Contacts of the helix formed by residues 178 - 202 (chain A) in PDB entry 2XGZ
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 THR 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.5 3.1 - - - +
177A LYS* 1.3 86.4 - - + +
179A PHE* 1.3 65.0 + - - +
180A ALA* 3.6 5.7 + - - +
181A GLU* 3.0 25.5 + - + +
182A ALA* 3.0 22.3 + - - +
416A GLU* 3.5 14.8 - - - +
425A PHE* 3.7 13.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.2 11.7 - - + -
147A PRO* 3.2 30.1 - - + -
149A PRO* 3.7 24.2 - - + -
178A THR* 1.3 67.4 - - - +
180A ALA* 1.3 67.8 + - - +
182A ALA* 3.0 2.3 + - - +
183A LEU* 2.9 38.3 + - + +
409A LEU* 3.5 29.2 - - + -
412A LEU* 3.4 46.7 - - + -
413A LEU* 3.8 18.2 - - + -
416A GLU* 2.9 22.9 + - - +
425A PHE* 3.6 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 3.3 5.6 - - - +
179A PHE* 1.3 73.5 - - - +
181A GLU* 1.3 63.3 + - - +
183A LEU* 3.4 1.7 + - - +
184A ARG* 3.0 24.0 + - - +
413A LEU* 3.7 22.6 - - + +
416A GLU* 2.7 20.9 + - - +
11B TYR* 4.4 2.1 + - - -
56B TRP* 5.6 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.7 7.6 - - + +
177A LYS* 2.8 37.3 + - - +
178A THR* 3.0 20.0 + - - +
180A ALA* 1.3 76.2 - - - +
182A ALA* 1.3 57.2 + - - +
184A ARG* 3.2 26.7 + - - +
185A ILE* 2.9 43.7 + - + +
240A LYS* 3.3 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 4.1 12.3 - - + -
173A PRO* 3.4 24.6 - - + +
176A ALA* 3.5 13.1 - - + +
178A THR 3.0 14.8 + - - +
179A PHE 3.0 8.0 + - - +
181A GLU* 1.3 76.6 - - - +
183A LEU* 1.3 56.6 + - - +
185A ILE* 3.5 1.0 - - - +
186A GLY* 2.9 25.5 + - - -
425A PHE* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 4.8 4.6 - - + +
151A LEU* 4.3 13.7 - - + -
179A PHE* 2.9 30.2 + - + +
180A ALA* 3.9 4.7 - - - +
182A ALA* 1.3 74.1 - - - +
184A ARG* 1.3 58.8 + - - +
186A GLY* 4.9 1.1 - - - -
187A SER* 2.9 31.7 + - - -
400A PRO* 4.6 11.0 - - + -
406A LEU* 5.3 0.7 - - + -
409A LEU* 3.8 59.2 - - + +
413A LEU* 4.0 6.7 - - + -
11B TYR* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA 3.0 18.5 + - - +
181A GLU* 3.2 21.4 + - - +
183A LEU* 1.3 74.3 - - - +
185A ILE* 1.3 81.9 + - - +
187A SER* 2.7 19.5 + - - -
188A GLU* 2.8 54.6 + - - +
237A HIS* 4.6 2.8 - - - -
11B TYR* 3.2 10.3 + - - +
54B SER 3.8 13.1 + - - -
55B LYS* 3.8 30.0 - - - +
56B TRP* 3.3 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PRO* 3.9 14.1 - - + -
176A ALA* 4.2 15.7 - - + +
181A GLU* 2.9 35.8 + - + +
182A ALA* 3.5 6.1 - - - +
184A ARG* 1.3 94.7 - - - +
186A GLY* 1.3 64.6 + - - +
188A GLU* 3.3 4.1 + - - +
189A VAL* 3.0 28.8 + - - +
237A HIS* 3.5 34.1 - - + +
240A LYS* 4.3 20.2 - - + -
241A ILE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.7 24.2 - - - -
