Contacts of the helix formed by residues 201 - 218 (chain E) in PDB entry 3N2N
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 VAL 201 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 3.6 46.2 - - + +
65E PHE* 4.1 16.2 - - + -
148E LEU* 4.2 14.4 - - + -
178E VAL* 3.5 10.1 - - + -
179E GLY 2.9 20.7 + - - +
180E VAL* 3.6 21.1 - - + -
181E LYS 5.5 0.2 - - - +
200E PRO* 1.3 72.2 - - - +
202E ASN* 1.3 79.4 + - - +
203E ASP 3.5 0.5 + - - -
204E GLY 3.5 6.2 + - - -
205E PHE* 4.1 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 202 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 4.9 9.9 + - - +
200E PRO* 3.3 4.4 - - + +
201E VAL* 1.3 90.9 - - - +
203E ASP* 1.3 58.4 + - + +
205E PHE* 4.9 3.9 + - - +
206E GLN* 5.1 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E PHE* 4.5 14.8 - - - -
200E PRO* 3.2 26.8 + - + +
202E ASN* 1.3 77.3 - - + +
204E GLY* 1.3 64.3 + - - +
205E PHE 3.3 2.5 + - - -
206E GLN* 3.5 13.5 + - - +
207E ALA* 3.5 20.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
65E PHE* 3.5 15.0 - - - -
178E VAL* 4.6 3.4 - - - -
199E PHE* 3.8 17.7 - - - -
200E PRO 2.7 17.5 + - - -
201E VAL 3.5 1.6 + - - -
203E ASP* 1.3 77.0 - - - +
205E PHE* 1.3 59.4 + - - +
207E ALA* 3.6 0.7 + - - +
208E LEU* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E PHE* 3.4 23.6 - - + -
68E GLN* 3.5 55.0 - - + +
69E LEU* 3.7 29.8 - - + +
72E LYS* 4.8 10.3 - - + -
201E VAL 4.1 4.9 + - - +
202E ASN 4.9 3.8 + - - +
203E ASP 3.3 0.6 - - - -
204E GLY* 1.3 74.9 - - - +
206E GLN* 1.3 83.5 + - + +
208E LEU* 4.2 0.8 - - - +
209E GLN* 2.7 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 206 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E ASN 5.1 7.6 - - - +
203E ASP* 3.5 14.9 + - - +
204E GLY 3.4 0.2 - - - -
205E PHE* 1.3 98.8 - - + +
207E ALA* 1.3 61.6 + - - +
209E GLN* 3.4 20.7 + - - +
210E GLY* 3.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLU* 5.1 11.2 - - - +
186D THR* 4.7 0.7 + - - -
199E PHE* 3.7 35.4 - - + -
203E ASP* 3.5 16.9 + - - +
204E GLY 4.1 2.0 - - - +
205E PHE 3.3 0.4 - - - -
206E GLN* 1.3 78.6 - - - +
208E LEU* 1.3 57.4 + - - +
210E GLY* 3.3 3.3 + - - -
211E ILE* 3.0 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E PHE* 3.6 26.0 - - + -
69E LEU* 4.8 2.2 - - + -
144E VAL* 5.4 1.6 - - + -
146E ILE* 3.9 27.1 - - + -
176E TYR* 3.9 31.6 - - + -
178E VAL* 3.6 19.1 - - + -
199E PHE* 4.5 13.0 - - + -
204E GLY 3.0 21.7 + - - +
205E PHE 4.2 0.7 - - - +
207E ALA* 1.3 73.1 - - - +
209E GLN* 1.3 60.8 + - - +
210E GLY 3.2 0.2 - - - -
211E ILE* 3.7 17.4 - - + +
212E ILE* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASN* 5.3 0.5 - - - +
69E LEU* 4.0 10.2 - - + +
72E LYS* 3.2 32.5 + - + +
73E PHE* 3.3 26.4 - - + -
205E PHE* 2.7 37.1 + - + +
206E GLN* 3.4 29.7 + - - -
208E LEU* 1.3 70.9 - - - +
210E GLY* 1.3 62.0 + - - +
213E HIS* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASN* 3.1 26.8 - - - +
186D THR* 4.0 6.3 - - - -
