Contacts of the helix formed by residues 165 - 183 (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 ASP 165 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PRO* 3.5 31.8 - - - +
116E THR 4.0 4.6 + - - +
117E LEU* 3.9 18.1 - - + +
163E SER 3.1 5.9 + - - +
164E GLU* 1.3 98.6 + - - +
166E PRO* 1.3 69.4 - - + +
167E ARG* 2.3 25.9 + - - -
168E GLU 2.9 1.0 + - - -
169E ARG* 4.0 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E GLU 4.1 0.4 - - - +
165E ASP* 1.3 99.6 - - + +
167E ARG* 1.3 62.3 + - + +
168E GLU 2.7 1.2 + - - -
169E ARG* 2.7 23.3 + - + +
170E ASP* 2.4 52.2 + - + +
213E GLU* 5.0 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E LEU* 3.3 40.5 - - - +
118E GLU 5.0 0.4 + - - -
121E TRP* 2.8 64.7 - - + +
164E GLU* 2.5 33.9 + - - +
165E ASP* 2.3 16.2 + - - -
166E PRO* 1.3 74.3 - - + +
168E GLU* 1.3 57.5 + - - +
170E ASP* 4.2 1.5 - - - +
171E PHE* 3.0 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E MET* 3.3 4.0 - - - +
95E ARG* 2.6 34.7 + - - -
97E LEU* 4.7 4.3 - - - +
118E GLU* 4.4 3.8 - - - +
121E TRP* 3.6 18.4 - - + -
124E LEU* 5.6 0.2 - - - -
128E TYR* 2.6 29.0 + - + +
160E LEU* 3.9 12.6 - - - +
163E SER 5.2 0.7 + - - +
164E GLU* 3.3 33.2 + - + +
165E ASP 2.9 6.3 + - - -
166E PRO 2.7 3.1 + - - -
167E ARG* 1.3 73.8 - - - +
169E ARG* 1.3 68.4 + - + +
171E PHE* 3.4 4.3 + - - +
172E LEU* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E LEU 5.2 0.2 - - - +
161E PHE* 4.6 7.2 - - + -
162E ASP 4.6 7.0 - - - +
163E SER* 4.0 29.1 + - - +
164E GLU 3.5 10.1 + - - +
165E ASP* 4.0 23.2 + - - +
166E PRO* 2.7 29.0 + - + +
168E GLU* 1.3 73.1 - - + +
170E ASP* 1.3 65.7 + - - +
172E LEU* 2.7 16.2 + - + +
173E LYS* 2.6 22.8 + - - +
209E ASN* 3.5 26.7 + - - +
210E GLY* 4.0 7.2 - - - -
213E GLU* 3.0 50.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E PRO* 2.4 46.3 + - + +
167E ARG* 4.2 3.4 - - - +
169E ARG* 1.3 66.3 - - - +
171E PHE* 1.3 67.7 + - + +
173E LYS* 2.8 42.9 + - - +
174E THR* 2.9 20.5 + - - -
213E GLU* 4.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E TRP* 4.2 11.2 - + - -
125E GLN* 4.1 15.5 - - + -
128E TYR* 3.1 41.1 - + + -
129E GLU* 3.5 48.2 - - + -
132E LEU* 4.2 16.3 - - + +
167E ARG* 3.0 24.5 - - - -
168E GLU 3.4 6.4 + - - +
169E ARG 3.2 0.6 - - - -
170E ASP* 1.3 82.3 - - + +
172E LEU* 1.3 51.0 + - - +
174E THR* 3.2 5.8 + - - +
175E THR* 2.4 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E TYR* 3.4 21.5 - - + +
157E LEU* 3.8 29.5 - - + +
160E LEU* 3.6 40.4 - - + +
161E PHE* 3.8 20.1 - - + +
168E GLU* 3.0 35.4 - - + +
169E ARG* 2.7 21.9 + - - +
171E PHE* 1.3 71.6 - - - +
173E LYS* 1.3 62.0 + - - +
175E THR* 4.1 4.3 - - - -
176E LEU* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E PHE* 3.8 4.2 - - - -
169E ARG 2.6 14.2 + - - +
170E ASP* 2.9 37.9 + - - +
172E LEU* 1.3 73.1 - - - +
174E THR* 1.3 66.8 + - - +
177E HIS* 3.1 19.5 + - + +
213E GLU* 4.2 21.8 - - + +
