Contacts of the helix formed by residues 162 - 185 (chain E) in PDB entry 4MNE
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 PRO 162 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E ARG 3.5 8.1 - - - +
161E ILE* 1.4 93.3 - - + +
163E GLU* 1.3 66.3 + - - +
164E GLN* 4.5 3.1 - - + +
165E ILE* 2.9 29.4 + - + +
166E LEU* 3.0 10.3 + - - +
374E TRP* 3.6 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ILE 3.7 2.2 + - - -
162E PRO* 1.3 69.8 - - - +
164E GLN* 1.3 62.2 + - + +
166E LEU* 3.0 11.6 + - - +
167E GLY* 2.8 26.3 + - - -
329E VAL 4.3 1.4 - - - +
330E PHE* 3.5 23.6 - - + -
331E SER* 2.7 47.1 + - - -
334E PHE* 3.2 34.1 - - + +
360E PHE* 4.3 7.2 - - + -
363E ARG* 3.0 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E PRO* 3.1 3.9 + - + +
163E GLU* 1.3 81.5 - - + +
165E ILE* 1.3 62.8 + - + +
167E GLY* 3.2 10.7 + - - -
168E LYS* 3.3 17.2 + - - +
363E ARG* 5.0 6.3 - - - +
364E SER* 5.3 1.9 - - - -
367E GLU* 3.3 35.0 - - - +
368E GLU 4.9 2.3 - - - +
369E VAL* 3.3 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ILE* 3.8 16.4 - - + -
162E PRO* 2.9 30.5 + - + +
164E GLN* 1.3 77.6 - - + +
166E LEU* 1.3 62.3 + - - +
168E LYS* 2.9 16.8 + - - +
169E VAL* 3.1 15.2 + - + +
369E VAL* 3.7 24.0 - - + -
370E ASP 4.6 0.4 - - - +
371E PHE* 3.4 37.0 - - + -
374E TRP* 3.7 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E ILE* 3.4 40.6 - - + +
162E PRO 3.0 14.1 + - - +
163E GLU* 3.2 9.0 - - - +
165E ILE* 1.3 75.5 - - - +
167E GLY* 1.3 49.8 + - - +
169E VAL* 3.1 11.0 + - + +
170E SER* 2.5 41.1 + - - -
253E LEU* 3.9 10.2 - - + +
256E MET* 4.0 27.8 - - + -
257E ALA* 3.5 33.7 - - + +
334E PHE* 3.9 22.7 - - + -
360E PHE* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E GLU 2.8 11.2 + - - -
164E GLN* 3.6 4.9 - - - -
165E ILE 3.2 0.8 - - - -
166E LEU* 1.3 76.3 - - - +
168E LYS* 1.3 61.4 + - - +
170E SER* 3.5 2.3 + - - -
171E ILE* 3.1 31.6 + - - +
360E PHE* 3.4 26.4 - - - -
361E ILE* 4.5 1.2 - - - +
364E SER* 3.7 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E GLN 3.3 11.7 + - - +
165E ILE* 2.9 9.6 + - - +
167E GLY* 1.3 71.9 - - - +
169E VAL* 1.3 61.3 + - - +
171E ILE* 3.1 17.6 + - + +
172E ALA* 2.9 27.2 + - - +
204E ILE* 4.4 13.0 - - + +
364E SER* 3.1 26.5 + - - +
365E ASP* 4.0 11.5 + - - +
367E GLU* 3.2 17.0 + - - -
369E VAL* 3.8 38.3 - - + +
371E PHE* 5.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU* 3.7 33.9 - - + -
161E ILE* 5.8 0.7 - - + -
165E ILE* 3.1 21.9 + - + +
166E LEU* 3.1 18.5 + - + +
168E LYS* 1.3 73.1 - - - +
170E SER* 1.3 53.6 + - - +
172E ALA* 2.8 8.1 + - - +
173E VAL* 2.7 48.0 + - + +
196E ILE* 4.5 9.2 - - + -
204E ILE* 4.1 20.9 - - + -
253E LEU* 4.9 4.0 - - + -
256E MET* 4.8 8.7 - - + -
371E PHE* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E LEU 2.5 29.2 + - - -
167E GLY 3.7 5.4 - - - -
169E VAL* 1.3 73.7 - - - +
171E ILE* 1.3 62.0 + - - +
173E VAL* 3.9 6.3 - - - +
174E ILE* 2.9 32.3 + - - +
249E MET* 4.6 4.9 - - - -
253E LEU* 3.6 19.7 - - - +
334E PHE* 5.3 0.3 - - - -
337E PHE* 4.1 17.7 - - - -
360E PHE* 3.9 7.6 - - - -
361E ILE* 4.0 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E TYR* 5.1 3.4 - - + +
167E GLY 3.1 23.7 + - - +
168E LYS* 3.3 21.3 - - + +
169E VAL 3.1 0.2 - - - -
170E SER* 1.3 75.0 - - - +
172E ALA* 1.3 66.3 + - - +
174E ILE* 3.1 6.1 + - - +
175E LYS* 2.9 51.4 + - + +
356E MET* 5.5 3.4 - - - -
361E ILE* 4.2 24.0 - - + -
364E SER* 4.0 7.6 - - - -
365E ASP* 3.6 45.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E TYR* 3.5 35.4 - - + +
168E LYS 2.9 11.7 + - - +
169E VAL 2.8 13.1 + - - +
171E ILE* 1.3 72.8 - - - +
173E VAL* 1.3 57.0 + - + +
175E LYS 3.4 0.3 + - - -
176E GLY* 3.0 23.4 + - - -
204E ILE* 3.7 38.1 - - + +
206E LEU* 5.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E VAL* 2.7 29.3 + - + +
170E SER* 3.9 4.3 - - - +
