Contacts of the helix formed by residues 228 - 243 (chain A) 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 ALA 228 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PRO* 3.7 5.1 + - + +
197A ALA* 5.7 1.6 - - - +
200A THR* 2.8 17.4 + - + +
227A GLY* 1.3 71.7 - - - -
229A PHE* 1.3 68.5 + - - +
230A PRO* 3.1 5.1 - - - +
231A PHE* 3.0 18.6 + - - +
232A THR* 3.1 22.5 + - + +
196F PRO* 6.1 1.1 - - + -
228F ALA* 3.8 29.2 - - + -
231F PHE* 4.5 5.2 - - - -
232F THR* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 3.2 14.9 + - + +
203A ILE* 3.6 37.0 - - + -
204A CYS* 4.7 5.8 - - - -
207A ILE* 4.1 16.2 - - + -
226A GLY* 3.3 16.8 - - - +
228A ALA* 1.3 74.6 - - - +
230A PRO* 1.3 64.4 - - + +
232A THR* 2.9 6.2 + - - -
233A VAL* 2.7 57.4 + - + +
236A ILE* 4.0 28.5 - - + -
255A PRO* 5.0 5.2 - - + -
259A LEU* 3.9 20.0 - - + -
262A PHE* 3.8 22.4 - + - -
281A ILE* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY 3.3 26.2 - - - +
226A GLY* 5.1 0.2 - - - -
228A ALA* 3.1 8.7 - - - +
229A PHE* 1.3 98.8 - - + +
231A PHE* 1.3 58.0 + - - +
233A VAL* 3.5 13.7 - - + +
264A THR* 5.9 0.2 - - + -
276A LEU* 4.2 5.6 - - + +
277A LEU* 3.7 21.5 - - + -
280A VAL* 3.8 36.4 - - + +
281A ILE* 4.9 3.8 - - + -
231F PHE* 3.8 23.8 - - + -
273F SER* 4.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ALA* 3.0 8.1 + - - +
230A PRO* 1.3 81.7 - - - +
232A THR* 1.3 64.3 + - + +
233A VAL 3.5 0.7 - - - -
234A GLY 4.6 2.1 + - - -
276A LEU* 4.2 3.8 - - + +
224F HIS 4.8 1.1 - - - -
225F GLY 4.2 4.9 - - - -
227F GLY 2.9 29.8 - - - -
228F ALA* 4.5 5.4 - - - -
230F PRO* 3.6 31.4 - - + -
231F PHE* 3.6 25.1 - - + -
268F VAL* 3.9 30.9 - - + +
273F SER* 2.8 55.3 + - - -
276F LEU* 4.3 16.4 - - + -
277F LEU* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 4.4 3.5 - - - +
228A ALA* 3.1 30.9 + - + +
229A PHE* 2.9 4.9 + - - -
231A PHE* 1.3 94.5 - - + +
233A VAL* 1.3 64.0 + - - +
234A GLY 3.1 3.1 - - - +
235A ARG* 3.2 15.4 + - + +
236A ILE* 3.0 33.8 + - - +
192F LEU 5.2 2.4 + - - -
196F PRO* 4.3 24.2 - - + -
227F GLY 3.9 11.2 - - - +
228F ALA* 5.0 0.2 - - - -
268F VAL 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 2.7 39.4 + - + +
230A PRO 3.5 20.4 - - - +
231A PHE 4.9 0.4 - - - -
232A THR* 1.3 74.0 - - - +
234A GLY* 1.3 61.2 + - - +
236A ILE* 3.8 8.5 - - + -
237A SER* 2.8 36.0 + - - -
255A PRO* 5.0 5.2 - - + -
256A LYS* 4.2 24.0 - - + -
259A LEU* 4.6 9.9 - - + -
280A VAL* 4.1 16.2 - - + -
270F ASP* 4.0 12.8 - - - +
273F SER* 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE 4.6 2.6 + - - -
232A THR* 3.1 1.8 - - - +
233A VAL* 1.3 83.0 - - - +
235A ARG* 1.3 57.8 + - - +
237A SER* 3.2 5.0 + - - -
238A HIS* 2.8 33.3 + - - +
256A LYS* 4.4 0.4 - - - -
268F VAL 4.2 3.4 - - - -
269F HIS* 3.9 13.2 - - - +
270F ASP* 3.7 29.2 + - - +
273F SER* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 3.2 15.2 + - + +
234A GLY* 1.3 75.9 - - - +
236A ILE* 1.3 60.8 + - - +
