Contacts of the helix formed by residues 193 - 209 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ALA* 4.4 8.5 - - + +
200A THR* 3.8 33.4 - - + +
201A ILE* 3.7 31.0 - - + -
204A CYS* 4.1 18.6 - - - -
236A ILE* 4.1 4.9 - - + -
184F MET* 5.0 1.3 - - + -
189F LEU* 2.8 17.8 + - + +
191F TRP 3.2 0.8 - - - -
192F LEU* 1.3 90.4 - - + +
194F GLY* 1.3 62.9 + - - +
196F PRO* 3.1 18.7 - - - +
197F ALA* 3.4 14.5 + - + +
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Residues in contact with GLY 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F MET* 3.7 11.3 - - - +
184F MET* 4.2 12.3 - - - +
189F LEU 2.8 11.2 + - - -
190F PRO* 3.2 14.4 - - - -
193F VAL* 1.3 76.1 - - - +
195F MET* 1.3 62.1 + - - +
197F ALA* 3.4 5.9 + - - +
198F GLU* 3.1 27.9 + - - +
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Residues in contact with MET 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 3.9 11.7 - - - +
174F HIS* 3.7 11.7 - - + -
175F PRO* 3.0 59.3 - - + +
176F TRP* 5.0 4.3 - - + -
178F MET* 3.9 16.2 - - + +
190F PRO 2.9 19.5 + - - +
191F TRP* 3.6 39.9 + - - +
194F GLY* 1.3 72.2 - - - +
196F PRO* 1.3 73.2 - - + +
197F ALA 3.2 0.3 + - - -
198F GLU* 3.2 4.3 + - - +
199F THR* 3.1 23.4 + - - -
224F HIS* 3.5 16.6 - - + +
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Residues in contact with PRO 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ALA* 6.1 0.9 - - + -
232A THR* 4.3 15.0 - - + -
235A ARG* 4.0 17.7 - - - +
191F TRP 3.9 2.0 - - - +
192F LEU 3.9 13.5 - - - +
193F VAL* 3.1 24.2 - - - +
195F MET* 1.3 93.2 - - + +
197F ALA* 1.3 55.2 + - - +
199F THR* 3.3 3.1 + - - +
200F THR* 3.0 31.5 + - - -
224F HIS* 5.5 6.3 - - + -
227F GLY* 3.5 31.3 - - - -
228F ALA* 4.4 3.8 - - + +
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Residues in contact with ALA 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 4.4 8.5 - - + +
197A ALA* 4.4 21.8 - - + -
193F VAL 3.4 11.7 + - - +
194F GLY* 3.8 9.4 - - - +
195F MET 3.2 0.8 - - - -
196F PRO* 1.3 74.0 - - - +
198F GLU* 1.3 63.3 + - - +
200F THR* 3.2 7.1 + - - -
201F ILE* 2.9 39.3 + - + +
228F ALA* 5.7 2.7 - - - -
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Residues in contact with GLU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 2.9 28.5 + - - -
145F THR* 3.1 24.4 + - - +
146F HIS* 2.5 35.7 + - - -
175F PRO* 3.9 8.1 - - + -
176F TRP 4.5 4.3 - - - +
177F ASP 5.1 1.3 - - - +
178F MET* 4.3 19.2 - - + -
194F GLY 3.1 16.2 + - - +
195F MET* 3.2 8.0 + - - +
197F ALA* 1.3 76.9 - - + +
199F THR* 1.3 61.5 + - - +
201F ILE* 3.5 13.8 + - - +
202F ALA* 3.1 21.7 + - - +
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Residues in contact with THR 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F THR* 4.0 9.6 - - + +
173F VAL 5.6 0.4 - - - +
175F PRO* 3.3 28.5 - - + +
195F MET 3.1 7.4 + - - -
196F PRO* 3.6 7.9 - - - +
197F ALA 3.3 0.2 - - - -
198F GLU* 1.3 76.3 - - - +
200F THR* 1.3 63.2 + - - +
202F ALA* 2.9 10.9 + - - +
203F ILE* 3.0 15.3 + - + +
222F PHE* 3.8 19.3 - - + -
223F ALA 3.7 13.3 + - - +
224F HIS* 4.8 1.0 - - - -
226F GLY* 3.6 34.5 - - - +
227F GLY* 4.2 2.2 + - - -
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Residues in contact with THR 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 3.7 26.2 - - + -
196F PRO 3.0 10.1 + - - -
197F ALA* 3.2 7.8 + - - -
199F THR* 1.3 77.7 - - - +
201F ILE* 1.3 63.7 + - - +
202F ALA 3.1 0.2 + - - -
203F ILE* 3.4 2.6 + - - +
204F CYS* 3.1 21.5 + - - -
226F GLY 3.7 4.2 + - - -
228F ALA* 2.7 38.6 + - + +
229F PHE* 3.0 18.2 + - + +
232F THR* 4.3 11.4 - - - +
236F ILE* 4.3 8.3 - - + -
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Residues in contact with ILE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 4.3 9.2 - - + +
184A MET* 4.0 26.2 - - + -
189A LEU* 4.2 17.4 - - + +
193A VAL* 3.7 23.8 - - + -
151F ASP* 3.9 21.8 - - - +
197F ALA* 2.9 27.5 + - + +
198F GLU* 3.7 23.1 - - - +
200F THR* 1.3 76.5 - - - +
202F ALA* 1.3 57.3 + - - +
