Contacts of the helix formed by residues 264 - 279 (chain E) in PDB entry 4HHM
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 ASP 264 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222E GLN* 3.9 20.6 - - - +
249E GLN 3.6 8.9 + - - +
261E GLY 4.8 0.2 - - - -
262E ALA 3.6 5.1 + - - +
263E GLY* 1.3 67.7 - - - -
265E LEU* 1.3 62.3 + - - +
266E ARG* 3.5 10.0 + - - +
267E ALA* 3.1 35.2 + - + +
268E ALA* 3.2 19.1 + - - +
250G SER* 6.0 2.1 - - - -
263G GLY 4.4 9.2 - - - +
264G ASP* 5.4 7.2 - - - +
265G LEU 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E GLY* 3.5 25.8 - - - +
263E GLY 3.0 6.9 + - - -
264E ASP* 1.3 72.9 + - - +
266E ARG* 1.3 57.7 + - - +
268E ALA* 3.2 4.0 + - - +
269E PHE* 3.1 22.7 + - - +
313E LEU* 4.2 20.9 - - + -
383E LEU* 4.6 3.8 - - + -
264G ASP* 5.8 0.2 + - - -
265G LEU* 3.8 25.1 - - + +
266G ARG* 3.6 23.5 - - + +
380G MET* 4.0 17.5 - - - -
383G LEU* 3.5 31.4 - - + -
384G LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E ASP* 3.4 7.7 + - - +
265E LEU* 1.3 73.8 - - - +
267E ALA* 1.3 64.0 - - - +
269E PHE* 3.4 8.0 - - - +
270E TRP* 2.8 57.6 + - + +
376E ASP* 2.6 50.6 + - - -
379E ALA* 4.3 2.0 + - - +
380E MET* 3.4 41.0 - - - +
383E LEU* 3.9 17.4 - - - +
145F SER* 5.6 0.8 - - - +
259G ARG* 4.3 0.4 - - - +
261G GLY 5.4 0.2 - - - +
262G ALA* 4.3 15.2 - - - +
263G GLY 4.3 11.6 - - - +
265G LEU* 3.8 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E VAL* 6.0 1.8 - - + -
222E GLN* 3.8 13.9 - - - +
228E PHE* 5.6 1.1 - - + +
229E PRO* 3.5 20.8 - - + +
264E ASP* 3.1 35.0 + - + +
265E LEU 3.3 0.4 - - - -
266E ARG* 1.3 75.8 - - - +
268E ALA* 1.3 61.2 + - - +
270E TRP* 4.5 5.2 - - - -
271E LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E VAL* 6.4 1.8 - - - -
260E PHE* 3.9 21.5 - - + -
261E GLY* 4.1 15.5 - - - +
264E ASP 3.2 11.5 + - - +
265E LEU 3.2 11.6 + - - +
267E ALA* 1.3 78.0 - - - +
269E PHE* 1.3 62.8 + - - +
271E LEU* 3.2 3.9 + - - +
272E VAL* 3.0 28.6 + - - +
313E LEU* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU 3.1 8.2 + - - +
266E ARG* 3.4 14.6 - - - +
268E ALA* 1.3 81.1 - - - +
270E TRP* 1.3 103.4 + + - +
272E VAL* 3.2 3.1 + - - +
273E ASP* 2.8 29.9 + - + +
313E LEU* 4.0 23.2 - - + +
316E ARG* 3.9 13.7 - - + -
317E ALA* 3.6 36.9 - - + +
320E PHE* 4.5 11.9 - + + -
379E ALA* 4.4 16.8 - - + -
383E LEU* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E PRO* 3.9 21.7 - - + +
266E ARG* 2.8 46.9 + - + +
267E ALA* 4.5 2.0 - - - -
269E PHE* 1.3 98.7 - + - +
271E LEU* 1.3 67.2 - - - +
273E ASP* 3.1 23.8 + - - +
274E LEU* 2.9 24.4 + - - +
320E PHE* 4.2 5.4 - + - -
321E ARG* 4.2 5.6 - - - -
376E ASP* 4.0 8.5 - - - -
379E ALA* 3.7 31.2 - - + -
146F GLY* 3.5 34.8 - - - +
147F ALA* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E VAL* 4.1 2.7 - - + -
