Contacts of the helix formed by residues 226 - 245 (chain B) in PDB entry 4D87
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 VAL 226 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP* 3.8 22.9 - - + -
108B ILE* 4.0 6.1 - - + -
109B TRP* 4.0 24.9 - - + -
114B MET* 4.0 8.7 - - + -
211B VAL* 5.1 1.6 - - + -
215B MET* 3.4 16.8 - - + -
224B ASP* 3.0 22.8 + - - +
225B PRO* 1.3 74.2 - - - +
227B PHE* 1.3 72.2 + - - +
228B PHE 3.0 1.6 - - - -
229B LEU* 3.5 30.5 - - + -
230B HIS* 2.7 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 3.4 44.0 - + - -
69B HIS* 4.1 3.4 - + - -
72B TYR* 4.2 21.1 - + - -
73B LEU* 5.4 0.2 - - + -
208B HIS* 3.6 13.9 - + - -
215B MET* 2.2 32.8 - - + +
221B ALA* 3.4 31.4 - - + +
222B PRO* 3.7 7.9 - - + -
224B ASP 2.9 13.2 + - - +
226B VAL* 1.3 75.6 - - - +
228B PHE* 1.3 75.4 + + + +
230B HIS* 3.0 4.9 - - - +
231B HIS* 2.9 54.3 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 5.7 0.9 - - + -
35B TYR* 2.7 36.1 - + - -
38B TYR* 4.4 9.0 - - + -
72B TYR* 3.7 30.3 - + - -
73B LEU* 4.0 18.4 - - + +
76B PHE* 2.3 49.6 - + + -
89B LEU* 3.7 19.1 - - + +
222B PRO* 4.0 11.2 - - + -
225B PRO* 3.2 16.4 - - + +
226B VAL 3.0 1.2 - - - -
227B PHE* 1.3 87.1 - + + +
229B LEU* 1.3 69.9 + - + +
231B HIS 3.9 1.0 - - - -
232B ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 4.3 9.4 - - + -
22B PHE* 3.8 27.1 - - + -
89B LEU* 4.7 0.9 - - + -
90B PRO* 3.6 21.3 - - + +
92B TRP* 3.1 30.8 + - + -
108B ILE* 3.8 9.0 - - + -
113B PHE* 3.4 8.1 - - + -
114B MET* 2.2 51.6 - - + -
225B PRO 4.1 7.4 - - - +
226B VAL* 2.9 21.2 + - + +
228B PHE* 1.3 78.8 - - + +
230B HIS* 1.3 66.1 + - - +
232B ALA* 3.1 11.8 - - - +
233B ASN 3.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP* 4.3 13.9 - - + +
94B TRP* 3.0 30.6 + + - +
204B HIS* 3.2 49.6 - + - -
207B VAL* 4.0 13.3 - - + +
208B HIS* 3.8 20.0 + + - -
215B MET* 4.8 2.7 - - + -
226B VAL 2.7 11.9 + - - +
227B PHE* 3.0 11.9 - - - +
229B LEU* 1.3 78.5 - - - +
231B HIS* 1.3 64.2 + + - +
233B ASN* 2.9 19.9 + - - +
234B VAL* 3.1 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.1 6.1 - + - -
69B HIS* 3.0 43.2 - + + +
73B LEU* 2.8 38.1 - - + +
204B HIS* 4.1 24.3 + + - -
208B HIS* 4.4 0.4 + - - -
227B PHE* 2.9 53.0 + + - +
228B PHE 3.7 0.2 + - - -
230B HIS* 1.3 81.7 - + - +
232B ALA* 1.3 60.7 + - - +
233B ASN 3.2 0.2 - - - -
234B VAL* 3.6 18.4 - - + +
235B ASP* 2.9 18.5 + - - +
401B CU 3.5 7.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 5.2 0.9 - - - +
73B LEU* 3.7 10.1 - - + -
89B LEU* 4.7 7.4 - - + +
90B PRO 3.4 8.1 - - - +
91B TYR* 3.3 23.3 - - + +
228B PHE 3.1 14.0 + - - +
229B LEU 3.1 12.8 - - - +
230B HIS 3.0 0.6 - - - -
231B HIS* 1.3 79.7 - - - +
233B ASN* 1.3 58.9 + - - +
235B ASP* 2.9 5.7 + - - +
236B ARG* 2.8 27.0 + - - +
286B TYR* 3.6 13.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.2 13.1 - - - -
92B TRP 3.2 31.7 + - - +
93B GLU* 3.5 5.3 - - - +
94B TRP* 3.6 17.7 - - - +
95B GLU* 3.0 31.7 + - - -
229B LEU 3.3 0.4 + - - -
230B HIS 2.9 9.3 + - - +
232B ALA* 1.3 78.8 - - - +
234B VAL* 1.3 66.8 + - - +
236B ARG* 2.8 31.2 + - - +
237B ILE* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.4 20.0 - - + -
66B LEU* 5.0 6.3 - - + -
69B HIS* 6.3 0.7 - - + -
94B TRP* 4.1 11.0 - - + -
194B LEU* 3.9 25.9 - - + +
204B HIS* 4.3 9.4 - - + -
230B HIS* 3.1 40.3 + - + +
231B HIS* 3.9 20.0 - - - +
233B ASN* 1.3 75.6 - - - +
235B ASP* 1.3 63.1 + - - +
237B ILE* 3.1 17.6 + - - +
238B TRP* 3.1 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 4.0 1.1 - - - -
69B HIS 6.1 0.2 - - - -
70B ARG* 2.6 46.6 + - + +
