Contacts of the helix formed by residues 183 - 204 (chain E) in PDB entry 2NPP
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 183 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E LEU* 5.0 11.2 - - + -
142E PRO* 4.0 15.3 - - + -
145E ALA* 3.9 18.8 - - + -
146E LYS* 3.8 35.4 - - + -
149E ILE* 4.3 16.6 - - + -
179E ILE* 2.9 45.4 + - + +
180E TYR 3.8 1.2 + - - +
181E GLY 3.7 1.6 - - - -
182E LYS* 1.3 98.1 - - + +
184E LEU* 1.3 66.4 + - - +
185E GLY 2.9 4.9 - - - +
186E LEU* 2.9 34.5 + - + +
187E ARG* 3.3 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E GLY 4.6 3.8 - - - +
182E LYS 4.0 1.7 + - - +
183E PHE* 1.3 72.0 - - - +
185E GLY* 1.3 57.7 + - - +
186E LEU 2.9 5.9 + - - -
187E ARG* 3.2 59.3 + - - +
188E ALA* 4.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E LYS* 5.9 4.3 - - - -
183E PHE* 2.9 4.5 - - - +
184E LEU* 1.3 76.0 - - - +
186E LEU* 1.3 70.6 + - - +
188E ALA* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ILE* 4.2 22.2 - - + +
150E ASP* 4.7 2.2 - - - +
151E GLN* 4.4 24.5 - - + +
154E VAL* 3.6 24.0 - - + -
179E ILE* 4.3 18.4 - - + +
183E PHE* 2.9 28.0 + - + +
184E LEU 2.9 1.2 + - - -
185E GLY* 1.3 86.9 - - - +
187E ARG* 1.3 71.8 + - - +
188E ALA* 2.7 6.1 + - - -
189E TYR* 2.9 17.4 + - + +
190E ILE* 2.8 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E TYR* 3.0 69.1 + - + +
181E GLY* 3.1 30.9 + - - -
183E PHE 3.5 7.2 - - - +
184E LEU* 3.2 38.7 - - - +
186E LEU* 1.3 76.4 - - - +
188E ALA* 1.3 65.5 + - - +
190E ILE* 3.5 0.8 + - - +
191E ARG* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E LEU 4.7 2.2 + - - +
185E GLY 6.2 0.4 - - - -
186E LEU* 2.7 6.0 + - - +
187E ARG* 1.3 78.9 - - - +
189E TYR* 1.3 68.5 + - - +
191E ARG* 2.6 27.9 + - - +
192E LYS* 2.9 14.6 + - + -
232E GLU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D GLU* 3.8 10.6 + - - -
151E GLN* 3.4 74.5 - - + +
154E VAL* 4.2 10.3 - - + -
155E LEU* 3.4 32.0 - - + +
186E LEU* 2.9 13.9 + - + +
188E ALA* 1.3 76.1 - - - +
190E ILE* 1.3 69.4 + - + +
191E ARG 2.8 1.6 + - - -
192E LYS* 4.3 10.7 - - + +
193E GLN* 2.8 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E VAL* 3.6 24.5 - - + -
158E LEU* 4.5 1.9 - - + +
176E LEU* 3.8 27.4 - - + -
179E ILE* 5.7 1.1 - - + -
180E TYR* 3.8 33.2 - - + +
186E LEU* 2.8 64.9 + - + +
187E ARG* 3.7 2.7 - - - +
189E TYR* 1.3 78.7 - - + +
191E ARG* 1.3 62.9 + - + +
193E GLN* 3.9 4.2 + - - +
194E ILE* 3.0 45.2 + - + +
217E ILE* 6.1 0.7 - - + -
221E ILE* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E TYR* 3.1 27.2 + - + +