172E ALA* 1.3 73.4 - - + +
174E ILE* 1.3 57.2 + - - +
176E GLY* 3.3 0.9 + - - -
177E LEU* 2.9 44.9 + - + +
191E VAL* 4.7 7.2 - - + -
196E ILE* 4.0 26.0 - - + -
206E LEU* 3.7 28.5 - - + +
249E MET* 3.6 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E SER 2.9 25.3 + - - +
171E ILE* 3.7 4.5 - - - +
173E VAL* 1.3 74.0 - - - +
175E LYS* 1.3 66.7 + - - +
177E LEU* 3.5 5.9 + - + +
178E THR* 3.0 32.2 + - - +
249E MET* 4.3 12.8 - - - -
337E PHE* 3.9 18.8 - - + -
352E LEU* 4.2 27.8 - - + +
355E LEU* 3.7 35.7 - - + +
356E MET* 3.6 27.4 - - + +
361E ILE* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E TYR* 3.0 49.2 + - + +
171E ILE* 2.9 42.1 + - + +
172E ALA 3.6 2.2 - - - +
174E ILE* 1.3 79.3 - - - +
176E GLY* 1.3 57.1 + - - +
178E THR* 3.3 6.5 + - - -
179E TYR* 2.8 29.8 + - - +
356E MET* 3.7 26.5 - - + -
365E ASP* 5.5 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E TYR* 3.8 15.7 - - - -
126E ILE* 4.0 7.4 - - - +
172E ALA 3.0 14.4 + - - -
173E VAL 3.8 2.2 - - - -
174E ILE 3.2 0.2 - - - -
175E LYS* 1.3 76.6 - - - +
177E LEU* 1.3 58.4 + - - +
179E TYR* 3.4 5.0 + - - +
180E LEU* 3.0 33.4 + - - +
206E LEU* 3.9 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E VAL* 2.9 34.1 + - + +
174E ILE* 4.0 4.0 - - - +
176E GLY* 1.3 74.7 - - - +
178E THR* 1.3 58.1 + - - +
180E LEU* 3.5 6.5 + - + +
181E ARG* 3.0 31.4 + - - +
186E ILE 5.0 0.3 - - - +
187E MET* 5.9 0.7 - - - -
188E HIS* 3.7 32.1 - - + +
191E VAL* 4.2 4.3 - - + -
206E LEU* 3.9 12.8 - - + +
242E VAL* 4.8 8.6 - - + +
245E ASP* 4.0 33.4 - - + +
246E ILE* 4.8 4.0 - - + +
249E MET* 5.4 3.1 - - - -
352E LEU* 4.0 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E ILE* 3.0 25.3 + - - +
175E LYS* 3.6 6.7 - - - -
177E LEU* 1.3 74.5 - - - +
179E TYR* 1.3 66.4 + - - +
181E ARG* 3.8 8.0 - - - +
182E GLU* 2.9 50.6 + - - +
352E LEU* 3.6 24.9 - - - +
356E MET* 4.8 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E GLU 3.8 2.3 + - - -
121E CYS* 3.7 9.0 - - - -
122E ASN* 2.8 40.2 + - - +
123E SER* 3.9 22.2 - - - +
125E TYR* 6.0 0.4 - - + -
126E ILE* 3.8 21.3 - - + -
175E LYS 2.8 20.4 + - - +
176E GLY* 3.6 5.4 - - - +
177E LEU 3.3 0.2 - - - -
178E THR* 1.3 72.7 - - - +
180E LEU* 1.3 68.7 + - + +
182E GLU* 5.0 0.4 - - - -
183E LYS* 2.9 57.2 + - + +
184E HIS* 3.0 34.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E CYS* 4.7 7.6 - - - -
126E ILE* 3.9 21.3 - - + -
176E GLY 3.0 23.1 + - - +
177E LEU* 3.9 7.4 - - + +
179E TYR* 1.3 83.5 - - + +
181E ARG* 1.3 63.4 + - - +
184E HIS* 2.9 15.8 + - + +
185E LYS 2.9 17.8 + - - -
186E ILE* 3.4 26.2 - - + +
187E MET 4.9 0.9 - - - +
188E HIS* 4.3 18.8 - - + -
206E LEU* 4.8 1.8 - - + -
209E PHE* 3.6 53.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E LEU 3.0 17.8 + - - +
178E THR* 4.0 12.2 + - - +
180E LEU* 1.3 76.0 - - - +
182E GLU* 1.3 95.6 + - - +
185E LYS* 3.1 30.4 + - + +
186E ILE 3.5 10.0 + - - +
242E VAL* 4.0 28.7 - - + -
352E LEU* 3.9 24.2 - - + +
353E LYS* 5.7 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E THR* 2.9 35.5 + - - +
179E TYR* 4.3 0.4 - - - +
181E ARG* 1.3 113.8 + - - +
183E LYS* 1.3 80.1 + - + +
184E HIS 3.5 0.3 + - - -
185E LYS* 4.4 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E TYR* 2.9 42.0 + - + +
182E GLU* 1.3 88.7 - - + +
184E HIS* 1.3 86.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E VAL* 4.3 17.6 - - + +
120E GLU* 2.8 31.0 - - + -
121E CYS* 3.7 18.3 - - - -
179E TYR* 3.0 41.9 + + - -
180E LEU* 2.9 10.5 + - + +
183E LYS* 1.3 96.0 + - + +
185E LYS* 1.3 74.3 + - - +
186E ILE* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E LEU 2.9 5.7 + - - -
181E ARG* 3.1 21.6 + - + +
182E GLU 4.4 2.6 + - - +
184E HIS* 1.3 79.3 - - - +
186E ILE* 1.3 60.2 + - - +
----------------------------------------------------------
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