73B LEU* 4.0 7.4 - - + -
231B HIS 2.9 15.0 + - - +
232B ALA 2.9 9.8 + - - +
234B VAL* 1.3 79.0 - - - +
236B ARG* 1.3 58.2 + - - +
238B TRP* 3.0 8.5 + - - +
239B ALA* 2.8 25.7 + - - +
279B HIS* 4.9 0.5 - - - +
284B TYR* 2.8 19.1 + - - -
286B TYR* 2.6 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 2.8 40.8 - - - -
93B GLU* 3.1 22.6 + - - -
95B GLU* 3.6 19.2 + - - -
232B ALA 2.8 8.5 + - - +
233B ASN* 2.8 19.2 + - - +
235B ASP* 1.3 74.4 - - - +
237B ILE* 1.3 75.9 + - - +
239B ALA* 3.6 9.0 - - + +
240B VAL* 3.0 48.1 + - + +
286B TYR* 3.5 34.1 - - + -
287B ASP 6.0 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
94B TRP* 5.2 6.3 - - + -
95B GLU* 3.6 18.2 - - - +
168B VAL* 3.4 34.3 - - + +
171B ALA* 6.0 2.0 - - + -
172B LEU* 3.6 22.5 - - + +
190B PHE* 4.7 2.7 - - + -
194B LEU* 4.2 19.7 - - + -
233B ASN* 2.8 35.9 + - - +
234B VAL* 3.1 7.6 + - - +
236B ARG* 1.3 89.7 - - - +
238B TRP* 1.3 56.9 + - - +
240B VAL* 3.2 7.7 - - + +
241B TRP* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.0 18.6 - - + -
67B PRO* 4.0 24.7 - - + -
70B ARG* 2.7 67.5 - - + -
177B TYR* 3.5 30.2 - + - -
190B PHE* 3.3 31.4 - + + -
194B LEU* 4.6 4.5 - - + -
234B VAL* 3.1 10.5 + - + +
235B ASP* 3.0 8.6 + - - +
237B ILE* 1.3 75.7 - - - +
239B ALA* 1.3 55.6 + - - +
241B TRP* 4.0 6.8 - + - +
242B GLN* 2.3 48.1 + - + +
276B VAL 4.0 2.0 - - - -
277B MET* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 4.5 1.1 - - - +
235B ASP* 2.8 15.7 + - - +
236B ARG* 3.6 11.0 - - + +
238B TRP* 1.3 77.0 - - - +
240B VAL* 1.3 58.8 + - - +
242B GLN* 3.0 26.7 - - - +
243B ILE* 3.5 7.8 + - - +
279B HIS* 3.1 43.3 + - + +
286B TYR* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.7 25.8 - - + -
236B ARG* 3.0 39.2 + - + +
237B ILE* 3.2 11.0 - - + +
239B ALA* 1.3 72.0 - - - +
241B TRP* 1.3 68.3 + - - +
242B GLN 2.9 2.2 + - - -
243B ILE* 3.0 15.8 + - + +
244B ILE* 3.3 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.6 21.1 - - + -
174B ILE 2.8 28.3 + - - -
175B THR 3.7 13.0 - - - -
176B GLN 3.9 2.0 - - - -
177B TYR* 3.6 43.1 - + + -
190B PHE* 3.6 52.7 - + + -
237B ILE 3.0 4.4 + - - +
238B TRP* 4.1 11.9 - + - +
240B VAL* 1.3 80.4 - - - +
242B GLN* 1.3 71.1 + - + +
244B ILE* 4.5 4.0 - - - -
245B HIS* 3.0 44.8 + + - -
248B GLN* 3.2 40.2 - - + -
249B ASN 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 1.8 38.9 + - - -
238B TRP* 2.3 46.5 - - + +
239B ALA* 3.0 15.0 - - - +
240B VAL 2.9 0.2 - - - -
241B TRP* 1.3 87.5 - - + +
243B ILE* 1.3 60.7 + - + +
245B HIS 3.1 4.7 - - - +
246B ARG* 2.9 26.3 + - - +
248B GLN 4.6 5.9 + - - +
277B MET* 3.2 31.2 + - - +
278B ASN* 4.8 0.6 - - - -
279B HIS* 4.3 5.3 - - + -
----------------------------------------------------------
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 ALA 3.5 6.4 + - - +
240B VAL* 3.0 10.1 + - + +
242B GLN* 1.3 81.0 - - + +
244B ILE* 1.3 89.1 + - + +
245B HIS 3.1 0.9 - - - -
246B ARG* 2.2 69.8 + - + +
280B ARG* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 4.2 24.5 - - + +
240B VAL* 3.3 18.3 + - + +
241B TRP 3.6 7.2 - - - +
243B ILE* 1.3 91.1 - - + +
245B HIS* 1.3 90.6 + - + +
246B ARG 3.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU 2.7 26.0 + - - -
173B LYS* 3.7 16.6 - - - -
174B ILE 3.8 5.8 + - - -
175B THR* 4.5 8.7 - - - +
241B TRP* 3.0 41.3 + + + +
242B GLN 3.1 9.1 - - - +
243B ILE 2.9 0.2 + - - -
244B ILE* 1.3 100.2 + - + +
246B ARG* 1.3 54.5 + - - +
247B ASN* 2.7 9.4 - - - +
248B GLN* 2.6 59.8 + - + +
----------------------------------------------------------
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