Contacts of the helix formed by residues 189 - 207 (chain A) in PDB entry 3IEU
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 SER 189 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 5.3 7.9 + - - -
187A ASP* 2.7 24.0 + - - -
188A ARG* 1.3 81.3 - - - +
190A GLN* 1.3 64.3 + - - +
191A ARG* 4.2 8.9 - - - +
192A PHE* 3.2 17.7 + - - +
193A MET* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG 3.5 3.0 + - - +
189A SER* 1.3 69.2 - - - +
191A ARG* 1.3 66.9 + - - +
193A MET* 3.0 11.5 + - - +
194A ALA* 2.9 21.1 + - - +
221A PHE* 3.9 27.0 - - + -
229A TYR* 3.6 26.0 + - - -
269A PHE* 3.5 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 4.7 6.1 - - - -
39A LYS* 4.3 40.0 - - - +
189A SER* 3.2 8.9 - - - +
190A GLN* 1.3 81.7 - - - +
192A PHE* 1.3 61.4 + - - +
194A ALA* 3.4 9.9 + - - +
195A SER* 3.4 14.3 + - - +
218A ILE* 3.1 42.7 + - + +
220A ARG 4.5 0.2 - - - +
221A PHE* 3.6 39.9 + - + +
307A SO4 3.0 44.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.9 30.3 - - + -
185A ILE* 4.2 15.9 - - + -
187A ASP* 3.4 56.5 - - + +
189A SER* 3.2 10.1 + - - +
191A ARG* 1.3 81.7 - - - +
193A MET* 1.3 71.1 + - - +
195A SER* 3.0 10.3 + - - -
196A GLU* 3.0 47.3 + - + -
199A ARG* 4.5 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 4.9 17.9 - - - -
188A ARG* 4.6 9.9 - - - +
189A SER 3.0 15.7 + - - +
190A GLN* 3.0 14.6 + - - +
192A PHE* 1.3 89.7 - - + +
194A ALA* 1.3 60.4 + - - +
196A GLU* 3.4 19.2 + - + -
197A ILE* 3.1 34.5 + - + +
268A MET* 3.6 40.6 - - + +
269A PHE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLN 2.9 11.0 + - - +
191A ARG 3.5 6.7 - - - +
192A PHE 3.1 0.2 - - - -
193A MET* 1.3 75.3 - - - +
195A SER* 1.3 65.3 - - - +
197A ILE* 3.0 13.2 + - - +
198A ILE* 3.1 16.8 + - - +
218A ILE* 3.5 24.7 - - + -
221A PHE* 4.4 14.1 - - + -
231A ILE* 4.8 1.3 - - + -
265A MET* 4.2 27.0 - - + +
269A PHE* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.2 39.6 - - - +
36A THR 5.2 0.3 + - - -
191A ARG* 3.4 7.3 + - - +
192A PHE* 3.0 8.4 + - - -
194A ALA* 1.3 77.8 - - - +
196A GLU* 1.3 63.4 + - - -
198A ILE* 3.0 3.5 + - - +
199A ARG* 2.9 24.8 + - - +
216A VAL* 4.1 17.7 - - - +
218A ILE* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.9 4.2 - - - +
185A ILE* 6.1 3.9 - - + +
192A PHE* 3.0 32.1 + - + +
193A MET* 3.7 26.0 - - + +
194A ALA 3.2 0.6 - - - -
195A SER* 1.3 77.3 - - - +
197A ILE* 1.3 57.9 + - + +
199A ARG* 3.1 41.9 + - - +
200A GLU* 3.0 33.4 + - + +
203A MET* 5.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A MET* 3.1 24.4 + - + +
194A ALA* 3.0 8.1 + - - +
196A GLU* 1.3 75.3 - - - +
198A ILE* 1.3 58.9 + - - +
200A GLU* 3.2 9.3 + - - +
201A LYS* 2.9 32.2 + - + +
261A ALA* 3.8 32.5 - - + +
264A ASP* 3.9 23.3 - - + +
265A MET* 3.8 33.9 - - + -
268A MET* 4.6 16.2 - - + -
269A PHE* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 3.1 8.4 + - - +
195A SER 3.0 6.4 + - - +
197A ILE* 1.3 73.6 - - - +
199A ARG* 1.3 55.6 + - - +
201A LYS* 3.0 6.8 + - - +
202A LEU* 2.8 38.0 + - + +