228E PHE* 3.8 22.7 - - + -
229E PRO* 3.6 13.4 - - + +
232E ILE* 3.7 33.0 - - + -
244E ILE* 4.3 2.0 - - + -
246E LEU* 3.7 28.9 - - + -
260E PHE* 3.8 20.9 - - + -
267E ALA 2.9 19.7 + - - +
268E ALA* 3.5 3.8 - - - +
270E TRP* 1.3 75.7 - - - +
272E VAL* 1.3 63.9 + - + +
274E LEU* 3.1 6.5 + - + +
275E LEU* 3.0 41.1 + - + +
310E TYR* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E PHE* 3.8 18.8 - - + -
268E ALA 3.0 21.0 + - - +
269E PHE 3.7 3.8 - - - +
271E LEU* 1.3 75.3 - - + +
273E ASP* 1.3 63.2 + - - +
275E LEU* 3.4 1.9 + - - +
276E GLU* 3.2 26.8 + - + +
310E TYR* 3.7 43.3 - - + +
313E LEU* 4.0 16.2 - - + +
314E LYS* 3.6 35.2 - - + +
317E ALA* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E PHE* 2.8 15.7 + - + +
270E TRP* 3.1 30.0 + - + +
272E VAL* 1.3 77.8 - - - +
274E LEU* 1.3 58.8 + - - +
276E GLU* 4.1 1.9 - - - +
277E SER* 3.0 35.4 + - - -
317E ALA* 3.8 23.3 - - + +
320E PHE* 4.7 1.7 - - - -
321E ARG* 2.9 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E PRO* 3.1 34.1 - - + +
232E ILE* 3.8 13.9 - - + -
233E ALA* 3.6 28.3 - - + +
236E LEU* 4.0 14.6 - - + -
270E TRP 2.9 13.0 + - - +
271E LEU* 3.4 9.0 - - + +
273E ASP* 1.3 78.5 - - - +
275E LEU* 1.3 60.0 + - + +
277E SER* 3.0 10.2 + - - +
278E ALA* 3.0 35.2 + - + +
150F ASP* 5.5 7.6 - - - +
151F VAL 6.4 0.4 - - - +
152F ARG* 5.2 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E ILE* 4.2 13.7 - - + -
236E LEU* 4.6 2.9 - - + -
241E LEU* 4.0 21.5 - - + -
244E ILE* 4.3 13.7 - - + -
246E LEU* 4.9 2.9 - - + -
271E LEU* 3.0 38.9 + - + +
272E VAL 4.0 3.4 - - - +
274E LEU* 1.3 75.7 - - - +
276E GLU* 1.3 58.6 + - - +
278E ALA* 3.8 1.9 - - - -
279E GLY 3.0 21.5 + - - -
280E TRP* 3.0 44.3 + - + -
284E ARG* 3.8 18.1 + - + +
310E TYR* 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E VAL* 3.2 21.6 + - + +
273E ASP* 4.1 2.7 - - - +
275E LEU* 1.3 72.1 - - - +
277E SER* 1.3 66.6 + - - +
279E GLY* 3.0 14.2 + - - -
284E ARG* 2.9 15.2 + - - +
310E TYR* 2.8 28.6 + - - +
314E LYS* 3.4 43.6 + - + +
317E ALA* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E ASP* 3.0 28.1 + - - -
274E LEU* 3.0 17.8 + - - +
276E GLU* 1.3 76.8 - - - +
278E ALA* 1.3 58.2 + - - +
279E GLY 3.6 0.2 + - - -
321E ARG* 5.5 10.5 - - - -
152F ARG* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E LEU* 4.1 25.6 - - + -
274E LEU* 3.0 22.5 + - + +
275E LEU* 3.9 3.4 - - - +
277E SER* 1.3 77.4 + - - +
279E GLY* 1.3 62.1 + - - +
280E TRP 4.5 2.5 - - - +
152F ARG* 4.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E LEU 3.0 4.8 + - - -
276E GLU* 3.0 13.7 + - - -
277E SER 3.3 0.6 + - - -
278E ALA* 1.3 79.8 - - - +
280E TRP* 1.3 66.8 + - - +
281E GLU* 3.2 15.4 + - - +
----------------------------------------------------------
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