Contacts of the helix formed by residues 196 - 213 (chain E) in PDB entry 2A27
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 LEU 196 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E HIS* 3.2 61.8 - - + +
134E LYS* 4.4 6.1 - - + -
135E ILE 3.4 38.8 - - - +
136E ALA* 3.9 5.4 - - + -
168E ILE* 3.8 22.6 - - + +
195E GLY* 1.3 71.1 - - - -
197E GLU* 1.3 69.9 + - + +
198E ALA 3.2 0.7 + - - -
199E ASP* 3.2 11.8 + - - +
200E MET* 3.8 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E GLU* 4.0 2.6 - - - +
193E PRO 5.3 0.7 - - - +
194E LEU* 4.1 1.9 - - - -
195E GLY* 3.1 24.4 + - - -
196E LEU* 1.3 82.6 - - + +
198E ALA* 1.3 61.9 + - - +
200E MET* 2.9 26.0 + - - +
260E THR* 3.7 47.3 + - - +
261E ARG* 5.8 0.5 - - - -
263E ARG* 2.8 26.3 + - + +
264E LEU 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PHE* 3.8 31.9 - - + -
185E ALA* 4.2 12.4 + - + +
187E GLU* 3.5 21.1 + - + +
188E ILE* 4.7 9.9 - - + -
194E LEU* 5.4 0.2 - - + -
195E GLY 3.5 4.2 + - - +
196E LEU 3.2 1.0 + - - -
197E GLU* 1.3 78.3 - - - +
199E ASP* 1.3 63.8 + - - +
201E TRP* 3.2 6.1 + - - +
202E SER* 3.1 23.5 + - - -
263E ARG* 3.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E VAL* 4.6 1.8 - - + -
131E HIS* 3.2 26.8 + - + +
136E ALA* 3.3 12.8 - - - +
137E HIS* 3.1 23.0 + - - -
138E PHE* 3.0 28.7 + - - -
139E ASP 4.4 0.5 + - - -
140E LEU* 3.5 25.9 + - + +
195E GLY 5.4 0.2 - - - -
196E LEU 3.2 9.2 + - - +
198E ALA* 1.3 78.3 - - - +
200E MET* 1.3 57.9 + - - +
202E SER* 3.3 7.2 + - - -
203E ILE* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 200 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E LEU* 4.9 0.7 - - + -
131E HIS* 3.9 12.3 - - + -
196E LEU 4.0 8.1 - - - +
197E GLU* 2.9 17.5 + - - +
199E ASP* 1.3 73.5 - - - +
201E TRP* 1.3 66.1 + - - +
203E ILE* 3.4 17.4 + - + +
204E GLY 3.2 16.3 + - - -
255E LEU* 3.5 27.9 - - + +
263E ARG* 4.1 7.4 - - - -
264E LEU 3.2 22.2 - - - +
265E THR* 3.6 10.5 - - - +
266E ILE* 3.6 48.5 - - + +
269E ALA* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 201 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E GLU 5.3 0.4 + - - -
183E PHE 4.0 4.2 + - - -
184E VAL 3.2 16.0 + - - -
185E ALA* 3.6 16.8 - - + -
186E PRO* 3.4 41.1 - - + -
197E GLU 3.3 2.8 + - - -
198E ALA 3.2 7.2 + - - +
200E MET* 1.3 76.0 - - - +
202E SER* 1.3 67.2 + - - +
204E GLY* 3.0 13.0 + - - -
205E VAL* 3.1 26.9 + - + +
217E PHE* 3.2 40.5 - + - -
229E ILE* 4.0 15.7 - - + +
232E VAL* 4.2 9.0 - - + -
255E LEU 4.0 9.2 - - - -
256E LEU* 3.6 9.7 - - + +
257E VAL 3.4 43.5 - - - -
258E LYS 4.1 0.7 - - - -
263E ARG* 3.4 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PHE 5.9 1.4 - - - -
140E LEU* 3.5 37.2 + - - +
183E PHE* 3.1 25.1 + - - -
185E ALA 5.4 0.3 + - - -
198E ALA 3.1 10.9 + - - -
199E ASP* 3.5 12.0 + - - -
201E TRP* 1.3 79.4 - - - +
203E ILE* 1.3 56.3 + - - +
205E VAL* 3.3 6.3 + - - +
206E ILE* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ILE* 5.3 4.5 - - + -
123E ILE* 4.8 12.3 - - + -
124E LEU* 4.1 27.1 - - + -
127E VAL* 4.1 25.4 - - + -
140E LEU* 4.1 10.1 - - + -
199E ASP 3.0 16.2 + - - +
200E MET* 3.6 33.0 - - + +
201E TRP 3.1 0.2 - - - -
202E SER* 1.3 74.3 - - - +
204E GLY* 1.3 56.9 + - - +
206E ILE* 3.2 9.9 + - + +
207E THR* 2.7 46.5 + - - +
251E PHE* 4.6 3.6 - - + -
255E LEU* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E MET 3.2 4.8 + - - -
201E TRP 3.0 8.6 + - - -
203E ILE* 1.3 77.7 - - - +
205E VAL* 1.3 60.0 + - - +
207E THR* 3.7 5.0 - - - -
208E TYR* 3.2 21.7 + - - +
252E ILE* 3.9 11.4 - - - +
