Contacts of the helix formed by residues 193 - 209 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ALA* 4.3 16.8 - - + +
200B THR* 3.7 30.3 - - + -
201B ILE* 3.9 28.9 - - + -
204B CYS* 4.1 18.8 - - - -
236B ILE* 4.5 2.2 - - + -
184C MET* 4.9 2.9 - - + -
189C LEU* 2.8 23.7 + - + +
192C LEU* 1.3 78.8 - - + +
194C GLY* 1.3 68.2 + - - +
195C MET 3.5 0.9 - - - -
196C PRO* 3.4 5.7 - - - +
197C ALA* 3.3 19.9 + - + +
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Residues in contact with GLY 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C MET* 3.7 13.6 - - - +
184C MET* 4.4 10.9 - - - +
189C LEU 2.9 11.3 + - - -
190C PRO* 3.1 12.6 - - - -
193C VAL* 1.3 77.4 - - - +
195C MET* 1.3 59.9 + - - +
197C ALA* 3.3 5.8 + - - +
198C GLU* 2.8 31.2 + - - +
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Residues in contact with MET 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 3.8 6.5 - - - +
174C HIS* 3.5 18.4 - - + -
175C PRO* 3.2 33.8 - - + +
176C TRP* 5.4 4.5 - - - -
178C MET* 4.1 16.6 - - + +
190C PRO 3.0 16.1 + - - +
191C TRP* 3.5 37.9 - - - +
194C GLY* 1.3 72.0 - - - +
196C PRO* 1.3 74.4 - - + +
198C GLU* 2.9 4.7 + - - +
199C THR* 2.9 26.0 + - - -
224C HIS* 2.7 41.5 - - + +
291C ASP* 5.8 1.1 - - - +
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Residues in contact with PRO 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 4.5 12.6 - - + -
235B ARG* 3.9 17.5 - - - +
191C TRP 3.9 4.7 - - - +
192C LEU 3.4 21.3 - - - +
193C VAL* 3.4 14.4 - - - +
195C MET* 1.3 94.4 - - + +
197C ALA* 1.3 55.7 + - - +
199C THR* 3.2 3.5 + - - +
200C THR* 2.9 30.7 + - - -
224C HIS* 5.3 6.0 - - + -
227C GLY* 3.4 33.5 - - - +
228C ALA* 4.5 2.5 - - + -
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.5 5.6 - - + +
197B ALA* 4.2 23.6 - - + -
193C VAL* 3.3 17.6 + - + +
194C GLY* 3.7 4.7 - - - +
195C MET 3.2 0.4 - - - -
196C PRO* 1.3 77.1 - - - +
198C GLU* 1.3 65.6 + - - +
200C THR* 3.2 8.3 + - - -
201C ILE* 3.1 34.7 + - + +
228C ALA* 5.6 2.2 - - - +
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG* 3.0 32.0 + - - -
145C THR* 3.1 24.7 + - - +
146C HIS* 2.7 32.2 + - - -
175C PRO* 4.0 8.3 - - + -
176C TRP 4.4 3.1 - - - +
177C ASP 4.5 0.2 - - - +
178C MET* 4.1 26.9 - - + +
194C GLY 2.8 19.0 + - - +
195C MET 2.9 7.6 + - - +
197C ALA* 1.3 73.0 - - - +
199C THR* 1.3 64.3 + - - +
201C ILE* 3.3 10.5 + - - +
202C ALA* 3.1 21.7 + - - +
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 4.0 8.9 - - + +
173C VAL 5.6 0.2 - - - +
175C PRO* 3.6 24.1 - - + +
195C MET 2.9 12.6 + - - -
196C PRO* 3.4 9.0 - - - +
198C GLU* 1.3 78.4 - - - +
200C THR* 1.3 57.6 + - - +
202C ALA* 3.3 1.9 + - - +
203C ILE* 2.9 28.8 + - + +
222C PHE* 4.0 19.3 - - + -
223C ALA 3.8 15.3 + - - +
224C HIS* 4.8 1.6 - - - -
226C GLY* 3.6 26.5 - - - -
227C GLY* 3.8 7.0 - - - +
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Residues in contact with THR 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.2 20.2 - - + -
196C PRO 2.9 9.5 + - - -
197C ALA* 3.2 7.6 + - - -
199C THR* 1.3 75.9 - - - +
201C ILE* 1.3 58.4 + - - +
203C ILE* 3.4 5.0 + - - +
204C CYS* 2.9 27.3 + - - -
226C GLY 4.2 4.5 + - - -
228C ALA* 3.0 33.7 + - + +
229C PHE* 3.5 24.2 + - + +
232C THR* 4.4 3.8 - - - +
236C ILE* 4.1 19.5 - - + -
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG* 3.9 14.1 - - + +
184B MET* 3.9 24.7 - - + -
189B LEU* 3.9 26.0 - - + -
193B VAL* 3.8 21.5 - - + -
151C ASP* 3.4 28.7 - - - +
197C ALA* 3.1 24.3 + - + +
198C GLU* 3.7 13.0 - - - +
200C THR* 1.3 74.4 - - - +
202C ALA* 1.3 53.0 + - - +
204C CYS* 3.2 8.1 + - - +
205C SER* 2.8 38.5 + - - +
