* 3.8 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ARG* 3.4 26.6 + - + -
253D GLU 2.9 12.0 + - - +
254D MSE 3.1 7.8 + - - +
256D CYS* 1.3 77.3 - - - +
258D ILE* 1.3 62.8 + - - +
261D GLY* 2.6 43.7 + - - +
262D LYS 3.1 16.5 + - - +
263D ALA* 4.9 0.2 - - + -
282D LEU* 4.3 22.2 - - + -
284D ARG* 3.3 37.7 - - + -
285D LEU* 3.7 57.0 - - + -
288D MSE 3.9 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 3.8 1.7 - - - +
217D ILE* 4.1 12.8 - - + +
218D LEU* 3.5 35.9 - - + -
221D ARG* 2.8 47.6 + - + +
222D SER* 4.9 1.8 - - - -
225D PHE* 4.0 13.5 - - + -
254D MSE 2.9 16.7 + - + +
255D MSE 3.1 26.7 + - + +
257D PHE* 1.3 74.5 - - - +
259D TYR* 1.3 68.3 + - + +
282D LEU* 3.9 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 3.6 2.9 - - - +
190D LEU* 3.0 54.4 - - + +
193D LEU* 4.5 2.2 - - + -
194D TRP* 3.4 48.9 - + + -
213D ALA* 3.4 8.3 - - - +
214D HIS* 2.6 52.2 + + - +
217D ILE* 3.8 30.5 - - + -
218D LEU* 4.5 10.3 - - + +
255D MSE 2.9 26.0 + - - +
256D CYS* 4.2 0.7 - - - +
258D ILE* 1.3 92.6 - - + +
260D THR* 1.3 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C CYS* 4.7 3.8 - - - -
186C LEU* 3.5 20.5 - - - +
187D ALA* 3.4 38.3 - - - +
188D ASP* 5.5 0.4 - - - -
191D GLY* 3.5 20.4 - - - -
194D TRP* 6.4 0.7 - - + -
256D CYS* 2.8 30.3 + - - +
259D TYR* 1.3 83.5 - - + +
261D GLY* 1.3 61.0 + - - +
262D LYS* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C CYS* 4.4 7.6 - - - -
221D ARG* 3.3 19.8 - - - +
257D PHE* 2.6 32.9 + - - -
260D THR* 1.3 71.9 - - - +
262D LYS* 1.3 60.2 + - - +
284D ARG* 2.8 31.4 + - - -
288D MSE 4.3 3.1 - - - +
----------------------------------------------------------
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