204F CYS* 3.5 6.5 + - - +
205F SER* 2.8 37.9 + - - +
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Residues in contact with ALA 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F THR* 3.8 33.0 - - + +
151F ASP* 5.5 1.6 - - - -
152F LEU* 4.2 10.8 - - + -
173F VAL* 4.4 0.4 - - + -
198F GLU 3.1 13.0 + - - +
199F THR* 2.9 10.6 + - - +
201F ILE* 1.3 74.6 - - - +
203F ILE* 1.3 67.8 + - - +
205F SER* 3.3 6.3 + - - -
206F MET* 3.1 27.7 + - - +
222F PHE* 4.3 11.7 - - + -
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Residues in contact with ILE 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F THR 3.0 16.3 + - - +
200F THR 3.8 5.4 - - - +
202F ALA* 1.3 75.0 - - - +
204F CYS* 1.3 60.3 + - - +
206F MET* 3.1 4.2 + - - +
207F ILE* 3.0 44.3 + - + +
212F PHE* 4.9 0.4 - - + -
222F PHE* 3.7 38.4 - - + -
226F GLY* 3.5 36.8 - - - +
229F PHE* 3.6 31.0 - - + -
262F PHE* 3.7 22.2 - - + -
264F THR* 5.1 0.4 - - + -
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Residues in contact with CYS 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 5.0 1.3 - - + -
189A LEU* 4.0 11.9 - - + -
192A LEU* 5.7 0.2 - - - -
193A VAL* 4.2 13.0 - - - -
200F THR 3.1 18.2 + - - +
201F ILE 3.7 6.5 - - - +
203F ILE* 1.3 73.0 - - - +
205F SER* 1.3 68.2 + - - +
206F MET 3.0 0.3 + - - -
207F ILE* 3.1 4.4 + - - +
208F MET* 2.8 60.5 + - + +
229F PHE* 4.3 5.2 - - - -
236F ILE* 3.9 31.0 - - - -
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Residues in contact with SER 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LYS* 3.9 7.4 - - - -
187A TYR* 4.2 12.0 - - - -
189A LEU* 4.8 2.1 - - - +
151F ASP* 3.7 21.3 + - - +
152F LEU 4.1 8.3 - - - -
153F ASN* 3.1 28.9 - - - +
201F ILE* 2.8 29.9 + - - +
202F ALA* 3.7 7.0 - - - -
204F CYS* 1.3 72.2 - - - +
206F MET* 1.3 58.3 + - - +
209F GLY* 2.8 28.2 + - - -
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Residues in contact with MET 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 3.7 40.6 - - + +
161F TYR* 4.2 15.5 - - + -
171F LEU* 5.3 1.3 - - + -
173F VAL* 5.0 1.1 - - + -
202F ALA 3.1 11.6 + - - +
203F ILE 3.7 2.0 - - - +
204F CYS 3.0 0.8 - - - -
205F SER* 1.3 75.7 - - - +
207F ILE* 1.3 66.3 + - - +
210F GLY 3.4 1.6 + - - -
211F VAL* 3.1 59.6 + - + +
212F PHE* 3.7 21.5 + - + -
218F LEU* 4.4 0.4 - - + -
220F VAL* 4.0 29.8 - - + -
222F PHE* 3.8 24.2 - - - -
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Residues in contact with ILE 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F ILE* 3.0 39.6 + - + +
204F CYS* 3.9 3.1 - - - +
206F MET* 1.3 77.6 - - - +
208F MET* 1.3 65.0 + - + +
209F GLY 3.3 0.2 + - - -
210F GLY* 3.4 3.1 + - - -
212F PHE* 4.2 22.3 + - + +
229F PHE* 3.7 19.7 - - + -
251F ASN* 2.9 26.2 + - - -
253F MET 4.8 2.0 - - - +
255F PRO* 3.6 37.0 - - + +
258F TYR* 3.5 32.4 - - + -
262F PHE* 4.2 9.0 - - + -
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Residues in contact with MET 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 3.6 40.4 - - + +
189A LEU* 4.7 1.6 - - + -
192A LEU* 4.0 14.6 - - + -
204F CYS* 2.8 51.9 + - + +
207F ILE* 1.3 83.1 - - + +
209F GLY* 1.3 60.1 + - - +
210F GLY 3.2 0.9 + - - -
236F ILE* 3.9 17.5 - - + -
240F PHE* 4.1 21.3 - - + -
247F CYS* 3.9 24.1 - - - +
250F ASP* 3.5 19.9 - - - +
251F ASN* 3.5 12.7 + - - +
253F MET 5.9 0.2 - - - -
255F PRO* 4.6 3.1 - - + -
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Residues in contact with GLY 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 3.6 16.4 + - - -
153F ASN* 3.6 11.3 - - - +
155F GLN* 5.6 0.3 + - - -
158F PHE* 4.0 15.2 - - - -
205F SER 2.8 23.8 + - - -
207F ILE 3.1 0.2 - - - -
208F MET* 1.3 79.5 - - - +
210F GLY* 1.3 57.8 + - - +
211F VAL* 3.5 4.4 + - - -
250F ASP* 4.4 10.5 - - - +
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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) + - + + + + + -
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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