187E ARG* 3.0 18.2 + - - +
188E ALA* 2.6 39.5 + - - +
190E ILE* 1.3 70.4 - - + +
192E LYS* 1.3 70.7 + - - +
194E ILE* 2.8 17.3 + - + +
195E ASN* 3.0 18.4 + - - +
218E LEU* 5.1 12.8 - - + -
221E ILE* 4.7 11.4 - - + -
225E PHE* 5.2 1.3 - - - -
232E GLU* 2.7 49.9 + - - +
233E HIS* 4.0 26.6 + - - -
236E PHE* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ASP* 5.4 15.9 - - - +
188E ALA* 2.9 11.5 + - + +
189E TYR* 2.9 19.6 + - + +
191E ARG* 1.3 70.4 - - - +
193E GLN* 1.3 61.7 + - - +
195E ASN* 2.6 39.7 + - + +
196E ASN* 3.0 21.2 + - - +
232E GLU* 5.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ASP 5.5 3.0 + - - -
179D PRO* 5.0 5.5 - - - +
216D GLU* 5.5 1.8 + - - -
217D GLN* 5.1 3.4 + - - +
155E LEU* 3.9 18.6 - - + +
158E LEU* 3.5 22.2 - - + -
189E TYR* 2.8 68.1 + - + +
190E ILE 4.0 0.2 - - - +
192E LYS* 1.3 78.2 - - - +
194E ILE* 1.3 56.6 + - - +
196E ASN* 3.1 28.8 + - - +
197E ILE* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LEU* 4.1 11.0 - - + -
176E LEU* 4.4 7.4 - - + -
190E ILE* 3.0 36.1 + - + +
191E ARG* 2.8 14.2 + - - +
193E GLN* 1.3 72.8 - - - +
195E ASN* 1.3 59.9 - - - +
197E ILE* 3.2 8.9 + - - +
198E PHE* 2.9 51.6 + - + -
214E LEU* 3.4 36.6 - - + +
217E ILE* 5.2 6.1 - - + -
218E LEU* 4.1 23.8 - - + -
221E ILE* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E ARG* 3.0 21.4 + - - +
192E LYS* 2.6 25.4 + - + +
194E ILE* 1.3 70.7 - - - +
196E ASN* 1.3 54.6 + - - +
198E PHE* 2.9 8.3 + - - +
199E TYR* 2.7 57.0 + - + -
232E GLU* 5.1 6.3 + - - -
236E PHE* 3.2 39.6 - - - +
240E VAL* 4.2 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ASP 4.5 4.9 + - - -
178D THR* 4.0 11.6 - - - +
179D PRO* 3.3 26.0 - - + +
180D MET* 3.5 26.4 - - + +
192E LYS* 3.0 20.1 + - - +
193E GLN* 3.3 34.9 + - - +
195E ASN* 1.3 80.1 - - - +
197E ILE* 1.3 65.0 + - + +
198E PHE 2.9 1.2 + - - -
199E TYR* 4.2 5.6 - - - -
200E ARG* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 6.4 0.4 - - + -
158E LEU* 3.7 48.5 - - + +
159E GLU* 4.9 2.0 - - - +
193E GLN* 2.9 21.1 + - + +
194E ILE* 3.2 9.6 + - - +
196E ASN* 1.3 77.0 - - + +
198E PHE* 1.3 63.1 + - + +
200E ARG* 4.3 5.6 - - - +
201E PHE* 3.5 18.2 + - - +
208E HIS* 3.3 36.9 + - + +
211E ILE* 6.0 0.4 - - + -
214E LEU* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E ILE* 2.9 24.1 + - + -
195E ASN* 3.3 7.6 - - - +
196E ASN 2.9 0.4 - - - -
197E ILE* 1.3 80.4 - - + +
199E TYR* 1.3 66.1 + - - +
200E ARG 3.2 1.1 - - - -
201E PHE* 2.8 6.9 + - + +
202E ILE* 2.8 27.9 + - + +
211E ILE* 3.8 37.2 - - + -