171A ILE* 3.7 15.2 - - - +
173A PRO* 4.3 4.9 - - - -
182A ALA 2.9 17.8 + - - -
183A LEU 3.9 0.2 - - - -
185A ILE* 1.3 75.0 - - - +
187A SER* 1.3 64.0 + - - +
189A VAL* 3.2 5.5 + - - +
190A TYR* 3.0 20.8 + - - +
241A ILE* 5.2 0.4 - - - -
400A PRO* 4.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.8 0.4 - - - +
183A LEU 2.9 16.0 + - - -
184A ARG* 2.7 19.6 + - - -
186A GLY* 1.3 75.0 - - - +
188A GLU* 1.3 57.3 + - - +
190A TYR* 3.1 3.5 + - - +
191A HIS* 3.0 36.4 + - - -
400A PRO* 4.0 21.4 - - - +
11B TYR* 3.7 17.5 - - - -
15B GLY 3.8 20.8 + - - -
56B TRP* 3.8 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 2.8 45.3 + - - +
185A ILE* 3.5 5.8 - - - +
186A GLY 3.2 0.2 - - - -
187A SER* 1.3 75.1 + - - +
189A VAL* 1.3 64.9 + - - +
191A HIS* 3.4 2.2 + - - +
192A ASN* 2.9 31.8 + - - -
235A ALA* 4.0 7.7 - - + +
237A HIS* 2.6 37.6 + - - +
54B SER 4.4 7.5 - - - +
55B LYS* 3.5 1.7 - - - -
56B TRP* 2.8 38.2 + - - +
57B MET* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 5.6 2.2 - - + -
171A ILE* 3.7 20.4 - - + -
185A ILE 3.0 16.6 + - - +
186A GLY 3.2 5.6 + - - +
188A GLU* 1.3 74.8 - - - +
190A TYR* 1.3 58.5 + - - +
192A ASN* 3.2 2.8 + - - +
193A LEU* 2.8 30.1 + - + +
228A ILE* 4.7 1.8 - - + +
231A ALA* 3.7 7.4 - - + +
232A ILE* 3.7 36.3 - - + +
235A ALA* 4.0 10.1 - - + -
237A HIS* 3.9 17.0 - - + -
241A ILE* 4.1 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 4.1 26.2 - - + -
171A ILE* 4.8 0.6 - - - +
186A GLY 3.0 8.1 + - - +
187A SER 3.1 8.0 + - - +
189A VAL* 1.3 76.9 - - - +
191A HIS* 1.3 72.8 + + - +
193A LEU* 3.3 7.9 + - + +
194A LYS* 2.9 51.9 + - + +
208A VAL* 3.4 17.0 - - - +
212A GLY 2.6 28.9 + - - -
213A GLY* 4.4 8.2 - - - -
214A VAL* 4.7 6.1 - - + -
399A ALA* 3.9 8.1 - - + -
400A PRO* 3.6 35.2 - - + -
401A ALA* 3.4 21.4 - - + +
14B ARG 4.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 3.0 29.6 + - - +
188A GLU* 4.0 0.8 - - - +
189A VAL 3.3 0.4 - - - -
190A TYR* 1.3 84.0 - + - +
192A ASN* 1.3 60.0 + - - +
194A LYS* 3.3 9.4 + - + +
195A SER* 3.0 29.1 + - - -
14B ARG 3.1 25.8 + - - -
15B GLY* 2.8 27.6 + - - -
16B ASN* 3.3 20.1 + - - -
17B PRO* 5.9 0.4 - - + -
56B TRP* 5.5 3.1 - + - -
57B MET* 3.7 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 2.9 27.9 + - - +
189A VAL 3.6 4.3 - - - +
191A HIS* 1.3 75.7 - - - +
193A LEU* 1.3 56.9 + - - +
195A SER* 3.3 7.7 + - - -
196A LEU* 2.8 33.2 + - - +
231A ALA* 3.8 18.6 - - - +
234A ALA* 3.6 21.0 + - + +
235A ALA* 3.5 24.9 - - - +
57B MET* 3.5 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 3.3 50.5 - - + +
154A LEU* 4.5 4.3 - - + -
189A VAL* 2.8 22.3 + - + +
190A TYR* 3.3 8.0 + - + +