206E GLN 3.2 12.2 + - - -
207E ALA 3.3 4.2 + - - -
208E LEU 3.2 0.6 - - - -
209E GLN* 1.3 85.1 - - - +
211E ILE* 1.3 58.0 + - - +
213E HIS* 3.4 1.1 + - - -
214E SER* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D THR* 3.4 26.4 + - + +
195D LYS* 3.6 17.0 - - - +
144E VAL* 5.9 1.1 - - + -
176E TYR* 3.7 46.7 - - + +
199E PHE* 4.4 10.1 - - + -
207E ALA* 3.0 24.3 + - + +
208E LEU* 3.3 19.9 + - + +
210E GLY* 1.3 75.3 - - - +
212E ILE* 1.3 59.5 + - + +
214E SER* 3.1 4.5 + - - -
215E ILE* 3.0 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PHE* 3.6 33.1 - - + -
45E LEU* 3.8 25.4 - - + -
69E LEU* 3.8 30.7 - - + -
73E PHE* 3.7 32.3 - - + -
78E LEU* 4.4 6.5 - - + -
144E VAL* 6.3 1.1 - - + -
146E ILE* 4.6 7.0 - - + -
208E LEU* 2.8 28.6 + - + +
209E GLN 4.0 2.5 - - - +
211E ILE* 1.3 74.5 - - + +
213E HIS* 1.3 63.5 + - - +
215E ILE* 3.3 1.1 + - + -
216E LEU* 3.0 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASN* 3.7 20.2 - - + +
187D GLN* 4.8 6.1 + - + -
73E PHE* 3.9 11.4 - - + -
209E GLN* 2.9 27.7 + - - +
210E GLY 3.5 4.5 - - - +
212E ILE* 1.3 75.3 - - - +
214E SER* 1.3 58.6 + - - +
216E LEU* 3.4 5.6 + - - +
217E LYS* 3.0 60.4 + - + +
222E ACT 2.8 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D THR* 3.7 27.8 - - - +
187D GLN* 3.0 37.8 + - - +
190D ARG* 4.2 8.1 + - - -
210E GLY 3.0 14.1 + - - -
211E ILE 3.4 8.3 - - - -
213E HIS* 1.3 78.0 - - - +
215E ILE* 1.3 62.6 + - - +
217E LYS* 3.3 6.1 + - - +
218E LYS* 3.2 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D THR* 6.2 1.1 - - + -
40E TYR* 3.9 17.2 - - + +
43E PHE* 3.6 47.1 - - + -
142E ALA* 3.6 24.0 - - + -
144E VAL* 4.1 15.9 - - + -
174E ILE* 6.2 1.8 - - + -
176E TYR* 6.1 0.4 - - + -
211E ILE* 3.0 37.8 + - + +
212E ILE* 5.5 0.2 - - + -
214E SER* 1.3 76.7 - - - +
216E LEU* 1.3 58.4 + - - +
218E LYS* 2.9 22.6 + - - +
219E SER* 3.2 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PHE* 3.8 19.7 - - + -
73E PHE* 3.6 36.8 - - + -
75E SER* 4.8 12.1 - - - +
77E GLN* 3.9 35.9 - - + +
78E LEU* 4.1 13.9 - - + +
212E ILE* 3.0 21.4 + - + +
213E HIS* 3.7 5.4 - - - +
215E ILE* 1.3 75.4 - - - +
217E LYS* 1.3 61.3 + - - +
218E LYS 3.1 0.2 - - - -
219E SER* 3.2 25.7 + - - +
222E ACT 4.0 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D GLU* 4.4 27.7 - - + +
187D GLN* 3.9 22.9 - - - +
190D ARG* 5.6 3.5 + - - +
213E HIS* 3.0 46.7 + - + +
214E SER 3.5 9.0 - - - +
215E ILE 3.2 0.2 - - - -
216E LEU* 1.3 75.4 - - + +
218E LYS* 1.3 57.1 - - - +
219E SER 3.3 6.0 + - - +
222E ACT 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D GLU* 5.3 4.7 + - - -
190D ARG* 5.0 25.9 - - - +
36E SER 2.7 25.1 + - - -
37E MET* 3.9 13.5 - - - +
38E ALA 3.3 21.5 - - - -
39E CYS* 3.2 13.1 - - + -
40E TYR* 2.7 61.6 + - + -
214E SER 3.2 10.5 + - - +
215E ILE* 2.9 14.8 + - - +
217E LYS* 1.3 78.4 - - - +
219E SER* 1.3 52.4 + - - -
----------------------------------------------------------
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