Contacts of the helix formed by residues 193 - 209 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D ALA* 4.3 13.2 - - + +
200D THR* 3.9 31.2 - - + -
201D ILE* 3.9 28.3 - - + -
204D CYS* 4.1 18.4 - - - -
236D ILE* 4.4 2.9 - - + -
184E MET* 4.8 2.7 - - + -
189E LEU* 2.8 29.0 + - + +
192E LEU* 1.3 80.3 - - + +
194E GLY* 1.3 59.2 + - - +
196E PRO* 3.1 9.7 - - - +
197E ALA* 3.0 26.5 + - + +
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Residues in contact with GLY 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E MET* 3.5 13.2 - - - -
184E MET* 4.3 10.4 - - - +
189E LEU 3.0 10.8 + - - -
190E PRO* 3.3 11.2 - - - -
193E VAL* 1.3 76.1 - - - +
195E MET* 1.3 59.4 + - - +
197E ALA* 3.7 6.5 - - - +
198E GLU* 2.8 34.5 + - - +
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Residues in contact with MET 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ARG* 2.9 28.3 - - - +
174E HIS* 4.6 7.9 - - + -
175E PRO* 3.5 28.1 - - + +
176E TRP* 5.3 4.5 - - - -
178E MET* 3.6 19.3 - - - +
190E PRO 2.8 21.9 + - - +
191E TRP* 3.6 32.5 - - + +
194E GLY* 1.3 71.9 - - - +
196E PRO* 1.4 71.5 - - + +
198E GLU* 3.2 4.7 + - - +
199E THR* 3.0 24.8 + - - -
224E HIS* 2.9 33.4 - - + +
291E ASP* 5.6 3.6 - - - +
296E LEU* 5.1 0.4 - - + -
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Residues in contact with PRO 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D ALA* 6.2 1.1 - - + -
232D THR* 4.3 15.0 - - + -
235D ARG* 4.0 17.0 - - - +
191E TRP 3.7 9.0 - - - +
192E LEU 3.6 13.7 - - - +
193E VAL* 3.1 16.4 - - - +
195E MET* 1.4 93.1 - - + +
197E ALA* 1.3 59.7 + - - +
199E THR* 3.4 1.8 + - - +
200E THR* 2.9 28.5 + - - -
224E HIS* 5.4 6.7 - - + -
227E GLY* 3.5 29.3 - - - -
228E ALA* 4.5 3.8 - - + +
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D VAL* 4.4 9.0 - - + +
197D ALA* 4.3 24.7 - - + -
193E VAL* 3.0 18.0 + - + +
194E GLY* 3.7 8.1 - - - +
196E PRO* 1.3 73.9 - - - +
198E GLU* 1.3 64.1 + - - +
200E THR* 3.2 8.1 + - - -
201E ILE* 3.1 32.2 + - + +
228E ALA* 6.0 1.3 - - - -
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Residues in contact with GLU 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ARG* 2.8 42.3 + - - -
145E THR* 3.3 25.4 + - - +
146E HIS* 3.0 18.6 + - - -
175E PRO* 4.0 7.2 - - + -
176E TRP 4.5 2.0 - - - +
178E MET* 3.6 28.4 - - + -
179E GLN 5.5 0.3 + - - -
194E GLY 2.8 18.8 + - - +
195E MET* 3.4 9.4 - - - +
197E ALA* 1.3 73.9 - - - +
199E THR* 1.4 61.5 + - - +
201E ILE* 3.4 13.4 + - - +
202E ALA* 3.1 16.5 + - - +
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Residues in contact with THR 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E THR* 4.0 9.3 - - + +
173E VAL 5.7 0.4 - - - +
175E PRO* 3.7 22.5 - - - +
195E MET 3.0 13.9 + - - -
196E PRO* 3.7 8.1 - - - +
197E ALA 3.3 0.4 - - - -
198E GLU* 1.4 73.4 - - - +
200E THR* 1.3 59.7 + - - +
202E ALA* 2.9 17.2 + - - +
203E ILE* 2.9 13.9 + - + +
222E PHE* 4.0 20.4 - - + -
223E ALA 3.9 12.4 + - - +
224E HIS* 4.6 2.3 - - - -
226E GLY* 3.4 31.2 - - - +
227E GLY* 3.7 6.9 + - - +
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Residues in contact with THR 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D VAL* 4.0 24.5 - - + -
196E PRO 2.9 6.7 + - - -
197E ALA* 3.2 7.9 + - - -
199E THR* 1.3 77.8 - - - +
201E ILE* 1.3 62.3 + - - +
203E ILE* 3.9 4.7 - - - +
204E CYS* 3.0 30.0 + - - -
226E GLY 4.3 4.9 - - - -
228E ALA* 2.9 33.7 + - + +
229E PHE* 3.4 23.1 + - + +
232E THR* 4.3 3.8 - - - +
236E ILE* 4.1 14.1 - - + -
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Residues in contact with ILE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ARG* 3.8 17.7 - - + +
184D MET* 3.9 27.4 - - + -
189D LEU* 4.3 12.3 - - + +
193D VAL* 3.9 23.3 - - + -
145E THR 5.7 1.3 - - - +
151E ASP* 3.7 24.9 - - - +
197E ALA* 3.1 28.4 + - + +