255E LEU* 3.4 29.8 - - - +
256E LEU* 3.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E GLU 3.9 15.7 - - - +
183E PHE* 3.6 27.8 - - + -
201E TRP* 3.1 35.1 + - + +
202E SER* 3.5 8.1 - - - +
203E ILE 3.1 0.4 - - - -
204E GLY* 1.3 73.9 - - - +
206E ILE* 1.3 66.1 + - - +
208E TYR* 3.1 16.6 + - - +
209E ILE* 3.1 25.1 + - + +
215E SER* 4.6 1.3 - - - +
216E PRO* 4.0 22.4 - - + -
217E PHE* 4.2 3.1 - - + -
256E LEU* 3.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E PHE* 3.7 27.5 - - + -
120E ILE* 5.6 2.7 - - + -
123E ILE* 5.2 8.1 - - + -
140E LEU* 3.9 31.6 - - + -
141E LYS* 3.9 5.2 - - - +
142E PRO* 4.1 16.8 - - + -
145E ILE* 4.0 24.9 - - + -
183E PHE* 4.3 6.1 - - + -
202E SER 3.0 28.2 + - - +
203E ILE* 3.2 10.1 + - + +
205E VAL* 1.3 76.4 - - - +
207E THR* 1.3 57.2 + - - +
209E ILE* 3.3 7.0 + - - +
210E LEU* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ILE* 3.9 17.5 - - + +
203E ILE* 2.7 25.2 + - - +
204E GLY* 3.7 7.0 - - - -
206E ILE* 1.3 75.9 - - - +
208E TYR* 1.3 65.8 + - - +
210E LEU* 3.1 7.4 + - - +
211E LEU* 3.0 31.2 + - + +
251E PHE* 3.7 14.6 - - + -
252E ILE* 3.8 21.3 - - + -
274E TRP* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E GLY 3.2 11.7 + - - +
205E VAL* 3.1 10.5 + - - +
207E THR* 1.3 79.0 - - - +
209E ILE* 1.3 56.2 + - - +
211E LEU* 3.7 1.3 + - - +
212E SER* 2.5 38.1 + - - -
214E ALA* 3.0 40.6 - - + +
215E SER 3.8 1.8 + - - -
216E PRO* 3.6 41.1 + - + +
234E TYR* 4.0 10.8 - + - -
235E ASP 2.8 22.9 + - - -
236E PHE* 3.9 14.1 - + - -
237E ASP* 4.7 1.6 + - - +
241E PHE* 3.4 32.6 - + - -
252E ILE* 3.8 28.9 - - + +
256E LEU* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E PHE* 3.7 20.2 - - + -
142E PRO* 5.0 2.2 - - + -
182E GLU* 3.8 14.6 - - - +
183E PHE* 3.6 32.5 - - + -
205E VAL* 3.1 22.7 + - + +
206E ILE* 3.8 5.8 - - - +
208E TYR* 1.3 72.7 - - - +
210E LEU* 1.3 61.3 + - - +
213E GLY* 2.8 37.4 + - - +
214E ALA 3.2 20.9 - - - +
215E SER* 3.9 10.8 - - - +
216E PRO* 4.5 0.9 - - + -
296E PHE* 3.2 6.5 - - + -
299E GLN* 6.2 0.4 - - + -
303E ARG* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU* 4.4 10.8 - - + -
102E PHE* 4.0 17.0 - - + -
105E LEU* 3.6 34.5 - - + -
111E LEU* 4.6 2.9 - - + -
116E ALA* 4.2 26.9 - - + +
119E PHE* 5.4 2.7 - - + -
120E ILE* 4.0 25.4 - - + -
123E ILE* 5.7 0.9 - - + -
206E ILE* 3.0 17.9 + - + +
207E THR* 3.1 7.2 + - - +
209E ILE* 1.3 81.5 - - - +
211E LEU* 1.3 61.8 + - + +
291E VAL* 3.1 27.7 - - + +
296E PHE* 3.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E GLU* 4.2 11.0 - - + +
116E ALA* 4.4 6.5 - - + -
120E ILE* 6.4 0.4 - - + -
207E THR* 3.0 19.2 + - + +
208E TYR 4.2 2.5 - - - +
210E LEU* 1.3 81.3 - - + +
212E SER* 1.3 59.7 + - - +
241E PHE* 5.0 3.1 - - + -
244E THR* 4.2 21.5 + - + +
248E ALA* 3.8 27.6 - - + -
252E ILE* 3.9 23.1 - - + -
274E TRP* 4.0 23.1 - - + -
290E VAL 5.1 0.3 - - - +
291E VAL* 3.4 27.6 - - + +
292E ASN* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E TYR* 2.5 21.6 + - - -
211E LEU* 1.3 79.0 - - - +
213E GLY* 1.3 54.2 + - - +
214E ALA* 3.2 14.0 + - - -
240E PHE* 3.9 13.5 - - - -
241E PHE* 3.2 40.2 - - - -
244E THR* 5.7 0.2 - - - -
292E ASN* 3.8 15.6 + - - +
295E ASN* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E ILE* 2.8 33.8 + - - +
211E LEU 3.8 0.4 - - - -
212E SER* 1.3 71.0 + - - +
214E ALA* 1.3 61.2 + - - +
295E ASN* 3.8 7.9 - - - -
296E PHE* 3.7 25.4 - - - -
299E GLN* 3.1 26.3 - - - +
303E ARG* 5.5 1.6 + - - -
----------------------------------------------------------
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