Contacts of the helix formed by residues 235 - 258 (chain B) in PDB entry 4DJH
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 PHE 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 5.1 2.0 - - + -
231B PHE* 3.2 32.3 + + + +
233B PHE 3.3 1.8 - - - -
234B ALA* 1.3 82.2 - - - +
236B VAL* 1.3 77.5 + - + +
237B ILE 3.3 1.3 - - - -
238B PRO* 3.3 3.8 - - - +
239B VAL* 2.9 49.6 + - + +
283B PHE* 6.1 3.1 - + - -
284B VAL* 4.7 8.7 - - + -
287B TRP* 4.4 4.3 - - + -
288B THR* 3.1 47.3 - - + -
291B HIS* 3.4 32.5 - + + +
292B ILE* 5.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 3.2 46.0 + - + +
232B ILE* 3.8 18.2 - - + +
235B PHE* 1.3 86.5 - - + +
237B ILE* 1.3 60.4 + - + +
239B VAL* 3.7 3.4 - - - +
240B LEU* 2.9 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.0 37.8 + - + +
233B PHE* 3.8 26.0 - - + +
236B VAL* 1.3 74.7 - - + +
238B PRO* 1.3 75.4 - - + +
240B LEU* 3.2 10.1 + - + +
241B ILE* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.5 27.1 - - + +
147B PHE* 4.9 7.2 - - + -
150B THR* 3.1 23.8 - - + +
233B PHE 3.2 19.7 - - - +
235B PHE 3.3 27.6 - - - +
237B ILE* 1.3 98.3 - - + +
239B VAL* 1.3 54.5 + - - +
241B ILE* 3.2 9.7 + - + +
242B ILE* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 5.1 8.5 - - + -
235B PHE* 2.9 48.4 + - + +
236B VAL* 3.7 3.6 - - - +
238B PRO* 1.3 75.1 - - - +
240B LEU* 1.3 61.4 + - + +
242B ILE* 3.1 10.6 + - + +
243B ILE* 2.8 47.0 + - + +
284B VAL* 4.1 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 2.9 39.0 + - + +
237B ILE* 3.5 8.7 - - + +
239B VAL* 1.3 77.4 - - + +
241B ILE* 1.3 65.3 + - + +
243B ILE* 2.8 21.1 + - + +
244B VAL* 2.8 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B THR* 3.8 27.6 - - + -
154B VAL* 4.0 19.1 - - + -
237B ILE* 3.0 34.7 + - + +
238B PRO* 3.5 6.5 - - + +
240B LEU* 1.3 76.8 - - + +
242B ILE* 1.3 59.4 + - - +
244B VAL* 3.2 8.4 + - + +
245B CYS* 2.8 32.8 + - - +
1303B OLC 4.5 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.8 8.5 - - + -
149B LEU* 4.2 6.7 - - + -
150B THR* 3.8 36.6 - - + +
153B SER* 3.8 22.0 - - - +
238B PRO 2.8 18.0 + - - +
239B VAL* 3.4 13.5 - - + +
241B ILE* 1.3 77.6 - - - +
243B ILE* 1.3 65.3 + - + +
245B CYS* 3.3 8.0 + - - +
246B TYR* 2.9 31.1 + - + +
277B LEU* 6.1 0.4 - - + -
280B VAL* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B VAL* 2.8 36.8 + - + +
240B LEU* 2.8 21.7 + - + +
242B ILE* 1.3 75.4 - - + +
244B VAL* 1.3 66.0 + - + +
246B TYR* 3.3 3.8 + - - +
247B THR* 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 2.8 20.9 + - + +
241B ILE* 3.5 10.1 - - + +
243B ILE* 1.3 77.7 - - + +
245B CYS* 1.3 65.6 + - - +
247B THR* 2.9 20.9 + - - -
248B LEU* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 4.3 11.2 - - - +
154B VAL* 3.6 44.6 - - - -
157B TYR* 3.8 26.2 - - + -
241B ILE* 2.8 25.5 + - - +
242B ILE* 3.5 7.4 - - - +
244B VAL* 1.3 77.8 - - - +
246B TYR* 1.3 59.3 + - + +
248B LEU* 3.3 4.1 + - - +
249B MET* 3.1 31.5 + - + +
1303B OLC 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 3.4 33.0 - - - -
156B ARG* 4.4 2.6 - - - +
242B ILE* 2.9 26.2 + - + +
243B ILE* 4.2 3.6 - - - +
245B CYS* 1.3 74.6 - - - +
247B THR* 1.3 63.5 + - - +
249B MET* 4.0 26.6 - - + +
250B ILE* 3.2 34.6 + - + +
273B THR* 3.5 17.8 + - + +
276B VAL* 3.0 29.4 - - + +
277B LEU* 3.1 55.8 + - + -