216E GLU* 2.7 45.1 + - - +
217E ILE* 3.2 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 3.9 28.7 - - + -
170E ASP* 2.9 20.0 + - - -
171E PHE* 3.8 7.0 - - - -
173E LYS* 1.3 76.7 - - - +
175E THR* 1.3 69.3 + - - +
177E HIS* 3.1 18.9 + - + +
178E ARG* 3.2 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E PHE* 5.3 3.6 - - + -
128E TYR* 4.6 8.1 - - + -
131E PHE* 3.9 27.1 - - + -
132E LEU* 4.2 23.4 - - + +
157E LEU* 4.5 13.0 - - + -
171E PHE* 2.4 36.1 + - - +
172E LEU* 3.5 6.0 - - - -
174E THR* 1.3 74.3 - - - +
176E LEU* 1.3 61.9 + - - +
178E ARG* 3.5 3.0 + - - +
179E ILE* 2.8 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E VAL* 4.4 11.9 - - + -
157E LEU* 4.4 14.7 - - + +
158E LEU* 3.8 22.0 - - + -
161E PHE* 3.7 17.0 - - + -
172E LEU 2.8 20.4 + - - +
175E THR* 1.3 73.0 - - - +
177E HIS* 1.3 66.3 + - - +
179E ILE* 2.9 13.4 + - + +
180E TYR* 2.7 22.5 + - + +
190E ILE* 3.8 31.9 - - + -
194E ILE* 4.4 15.0 - - + -
214E LEU* 4.6 0.4 - - + -
217E ILE* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E LYS* 3.1 15.5 + - + +
174E THR* 3.1 14.8 + - + +
176E LEU* 1.3 76.7 - - - +
178E ARG* 1.3 63.5 + - + +
180E TYR* 3.0 14.1 + + + +
181E GLY* 2.9 25.4 + - - -
217E ILE* 4.1 22.2 - - + +
220E SER* 3.9 31.4 + - - -
221E ILE* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 3.4 19.5 - - + +
136E GLU* 2.6 60.7 + - - -
174E THR* 3.2 25.2 + - - +
175E THR* 4.1 6.1 - - - +
177E HIS* 1.3 81.3 + - + +
179E ILE* 1.3 67.1 + - + +
180E TYR 3.0 1.8 - - - -
181E GLY* 3.0 3.1 + - - +
182E LYS* 2.9 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E PHE* 4.6 7.2 - - + -
149E ILE* 4.4 13.0 - - + -
153E PHE* 4.2 14.6 - - + -
154E VAL* 5.5 4.9 - - + -
157E LEU* 3.4 32.5 - - + -
175E THR* 2.8 36.0 + - + +
176E LEU* 2.9 11.1 + - + +
178E ARG* 1.3 76.0 - - + +
180E TYR* 1.3 61.0 + - - +
183E PHE* 2.9 51.2 + - + +
186E LEU* 4.3 18.3 - - + +
190E ILE* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E LEU* 2.7 12.3 + - + +
177E HIS* 3.1 16.4 - + - +
179E ILE* 1.3 79.8 - - - +
181E GLY* 1.3 61.5 + - - +
182E LYS 3.3 1.0 + - - -
183E PHE 3.8 3.2 + - - +
187E ARG* 3.0 89.4 + - + +
190E ILE* 3.8 30.7 - - + -
191E ARG* 3.1 27.2 + - + -
217E ILE* 5.6 0.7 - - + -
221E ILE* 3.3 49.6 - - + +
225E PHE* 5.1 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E HIS* 2.9 15.4 + - - -
178E ARG* 3.0 5.1 + - - -
180E TYR* 1.3 81.8 - - - +
182E LYS* 1.3 62.0 + - - +
184E LEU* 4.6 1.9 - - - +
187E ARG* 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E LEU* 3.3 35.3 + - + +
136E GLU* 3.9 13.5 - - - +
137E SER 4.9 2.2 + - - +
142E PRO* 4.0 19.8 - - + +
178E ARG* 2.9 34.7 + - + +
179E ILE 3.5 0.2 + - - -
180E TYR 3.2 0.2 - - - -
181E GLY* 1.3 83.7 - - - +
183E PHE* 1.3 79.7 + - + +
184E LEU* 4.0 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
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
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