192A ASN* 1.3 70.7 - - - +
194A LYS* 1.3 56.5 + - - +
196A LEU* 3.8 2.9 - - - +
197A THR* 2.7 44.1 + - - +
214A VAL* 4.0 9.4 - - + -
227A LEU* 3.6 48.0 - - + +
228A ILE* 4.3 8.3 - - + +
231A ALA* 3.6 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 2.9 50.0 + - + +
191A HIS* 3.7 10.5 - - + +
193A LEU* 1.3 75.5 - - - +
195A SER* 1.3 63.3 + - - +
197A THR* 3.4 2.0 + - - -
198A LYS* 3.0 34.9 + - + +
206A GLY* 2.8 35.2 + - - +
207A ASN* 4.7 4.8 - - - +
208A VAL* 3.9 10.5 - - - +
214A VAL* 4.0 15.9 - - + +
210B ASP* 4.5 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A HIS 3.0 17.7 + - - -
192A ASN* 3.4 8.1 - - - -
194A LYS* 1.3 75.6 - - - +
196A LEU* 1.3 64.6 + - - +
198A LYS* 3.3 8.2 + - - +
199A LYS* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 2.8 23.4 + - - +
193A LEU* 3.8 4.0 - - - +
195A SER* 1.3 73.9 + - - +
197A THR* 1.3 56.8 + - - +
199A LYS* 3.4 6.7 + - + +
200A ARG* 2.9 57.3 + - + +
227A LEU* 4.1 15.7 - - + +
230A ASP* 3.9 17.7 - - + +
231A ALA* 3.8 32.8 - - + +
234A ALA* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 2.7 29.5 + - - +
194A LYS* 3.7 7.0 - - - -
196A LEU* 1.3 71.8 - - - +
198A LYS* 1.3 57.5 + - - +
201A TYR* 2.8 39.7 + - + +
202A GLY 3.8 0.3 + - - +
205A ALA* 3.5 32.5 - - + +
206A GLY* 4.3 0.7 - - - +
214A VAL* 3.9 13.6 - - + +
216A PRO* 3.9 24.2 - - + -
227A LEU* 3.7 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 3.0 28.8 + - + +
195A SER* 3.8 6.3 - - - +
197A THR* 1.3 76.5 - - - +
199A LYS* 1.3 57.8 + - - +
202A GLY* 3.0 32.4 + - - +
203A ALA* 3.8 32.7 + - - +
206A GLY* 3.7 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER* 3.1 17.1 + - - +
196A LEU* 3.7 9.4 - - + +
198A LYS* 1.3 79.0 - - - +
200A ARG* 1.3 63.6 + - + +
202A GLY* 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 2.9 38.2 + - + +
199A LYS* 1.3 83.2 - - + +
201A TYR* 1.3 81.2 + - + +
202A GLY 3.7 0.4 - - - -
226A ASP* 5.3 1.0 - - - +
227A LEU* 3.4 31.6 - - - +
230A ASP* 2.7 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A THR* 2.8 30.8 + - + +
200A ARG* 1.3 95.1 + - + +
202A GLY* 1.3 61.6 + - - +
204A SER* 5.2 2.3 + - - -
205A ALA* 3.5 21.3 + - + +
216A PRO* 3.9 11.7 - - + -
217A ASN* 4.1 17.7 - - + +
218A ILE* 3.9 13.4 - - + +
223A GLU* 2.7 40.5 + - - +
227A LEU* 3.9 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 3.0 26.7 + - - -
199A LYS 4.6 1.0 + - - -
200A ARG 3.7 1.0 - - - -
201A TYR* 1.3 79.9 - - - +
203A ALA* 1.3 66.6 + - - -
204A SER* 3.1 6.2 + - - -
205A ALA* 3.2 12.8 + - - +
206A GLY 3.9 0.2 + - - -
----------------------------------------------------------
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