238A HIS* 4.7 0.2 - - - -
239A GLY* 3.1 21.5 + - - -
191F TRP* 2.9 33.1 + - - +
192F LEU* 3.8 21.5 + - + +
195F MET* 3.9 23.3 - - - +
196F PRO* 4.0 15.4 - - - +
224F HIS* 3.1 43.2 + - - +
267F LEU 5.0 1.5 + - - +
268F VAL* 4.3 5.1 + - - +
269F HIS* 3.6 28.6 + - + +
296F LEU* 3.8 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 4.1 8.3 - - + -
204A CYS* 3.7 25.1 - - - -
208A MET* 4.1 19.5 - - + -
229A PHE* 4.0 21.1 - - + -
232A THR* 3.0 35.6 + - - +
233A VAL* 3.9 4.9 - - - +
235A ARG* 1.3 75.4 - - - +
237A SER* 1.3 58.2 + - - +
239A GLY* 4.0 0.3 - - - -
240A PHE* 3.0 29.1 + - - +
255A PRO* 3.9 24.5 - - + -
192F LEU* 4.0 31.9 - - + +
193F VAL* 4.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 2.8 21.0 + - - -
234A GLY 3.5 3.4 - - - -
236A ILE* 1.3 75.4 - - - +
238A HIS* 1.3 63.2 + - - +
240A PHE* 3.6 2.8 - - - +
241A SER* 2.8 24.8 + - - -
254A ASN* 2.8 39.5 + - - +
255A PRO* 4.5 4.7 - - - -
256A LYS* 3.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLY 2.8 19.5 + - - +
235A ARG 4.1 1.6 - - - +
237A SER* 1.3 72.1 - - - +
239A GLY* 1.3 54.8 + - - +
241A SER* 3.1 9.2 + - - -
242A MET* 2.8 62.5 + - + +
269F HIS* 3.5 23.6 - + + -
295F PRO 3.2 20.0 + - - -
296F LEU* 3.2 24.2 - - + -
297F GLY 3.3 15.2 + - - -
298F GLU* 5.9 0.2 - - - -
299F LEU* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG 3.1 17.2 + - - -
238A HIS* 1.3 73.2 - - - +
240A PHE* 1.3 65.8 + - - +
242A MET* 3.6 3.5 - - - -
243A ARG* 2.8 22.9 + - - -
247A CYS* 4.4 1.4 - - - -
188F TRP* 3.8 29.4 - - - -
192F LEU* 4.0 7.6 - - - -
296F LEU* 4.2 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A MET* 4.1 17.0 - - + -
236A ILE 3.0 19.6 + - - +
237A SER 3.6 4.9 - - - +
239A GLY* 1.3 78.3 - - - +
241A SER* 1.3 66.8 + - - +
243A ARG 3.5 6.4 + - - -
244A PRO* 3.6 15.8 - - - +
247A CYS* 3.3 43.3 - - + +
248A ALA* 3.4 22.9 - - + -
251A ASN 3.5 12.1 - - - -
252A PRO 4.1 7.0 - - - -
253A MET 3.2 27.8 - - - -
254A ASN* 3.7 24.0 - - + -
255A PRO* 3.6 16.6 - - + -
257A LYS* 5.4 0.2 - - - -
192F LEU* 4.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER* 2.8 15.8 + - - -
238A HIS* 3.1 10.5 + - - -
240A PHE* 1.3 83.5 - - - +
242A MET* 1.3 77.0 + - - +
244A PRO* 3.5 10.4 - - - +
254A ASN* 3.2 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A HIS* 2.8 56.6 + - + +
239A GLY* 3.1 7.6 + - - +
241A SER* 1.3 89.0 - - - +
243A ARG* 1.3 70.6 + - + +
244A PRO* 3.4 5.6 - - - +
188F TRP* 4.7 3.1 - - + -
295F PRO* 3.4 32.2 - - + +
296F LEU 5.1 0.2 - - - +
299F LEU* 4.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLY 2.8 11.9 + - - -
240A PHE 3.7 4.0 - - - -
242A MET* 1.3 84.5 - - + +
244A PRO* 1.4 63.2 - - - +
245A ASP* 3.1 32.2 + - - +
246A LEU* 3.1 49.0 + - + +
247A CYS* 3.2 13.7 + - - +
47F ARG* 6.0 3.6 - - - +
188F TRP* 3.8 37.6 - - + +
295F PRO* 5.2 13.7 - - + +
----------------------------------------------------------
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