Contacts of the helix formed by residues 193 - 209 (chain D) in PDB entry 4IGM
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 193 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D MET* 4.8 0.9 - - + -
189D LEU* 2.7 26.7 + - + +
192D LEU* 1.3 82.2 - - + +
194D GLY* 1.3 66.6 + - - +
195D MET 3.2 2.0 - - - -
196D PRO* 3.2 7.6 - - - +
197D ALA* 3.0 21.4 + - + +
197E ALA* 4.4 16.8 - - + +
200E THR* 4.0 27.1 - - + -
201E ILE* 3.9 31.6 - - + -
204E CYS* 4.3 16.8 - - - -
236E ILE* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D MET* 3.8 11.8 - - - +
184D MET* 4.1 15.4 - - - +
189D LEU 2.9 10.5 + - - -
190D PRO* 3.4 11.0 - - - -
193D VAL* 1.3 78.7 - - - +
195D MET* 1.3 56.9 + - - +
197D ALA* 3.2 7.2 + - - +
198D GLU* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D HIS* 4.6 6.7 - - + -
175D PRO* 3.3 35.1 - - + +
176D TRP* 5.6 1.8 - - - -
178D MET* 3.7 23.3 - - + -
190D PRO 3.0 17.2 + - - +
191D TRP* 3.4 30.1 - - + +
194D GLY* 1.3 73.9 - - - +
196D PRO* 1.3 71.5 - - + +
198D GLU* 3.5 0.9 + - - -
199D THR* 3.3 25.0 + - - -
224D HIS* 3.5 18.4 - - + +
296D LEU* 4.4 0.7 - - + -
235E ARG* 2.3 39.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D TRP 3.8 4.9 - - - +
192D LEU 3.4 19.7 - - - +
193D VAL* 3.2 14.4 - - - +
195D MET* 1.3 96.4 - - + +
197D ALA* 1.3 58.0 + - - +
199D THR* 3.5 0.8 + - - +
200D THR* 2.9 28.0 + - - -
224D HIS* 5.5 5.6 - - + -
227D GLY* 3.4 30.7 - - - -
228D ALA* 4.4 3.1 - - + +
228E ALA* 6.2 0.4 - - + -
232E THR* 4.4 15.0 - - + -
235E ARG* 3.9 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D VAL* 3.0 15.7 + - + +
194D GLY* 3.5 11.7 - - - +
195D MET 3.2 0.4 - - - -
196D PRO* 1.3 72.5 - - - +
198D GLU* 1.3 66.8 + - - +
200D THR* 3.3 9.7 + - - -
201D ILE* 3.1 31.2 + - + +
228D ALA* 5.8 1.3 - - - -
193E VAL* 4.3 6.8 - - + +
197E ALA* 4.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D THR* 2.9 35.5 + - - +
146D HIS* 2.7 33.0 + - - -
175D PRO* 4.1 5.8 - - + -
176D TRP 4.0 8.5 - - - +
177D ASP 4.7 2.2 - - - +
178D MET* 4.3 15.9 - - + -
194D GLY 3.0 19.1 + - - +
195D MET 3.7 5.4 - - - +
197D ALA* 1.3 75.7 - - - +
199D THR* 1.3 61.9 + - - +
201D ILE* 3.2 13.0 + - - +
202D ALA 3.2 16.6 + - - -
183E ARG* 3.0 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D THR* 4.0 10.6 - - + +
173D VAL 5.6 0.4 - - - +
175D PRO* 3.6 22.5 - - - +
195D MET 3.3 12.9 + - - -
196D PRO* 3.8 8.6 - - - +
197D ALA 3.3 0.4 - - - -
198D GLU* 1.3 74.5 - - - +
200D THR* 1.3 64.6 + - - +
202D ALA* 3.3 2.1 + - - +
203D ILE* 3.2 22.6 + - + +
222D PHE* 3.8 19.3 - - + -
223D ALA 3.7 14.6 + - - +
224D HIS* 4.7 1.4 - - - -
226D GLY* 3.4 30.7 - - - -
227D GLY* 4.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PRO 2.9 16.5 + - - -
197D ALA* 3.5 9.5 - - - -
199D THR* 1.3 79.1 - - - +
201D ILE* 1.3 60.5 + - - +
203D ILE* 3.6 2.4 + - - +
204D CYS* 3.1 23.3 + - - -
226D GLY 3.9 5.8 + - - -
228D ALA* 3.0 27.2 + - + +
229D PHE* 3.5 18.5 + - + +
232D THR* 4.4 5.4 - - - +
236D ILE* 4.1 16.4 - - + -
193E VAL* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ASP* 3.5 33.0 - - - +
197D ALA* 3.1 23.4 + - + +
198D GLU* 3.2 13.6 + - - +