198E GLU* 3.5 20.6 - - - +
200E THR* 1.3 74.4 - - - +
202E ALA* 1.3 58.5 + - - +
204E CYS* 3.5 5.2 + - - +
205E SER* 2.8 36.3 + - - +
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Residues in contact with ALA 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E THR* 3.8 31.4 - - + +
151E ASP* 6.3 0.2 - - - -
152E LEU* 3.9 21.9 - - + +
198E GLU 3.1 5.4 + - - +
199E THR 2.9 10.2 + - - +
201E ILE* 1.3 75.6 - - - +
203E ILE* 1.3 66.1 + - - +
205E SER* 3.9 4.9 - - - -
206E MET* 3.0 28.2 + - - +
222E PHE* 4.0 13.0 - - + -
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Residues in contact with ILE 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E THR* 2.9 18.8 + - + +
200E THR 4.0 3.6 - - - +
202E ALA* 1.3 75.9 - - - +
204E CYS* 1.3 57.6 + - - +
206E MET* 3.3 1.8 + - - +
207E ILE* 2.9 54.3 + - + +
212E PHE* 5.5 0.7 - - + -
222E PHE* 3.7 31.0 - - + -
226E GLY* 3.6 26.2 - - - +
229E PHE* 3.5 40.8 - - + -
262E PHE* 3.8 28.3 - - + -
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Residues in contact with CYS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 4.9 0.2 - - - -
189D LEU* 4.1 10.8 - - + -
192D LEU* 6.0 0.2 - - - -
193D VAL* 4.3 11.4 - - - -
200E THR* 3.0 23.0 + - - +
201E ILE* 3.9 3.4 - - - +
203E ILE* 1.3 75.1 - - - +
205E SER* 1.3 60.5 + - - +
207E ILE* 4.4 5.6 - - - +
208E MET* 2.8 54.9 + - + +
229E PHE* 4.6 6.5 - - - -
236E ILE* 3.9 42.0 - - - -
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Residues in contact with SER 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LYS* 4.1 4.3 - - - -
187D TYR* 4.1 11.4 - - - -
189D LEU* 4.6 4.2 - - - +
151E ASP* 3.2 30.6 + - - +
152E LEU* 4.3 3.8 - - - -
153E ASN* 3.5 26.8 - - - +
201E ILE* 2.8 23.1 + - - +
202E ALA* 3.9 4.5 - - - -
204E CYS* 1.3 76.8 - - - +
206E MET* 1.3 55.6 + - - +
209E GLY* 2.7 35.3 + - - -
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Residues in contact with MET 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ILE* 6.3 0.2 - - - -
152E LEU* 3.8 30.1 - - + +
161E TYR* 4.6 8.7 - - + -
171E LEU* 5.1 2.5 - - + -
173E VAL* 5.0 3.6 - - - -
202E ALA 3.0 17.3 + - - +
203E ILE* 3.7 2.0 - - - +
205E SER* 1.3 79.4 - - - +
207E ILE* 1.3 60.6 + - - +
211E VAL* 3.2 63.0 + - + +
212E PHE* 3.6 37.8 + - + -
218E LEU* 4.0 5.2 - - + -
220E VAL* 3.9 18.4 - - + -
222E PHE* 4.0 23.1 - - - -
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Residues in contact with ILE 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E ILE* 2.9 39.5 + - + +
204E CYS* 3.8 5.4 - - - +
205E SER 3.3 0.2 - - - -
206E MET* 1.3 75.2 - - - +
208E MET* 1.3 66.8 + - + +
210E GLY* 3.2 11.8 + - - -
212E PHE* 4.2 18.7 + - + +
229E PHE* 3.9 21.5 - - + -
236E ILE* 6.4 0.2 - - + -
251E ASN* 3.3 17.7 + - - -
253E MET 4.9 2.7 - - - +
255E PRO* 3.8 30.1 - - + +
258E TYR* 3.6 41.0 - - + -
262E PHE* 4.4 4.0 - - + -
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Residues in contact with MET 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 3.7 49.2 + - + +
189D LEU* 4.0 6.5 - - + -
192D LEU* 4.9 8.1 - - + -
204E CYS* 2.8 54.3 + - + +
207E ILE* 1.3 82.1 - - + +
209E GLY* 1.3 59.6 + - - +
210E GLY 3.2 0.8 + - - -
236E ILE* 5.0 4.9 - - + -
240E PHE* 4.0 33.4 - - + -
247E CYS* 4.0 19.0 - - - +
250E ASP* 3.4 17.5 + - - +
251E ASN* 3.5 15.8 + - - +
253E MET 5.9 0.2 - - - -
255E PRO* 4.7 5.8 - - + -
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Residues in contact with GLY 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 3.2 18.1 + - - -
153E ASN* 3.7 11.7 - - - +
155E GLN* 5.4 2.4 + - - -
158E PHE* 4.2 12.3 - - - -
205E SER 2.7 21.0 + - - -
208E MET* 1.3 78.1 - - - +
210E GLY* 1.3 58.5 + - - +
211E VAL* 3.4 5.5 + - - -
214E LYS* 4.5 2.6 - - - -
250E ASP* 3.8 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