280B VAL* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 3.0 30.7 + - + +
244B VAL* 2.9 22.4 + - - +
246B TYR* 1.3 78.1 - - - +
248B LEU* 1.3 70.1 + - - +
250B ILE* 3.4 12.2 - - + +
251B LEU* 3.1 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TYR* 3.5 39.5 - - + +
161B CYS* 3.6 12.5 - - - -
244B VAL* 3.0 38.8 + - + +
245B CYS* 3.3 1.5 + - - +
247B THR* 1.3 82.1 + - - +
249B MET* 1.3 63.3 + - - +
251B LEU* 3.8 14.1 + - + +
252B ARG* 3.3 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER 3.4 8.5 - - - +
156B ARG* 3.4 23.1 - - + +
157B TYR* 3.2 40.8 - - + +
160B VAL* 4.1 17.0 - - + -
161B CYS* 4.2 6.5 - - - -
245B CYS 3.1 16.0 + - - +
246B TYR* 4.0 35.2 - - + +
248B LEU* 1.3 75.5 - - - +
250B ILE* 1.3 64.9 + - + +
252B ARG* 2.9 5.2 + - - +
253B LEU* 2.8 35.7 + - + +
273B THR* 4.0 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.2 23.1 + - + +
247B THR* 3.4 18.8 - - + +
249B MET* 1.3 82.8 - - + +
251B LEU* 1.3 66.4 + - + +
253B LEU* 3.8 12.2 - - + +
254B LYS* 2.7 37.0 + - - +
257B ARG* 5.0 1.9 + - - +
277B LEU* 6.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B THR* 3.1 30.2 + - - +
248B LEU* 3.9 16.4 - - + +
249B MET 3.1 0.4 - - - -
250B ILE* 1.3 92.6 - - + +
252B ARG* 1.3 56.8 + - - +
254B LYS* 3.6 7.3 + - + +
255B SER* 3.0 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 3.7 12.9 + - + +
161B CYS* 3.6 46.0 + - - +
163B PRO* 5.8 1.2 - - - +
248B LEU 3.3 9.8 + - - +
249B MET 2.9 7.6 + - - +
251B LEU* 1.3 76.7 - - - +
253B LEU* 1.3 61.7 + - - +
255B SER* 3.5 10.0 + - - -
256B VAL* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 3.7 29.6 - - + -
249B MET* 2.8 29.0 + - + +
250B ILE* 3.8 11.7 - - + +
252B ARG* 1.3 75.4 - - - +
254B LYS* 1.3 59.2 + - - +
256B VAL* 3.2 6.1 + - + +
257B ARG* 2.8 52.6 + - + +
268B ASN 3.7 19.7 - - - +
269B LEU* 4.2 15.9 - - + -
270B ARG 5.5 0.4 - - - +
273B THR* 5.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE 2.7 21.9 + - - +
251B LEU* 3.7 7.9 - - + +
253B LEU* 1.3 73.7 - - - +
255B SER* 1.3 62.3 + - - +
257B ARG* 3.4 26.6 + - - +
258B LEU* 3.5 17.3 + - - +
1157B THR* 6.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU 3.0 20.4 + - - -
252B ARG* 3.5 16.1 + - - -
253B LEU 3.1 0.2 - - - -
254B LYS* 1.3 78.6 - - - +
256B VAL* 1.3 56.6 + - - +
258B LEU* 2.5 31.4 - - - +
259B LEU* 3.5 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 2.9 30.7 + - + +
253B LEU* 3.9 6.7 - - + +
255B SER* 1.3 75.7 - - - +
257B ARG* 1.3 61.5 + - + +
258B LEU 3.0 2.2 - - - -
259B LEU* 2.8 32.8 + - + +
260B SER* 3.3 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 5.0 2.2 + - - +
253B LEU* 2.8 40.6 + - + +
254B LYS* 3.4 23.2 + - - +
256B VAL* 1.3 75.7 - - + +
258B LEU* 1.3 56.8 + - - +
259B LEU 3.2 0.7 - - - -
260B SER* 2.8 25.2 + - - +
267B ARG 5.4 1.3 - - - -
268B ASN* 3.0 55.7 + - - +
1158B TRP* 3.3 16.7 - - + +
1159B ASP* 3.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LYS 3.5 8.8 + - - +
255B SER* 2.5 38.8 - - - +
256B VAL 3.0 1.4 - - - -
257B ARG* 1.3 77.4 - - - +
259B LEU* 1.3 73.5 + - + +
260B SER 3.4 0.4 - - - -
261B GLY 4.6 2.1 + - - +
1094B VAL* 4.2 15.4 - - + +
1156B GLY 4.4 13.5 - - - +
1157B THR* 4.9 17.3 - - + -
1158B TRP* 3.3 26.8 + - + +
----------------------------------------------------------
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