214E LEU* 4.0 26.2 - - + -
215E LEU* 4.0 21.8 - - + -
218E LEU* 3.5 26.7 - - + -
236E PHE* 4.7 3.1 - + - -
240E VAL* 3.9 28.3 - - + -
241E LEU* 5.8 1.1 - - + -
244E LEU* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU* 5.6 0.2 - - - -
140D TRP* 2.9 30.0 - + - -
141D PHE* 3.5 36.1 - + + -
178D THR* 6.0 0.9 - - + -
180D MET* 3.8 26.7 - - + -
195E ASN* 2.7 38.2 + - + +
196E ASN* 3.2 4.9 + - - +
198E PHE* 1.3 71.9 - - - +
200E ARG* 1.3 65.5 + - - +
201E PHE 3.0 0.3 + - - -
202E ILE* 3.1 3.3 + - + -
203E TYR* 2.8 42.0 + + - +
204E GLU* 4.9 0.4 - - - -
235E ILE* 5.0 2.8 - - - +
239E LYS* 3.4 14.3 - - - +
240E VAL* 3.0 37.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D MET* 4.8 0.6 - - - +
183D ARG* 3.6 26.9 - - - +
217D GLN* 5.9 1.8 - - - +
218D ASP* 5.6 0.8 + - - -
219D SER* 3.3 34.7 + - - -
196E ASN 3.0 14.4 + - - +
197E ILE* 4.3 7.2 - - - +
199E TYR* 1.3 80.0 - - - +
201E PHE* 1.3 56.7 + - - +
204E GLU* 2.9 54.2 + - + +
205E THR* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E ILE 3.5 14.1 + - - +
198E PHE* 2.8 12.3 + + - +
200E ARG* 1.3 80.7 - - - +
202E ILE* 1.3 68.9 + - + +
205E THR* 3.1 18.6 - - - +
206E GLU* 3.4 19.2 - - - +
207E HIS* 3.5 38.4 - - - -
208E HIS* 3.5 21.1 - - + -
211E ILE* 3.8 31.9 - - + -
244E LEU* 4.5 6.7 - - + -
247E VAL* 3.8 18.1 - - + +
249E SER* 3.6 22.7 - - - -
253E TYR* 3.6 25.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E PHE* 2.8 19.6 + - + +
199E TYR* 3.8 4.7 - - + +
201E PHE* 1.3 83.9 - - + +
203E TYR* 1.3 89.2 + - + +
206E GLU* 3.9 6.9 - - - +
240E VAL* 3.6 27.1 - - + +
243E PRO* 3.7 22.0 - - + +
244E LEU* 3.8 32.3 - - + +
246E LYS* 4.4 8.4 - - + +
247E VAL* 4.3 11.8 - - + +
302F ARG* 2.8 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU* 3.4 42.5 + - + +
101D GLU* 4.1 2.0 - - - -
102D THR* 3.3 38.7 + - + +
105D ARG* 4.4 8.3 - - - +
141D PHE* 4.2 20.9 - + + -
142D THR* 5.9 0.2 - - + -
199E TYR* 2.8 40.0 + + - +
202E ILE* 1.3 100.9 - - + +
204E GLU* 1.3 62.7 + - + +
239E LYS 5.0 0.4 - - - -
243E PRO* 3.6 18.7 - - - +
246E LYS* 3.7 20.6 + - - -
282E TYR* 4.8 1.0 + - - -
302F ARG* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 6.0 2.5 - - - +
180D MET* 3.9 20.3 - - - +
183D ARG* 2.9 47.7 + - - +
199E TYR 5.7 0.2 - - - -
200E ARG* 2.9 35.4 + - + +
202E ILE 3.8 0.6 - - - -
203E TYR* 1.3 79.5 - - + +
205E THR* 1.3 66.8 + - + +
206E GLU 3.5 3.2 + - - -
302F ARG* 3.6 19.3 - - - +
----------------------------------------------------------
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