216A VAL* 3.9 26.9 - - + -
218A ILE* 4.0 27.4 - - + -
233A GLY* 4.3 9.4 - - - -
235A ILE* 4.3 20.9 - - + -
257A ILE* 4.9 2.4 - - + +
261A ALA* 4.4 7.0 - - + -
265A MET* 4.3 17.0 - - + -
275A LEU* 5.0 1.3 - - + -
277A LEU* 4.2 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 3.9 26.5 - - - +
33A ILE* 2.6 63.5 + - + +
34A SER* 4.3 3.4 - - - +
35A ILE* 3.4 26.1 - - + +
192A PHE* 4.5 4.9 - - - -
195A SER 2.9 16.2 + - - +
196A GLU* 3.1 35.6 + - - +
198A ILE* 1.3 76.5 - - - +
200A GLU* 1.3 62.6 + - - +
202A LEU* 3.6 5.2 - - - +
203A MET* 3.0 55.2 + - - +
216A VAL* 4.1 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 3.0 23.1 + - + +
197A ILE* 3.6 8.5 - - - +
198A ILE 3.1 0.4 - - - -
199A ARG* 1.3 78.0 - - - +
201A LYS* 1.3 82.8 + - - +
203A MET* 3.3 18.8 + - + +
204A ARG* 2.8 63.7 + - - +
264A ASP* 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 2.9 23.4 + - + +
198A ILE* 3.0 5.6 + - - +
200A GLU* 1.3 100.2 + - - +
202A LEU* 1.3 59.9 + - - +
204A ARG* 3.5 20.4 - - + +
205A PHE* 3.0 45.2 + - + +
257A ILE* 4.1 19.8 - - + +
260A GLU* 3.7 37.7 - - + -
261A ALA* 4.0 8.3 - - + +
264A ASP* 2.7 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.8 13.9 - - + -
198A ILE* 2.8 24.1 + - + +
199A ARG* 3.6 4.9 - - - +
201A LYS* 1.3 73.2 - - - +
203A MET* 1.3 62.6 + - - +
206A LEU* 3.0 48.7 + - + +
210A LEU* 4.5 0.2 - - - -
214A VAL* 4.3 13.2 - - + -
216A VAL* 3.9 27.6 - - + -
235A ILE* 4.0 36.1 - - + -
246A VAL* 4.6 6.3 - - + -
257A ILE* 3.5 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 5.6 8.7 - - - +
32A LYS* 6.1 3.1 - - - -
33A ILE* 3.3 22.7 - - + -
196A GLU* 5.1 3.6 - - - +
199A ARG* 3.0 46.1 + - - +
200A GLU* 3.7 17.3 - - + +
202A LEU* 1.3 76.2 - - - +
204A ARG* 1.3 63.4 + - - +
206A LEU* 5.3 0.2 - - - -
207A GLY* 3.8 13.2 + - - -
210A LEU* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLU* 2.8 42.4 + - - +
201A LYS* 3.5 23.4 - - + +
202A LEU 3.2 0.6 - - - -
203A MET* 1.3 79.9 - - - +
205A PHE* 1.3 84.6 + - + +
207A GLY* 4.1 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LYS* 3.0 38.9 + - + +
204A ARG* 1.3 98.5 - - + +
206A LEU* 1.3 64.9 + - - +
209A GLU* 4.1 4.5 - - - +
253A LYS* 3.7 30.6 + - + +
256A THR* 3.6 23.1 - - + -
257A ILE* 4.1 23.3 - - + -
260A GLU* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.0 34.8 + - + +
205A PHE* 1.3 81.5 - - - +
207A GLY* 1.3 61.1 + - - +
208A ALA 3.2 0.2 + - - -
209A GLU* 2.7 41.4 + - + +
210A LEU* 3.4 39.3 - - + +
211A PRO* 4.7 5.6 - - + -
214A VAL* 5.8 3.6 - - + -
245A MET* 4.1 22.2 - - + +
246A VAL* 4.2 24.7 - - + -
253A LYS* 4.2 14.8 - - + -
257A ILE* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 5.7 0.9 + - - -
203A MET 3.8 14.3 + - - -
204A ARG 4.1 4.4 + - - -
205A PHE 3.5 1.6 - - - -
206A LEU* 1.3 77.4 - - - +
208A ALA* 1.3 63.3 + - - -
209A GLU 3.4 0.5 + - - -
210A LEU* 3.6 15.5 + - - +
----------------------------------------------------------
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