Contacts of the helix formed by residues 270 - 287 (chain B) in PDB entry 5EJC
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 270 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 4.5 7.8 - - - +
246B PHE* 3.9 33.7 - - - -
267B PRO* 4.0 2.2 + - - +
268B GLN 3.4 0.4 - - - -
269B ASP* 1.3 86.8 + - - +
271B SER* 1.3 63.1 + - - +
272B ASP 3.2 3.1 - - - -
273B ALA* 3.1 20.7 + - - +
274B ILE* 3.2 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.9 18.6 - - - +
216B PRO* 3.1 32.5 - - - +
219B SER* 3.6 6.3 + - - -
267B PRO 4.4 2.6 + - - -
268B GLN* 2.6 27.2 + - - -
269B ASP 3.3 0.4 - - - -
270B SER* 1.3 76.9 - - - +
272B ASP* 1.3 63.7 + - - +
274B ILE* 3.7 14.0 - - - +
275B VAL* 3.2 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 3.6 12.4 + - - +
222B ARG* 3.1 34.3 + - - +
269B ASP 4.3 8.4 + - - +
270B SER 3.1 0.6 + - - -
271B SER* 1.3 81.8 + - - +
273B ALA* 1.3 63.6 + - - +
276B SER* 3.4 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 6.5 0.4 - - + -
270B SER* 3.1 12.2 + - - +
272B ASP* 1.3 78.6 - - - +
274B ILE* 1.3 65.0 + - + +
276B SER* 3.0 8.2 + - - -
277B LYS* 2.9 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 5.3 5.2 - - + -
238B VAL* 4.3 11.0 - - + +
241B GLU* 3.4 22.1 - - + +
242B ILE* 4.1 26.9 - - + +
245B THR* 3.5 27.4 - - + +
246B PHE* 3.9 28.9 - - + -
266B ILE* 5.0 4.9 - - + -
267B PRO 5.4 0.2 - - - +
270B SER 3.2 17.4 + - - +
271B SER* 3.7 17.5 - - - +
272B ASP 3.3 0.4 - - - -
273B ALA* 1.3 77.4 - - + +
275B VAL* 1.3 60.6 + - + +
277B LYS* 4.7 0.7 - - - -
278B ALA* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 4.3 13.9 - - + -
219B SER* 3.9 18.2 - - - +
222B ARG* 3.7 32.8 - - + +
223B VAL* 3.7 32.8 - - + -
238B VAL* 5.5 1.8 - - + -
271B SER 3.2 15.2 + - - +
274B ILE* 1.3 76.9 - - + +
276B SER* 1.3 65.0 + - - +
278B ALA* 3.2 6.8 + - - +
279B ILE* 3.0 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG* 3.1 28.0 + - - +
272B ASP* 3.4 6.9 + - - -
273B ALA* 3.0 11.5 + - - -
275B VAL* 1.3 80.6 - - - +
277B LYS* 1.3 62.1 + - - +
279B ILE* 3.4 6.3 + - - +
280B ASP* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLU* 3.5 35.7 + - + +
245B THR* 5.0 3.5 + - - +
273B ALA* 2.9 30.5 + - + +
276B SER* 1.3 73.7 - - - +
278B ALA* 1.3 60.9 + - - +
280B ASP* 3.3 10.4 + - - +
281B LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 4.4 2.2 - - + -
237B PHE* 3.4 29.1 - - - +
238B VAL* 3.6 27.1 - - + +
241B GLU* 3.9 4.5 - - + +
274B ILE 2.8 20.2 + - - +
275B VAL 3.5 4.7 - - - +
277B LYS* 1.3 77.3 - - - +
279B ILE* 1.3 58.8 + - + +
281B LEU* 3.3 6.0 + - - +
282B TRP* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG 5.3 1.6 - - - +
50B PRO* 6.4 1.3 - - + -
222B ARG* 4.3 21.3 - - + +
223B VAL* 5.5 1.6 - - + +
226B LYS* 4.2 25.8 - - + +
234B ILE* 4.2 20.0 - - + -
238B VAL* 6.3 0.4 - - + -
275B VAL* 3.0 39.2 + - + +
276B SER* 3.7 5.4 - - - +
277B LYS 3.2 0.2 - - - -
278B ALA* 1.3 75.0 - - + +
280B ASP* 1.3 63.2 + - - +
282B TRP* 3.2 9.0 + - + +
283B HIS* 2.8 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER 3.2 14.1 + - - +
277B LYS* 3.3 11.5 + - - +
279B ILE* 1.3 80.0 - - - +
281B LEU* 1.3 57.6 + - - +
283B HIS* 3.3 10.2 + - - +
284B LYS* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU* 3.6 31.6 - - + +
237B PHE* 4.0 24.5 - - + +
240B VAL* 3.9 26.9 - - + -
241B GLU* 3.7 22.0 - - + +
244B LEU* 4.1 6.1 - - + -
277B LYS 2.9 11.7 + - - +
278B ALA 3.4 9.4 - - - +
280B ASP* 1.3 75.9 - - - +
282B TRP* 1.3 61.7 - - - +
284B LYS* 3.4 16.7 + - + +
285B HIS* 3.2 33.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 3.2 39.9 - - + -
226B LYS* 3.6 25.6 - - + -
231B SER* 3.4 27.7 + - - -
233B LYS* 4.4 3.4 - - - +
234B ILE* 3.6 33.3 - - + +
237B PHE* 3.7 32.1 - + + -
278B ALA 2.9 17.4 + - - +
279B ILE* 3.5 9.9 - - + +
281B LEU* 1.3 73.3 - - - +
283B HIS* 1.3 91.4 + + - +
285B HIS 3.4 0.3 + - - -
286B CYS* 3.0 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 3.4 23.7 + - - +
48B ARG* 3.8 53.1 + - - +
279B ILE* 2.8 42.3 + - + +
280B ASP* 3.6 9.6 + - - +
282B TRP* 1.3 91.9 - + - +
284B LYS* 1.3 58.3 - - - +
286B CYS 5.2 0.2 - - - -
287B GLY* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU* 3.1 33.3 + - - -
280B ASP 2.9 17.5 + - - +
281B LEU* 3.5 14.7 - - + +
282B TRP 3.2 0.4 - - - -
283B HIS* 1.3 79.5 - - - +
285B HIS* 1.3 76.4 + - + +
287B GLY* 4.1 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 3.7 25.6 + + + -
183B LEU* 4.3 25.5 - - + +
184B GLU* 2.8 32.9 + - + +
237B PHE* 3.6 33.2 - + + -
281B LEU* 3.2 25.9 + - + +
284B LYS* 1.3 93.9 - - + +
286B CYS* 1.3 61.5 + - - +
287B GLY 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 4.4 1.8 - - - -
233B LYS* 3.2 38.6 - - - +
237B PHE* 4.0 10.8 - - - -
282B TRP* 3.0 40.6 + - + +
283B HIS* 3.9 0.7 - - - -
285B HIS* 1.3 82.6 - - - +
287B GLY* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG* 4.1 21.8 + - - -
283B HIS* 2.8 26.8 + - - -
284B LYS 4.1 3.4 + - - -
285B HIS 3.6 1.8 - - - -
286B CYS* 1.3 80.6 - - - +
----------------------------------------------------------
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