200D THR* 1.3 75.5 - - - +
202D ALA* 1.3 58.8 + - - +
204D CYS* 3.7 6.0 - - - +
205D SER* 2.8 37.1 + - - +
183E ARG* 3.9 15.3 - - - +
184E MET* 3.7 32.3 - - + -
189E LEU* 4.8 13.2 - - + -
193E VAL* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D THR* 3.7 25.4 - - + +
151D ASP* 5.0 0.2 - - - -
152D LEU* 3.6 26.6 - - + +
173D VAL* 4.3 0.2 - - + -
198D GLU 3.2 11.4 + - - +
199D THR 3.7 7.0 - - - +
200D THR 3.2 0.4 - - - -
201D ILE* 1.3 75.1 - - - +
203D ILE* 1.3 59.9 + - - +
205D SER* 3.3 5.3 + - - -
206D MET* 2.8 35.2 + - - +
222D PHE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D THR 3.2 10.5 + - - +
200D THR 3.9 5.4 - - - +
202D ALA* 1.3 76.8 - - - +
204D CYS* 1.3 62.2 + - - +
206D MET* 3.2 2.7 + - - +
207D ILE* 2.9 41.0 + - + +
212D PHE* 5.4 0.7 - - + -
222D PHE* 3.6 39.0 - - + -
226D GLY* 3.8 25.6 - - - +
229D PHE* 3.8 49.1 - - + -
262D PHE* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D THR 3.1 23.4 + - - +
201D ILE 3.8 3.6 - - - +
203D ILE* 1.3 75.4 - - - +
205D SER* 1.3 56.9 + - - +
207D ILE* 3.3 5.1 + - - -
208D MET* 2.7 54.9 + - + +
229D PHE* 4.5 5.8 - - - -
236D ILE* 3.7 43.3 - - - -
187E TYR* 5.0 0.7 - - + -
189E LEU* 4.1 13.7 - - + -
192E LEU* 5.9 0.2 - - - -
193E VAL* 4.1 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ASP* 3.6 23.3 + - - +
152D LEU 4.1 3.6 - - - -
153D ASN* 3.2 39.3 + - - +
201D ILE* 2.8 30.3 + - - +
202D ALA* 3.8 3.6 - - - -
204D CYS* 1.3 72.0 - - - +
206D MET* 1.3 57.7 + - - +
209D GLY* 2.9 22.3 + - - -
186E LYS* 4.3 5.4 - - - -
187E TYR* 4.1 12.1 - - - -
189E LEU* 4.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU* 3.7 37.9 - - + +
161D TYR* 4.4 11.4 - - + -
171D LEU* 4.9 3.6 - - + -
173D VAL* 5.0 1.1 - - + -
202D ALA 2.8 18.6 + - - +
203D ILE* 3.9 1.6 - - - +
205D SER* 1.3 72.4 - - - +
207D ILE* 1.3 59.4 + - - +
211D VAL* 2.8 59.9 + - + +
212D PHE* 3.6 22.6 + - + -
218D LEU* 4.4 4.7 - - + -
220D VAL* 4.1 29.4 - - + -
222D PHE* 3.7 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ILE* 2.9 37.2 + - + +
204D CYS* 3.7 4.9 - - - +
206D MET* 1.3 77.0 - - - +
208D MET* 1.3 62.4 + - + +
210D GLY* 2.9 18.7 + - - -
212D PHE* 4.1 22.2 - - + +
229D PHE* 3.9 19.1 - - + -
251D ASN* 3.3 15.4 + - - -
253D MET 4.7 2.9 - - - +
255D PRO* 3.8 39.0 - - + +
258D TYR* 3.4 35.9 - - + -
262D PHE* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D CYS* 2.7 43.8 + - + +
207D ILE* 1.3 82.8 - - + +
209D GLY* 1.3 57.0 + - - +
210D GLY 3.1 0.4 - - - -
236D ILE* 3.9 24.7 - - + +
240D PHE* 4.2 15.0 - - + -
247D CYS* 3.7 36.0 - - - +
250D ASP* 3.4 12.6 + - - +
251D ASN* 3.3 23.5 + - - +
253D MET 6.1 0.2 - - - -
255D PRO* 4.7 4.5 - - + -
187E TYR* 3.7 38.7 + - + +
189E LEU* 5.1 1.3 - - + -
192E LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ASN* 3.7 10.3 - - - +
158D PHE* 3.9 16.3 - - - -
205D SER 2.9 19.6 + - - -
208D MET* 1.3 76.8 - - - +
210D GLY* 1.3 60.0 + - - +
211D VAL* 3.3 5.4 + - - +
214D LYS* 4.7 2.8 + - - -
250D ASP* 4.1 10.3 - - - +
187E TYR* 3.0 21.6 + - - -
----------------------------------------------------------
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