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C THR* 3.8 29.8 + - + +
151C ASP* 5.2 0.7 - - - -
152C LEU* 3.9 19.2 - - + +
198C GLU 3.1 12.7 + - - +
199C THR* 3.4 9.0 - - - +
201C ILE* 1.3 78.1 - - - +
203C ILE* 1.3 63.1 + - - +
205C SER* 3.2 7.0 + - - -
206C MET* 3.0 28.4 + - - +
222C PHE* 4.3 10.5 - - + -
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Residues in contact with ILE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C THR* 2.9 21.5 + - + +
200C THR 3.7 4.3 - - - +
201C ILE 3.3 0.2 - - - -
202C ALA* 1.3 74.8 - - - +
204C CYS* 1.3 63.8 + - - +
205C SER 3.2 0.3 + - - -
206C MET* 3.2 3.0 + - - +
207C ILE* 3.1 34.3 + - + +
212C PHE* 5.5 0.7 - - + -
222C PHE* 3.7 36.6 - - + -
226C GLY* 3.5 39.0 - - - +
229C PHE* 3.7 41.1 - - + -
262C PHE* 4.1 14.4 - - + -
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Residues in contact with CYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 5.1 0.7 - - - -
189B LEU* 4.0 13.2 - - + -
193B VAL* 4.1 14.1 - - - -
200C THR* 2.9 22.0 + - - +
201C ILE 3.4 7.6 - - - +
203C ILE* 1.3 72.3 - - - +
205C SER* 1.3 53.7 + - - +
207C ILE* 4.7 4.5 - - - -
208C MET* 2.7 65.9 + - + +
229C PHE* 4.8 4.3 - - - -
236C ILE* 3.9 33.7 - - - -
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Residues in contact with SER 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LYS* 3.7 12.5 - - - -
187B TYR* 4.3 7.1 - - - -
189B LEU* 4.8 1.2 - - - +
151C ASP* 3.4 25.7 - - - +
152C LEU 4.0 3.1 - - - -
153C ASN* 3.4 28.8 - - - +
201C ILE* 2.8 23.2 + - - +
202C ALA* 3.6 7.0 - - - -
203C ILE 3.2 0.2 - - - -
204C CYS* 1.3 73.3 - - - +
206C MET* 1.3 60.1 + - - +
209C GLY* 2.8 29.5 + - - -
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Residues in contact with MET 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 6.5 0.2 - - - -
152C LEU* 3.6 33.2 - - + +
161C TYR* 4.7 10.5 - - + -
171C LEU* 5.8 1.6 - - + -
173C VAL* 5.0 2.2 - - - -
202C ALA 3.0 14.7 + - - +
203C ILE* 3.9 3.4 - - - +
205C SER* 1.3 79.7 - - - +
207C ILE* 1.3 59.8 + - - +
210C GLY 3.3 0.9 + - - -
211C VAL* 2.8 58.0 + - + +
212C PHE* 3.8 35.2 + - + -
218C LEU* 4.8 1.8 - - + -
220C VAL* 3.9 18.2 - - + -
222C PHE* 3.8 24.7 - - - -
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Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE* 3.1 34.5 + - + +
204C CYS* 3.9 4.3 - - - +
206C MET* 1.3 74.3 - - - +
208C MET* 1.3 65.2 + - + +
210C GLY* 3.1 5.9 + - - -
211C VAL 5.1 0.4 - - - +
212C PHE* 3.6 26.0 - - + -
229C PHE* 4.1 19.3 - - + -
251C ASN* 3.1 24.7 + - - +
253C MET 5.3 0.4 - - - +
255C PRO* 3.6 37.7 - - + +
258C TYR* 3.6 29.0 - - + -
262C PHE* 4.2 10.5 - - + -
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Residues in contact with MET 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.7 49.1 + - + +
189B LEU* 4.4 5.2 - - + -
192B LEU* 4.5 4.7 - - + -
204C CYS* 2.7 60.6 + - + +
207C ILE* 1.3 77.4 - - + +
209C GLY* 1.3 56.6 + - - +
210C GLY 3.1 1.6 + - - -
236C ILE* 4.3 13.2 - - + -
240C PHE* 4.0 22.7 - - + -
247C CYS* 3.9 26.5 - - - +
250C ASP* 3.6 15.9 - - - +
251C ASN* 3.6 12.1 + - - +
255C PRO* 4.6 9.4 - - + -
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Residues in contact with GLY 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.3 18.3 + - - -
153C ASN* 3.9 9.3 - - - +
158C PHE* 4.0 15.2 - - - -
205C SER 2.8 20.5 + - - -
207C ILE 3.2 0.2 - - - -
208C MET* 1.3 78.1 - - - +
210C GLY* 1.3 61.1 + - - +
211C VAL* 3.4 4.0 - - - -
214C LYS* 4.7 2.4 + - - +
250C ASP* 4.3 14.0 - - - +
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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