Contacts of the helix formed by residues 192 - 208 (chain B) in PDB entry 3MI9
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 THR 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.8 20.6 - - + +
191B TYR* 1.3 75.8 - - - +
193B PRO* 1.3 76.1 - - - +
194B PRO* 3.3 14.0 - - - +
195B VAL* 2.9 33.5 + - + +
196B VAL* 3.1 9.2 + - - +
226B ASP* 4.1 5.9 + - - -
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Residues in contact with PRO 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.6 14.4 - - - +
151B ASP* 3.1 50.5 - - + +
152B HIS* 3.9 14.6 - - - -
153B PRO* 3.5 11.7 - - + +
156B HIS* 4.0 3.8 - - + -
191B TYR 3.7 1.5 - - - +
192B THR* 1.3 88.0 - - - +
194B PRO* 1.3 62.5 - - + +
196B VAL* 3.4 7.3 + - + -
197B ALA* 2.9 29.5 + - - +
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Residues in contact with PRO 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 4.4 2.0 - - - +
156B HIS* 3.7 35.0 - - + +
192B THR* 3.2 15.0 - - - +
193B PRO* 1.3 99.4 - - + +
195B VAL* 1.3 61.2 + - - +
197B ALA* 3.2 4.2 + - - +
198B CYS* 3.1 26.0 + - - -
225B VAL* 3.6 23.7 - - + +
226B ASP* 3.9 15.0 - - + +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 4.0 20.0 - - + -
192B THR* 2.9 25.0 + - + +
194B PRO* 1.3 73.5 - - - +
196B VAL* 1.3 67.9 + - - +
198B CYS* 3.0 5.7 + - - +
199B VAL* 3.0 21.7 + - + +
226B ASP* 3.7 12.8 - - - +
228B THR* 4.3 6.5 - - - +
229B VAL* 3.7 25.4 - - + -
233B LEU* 4.0 25.1 - - + -
234B LEU* 5.3 1.3 - - + -
237B LEU* 4.4 11.7 - - + -
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PRO* 3.6 19.1 - - + -
181B SER* 3.5 31.6 - - - +
187B PHE* 3.9 32.1 - - + +
188B SER* 4.8 3.1 - - - +
191B TYR* 3.6 22.0 - - + +
192B THR 3.1 14.1 + - - +
193B PRO* 3.8 7.4 - - + +
195B VAL* 1.3 76.0 - - - +
197B ALA* 1.3 62.8 + - - +
199B VAL* 3.2 10.6 + - + +
200B CYS* 3.0 24.3 + - - -
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO* 3.6 6.5 - - - +
156B HIS* 3.6 23.6 - - + -
157B VAL* 3.6 27.8 - - + +
193B PRO 2.9 14.3 + - - +
194B PRO 3.3 10.5 - - - +
195B VAL 3.1 0.4 - - - -
196B VAL* 1.3 77.2 - - - +
198B CYS* 1.3 61.4 + - - +
200B CYS* 3.3 4.4 + - - +
201B ILE* 3.1 28.6 + - + +
225B VAL* 4.6 2.9 - - + -
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Residues in contact with CYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B PRO 3.1 12.4 + - - -
195B VAL 3.0 10.2 + - - +
197B ALA* 1.3 74.1 - - - +
199B VAL* 1.3 59.9 + - - +
201B ILE* 3.2 1.0 + - - -
202B HIS* 2.8 31.9 + - - +
221B TRP* 3.3 18.3 - - + -
222B TRP* 3.8 23.8 - - - -
225B VAL* 3.5 31.0 - - - -
226B ASP 4.6 0.7 - - - -
229B VAL* 4.2 13.0 - - + -
234B LEU* 3.7 18.6 - - + -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PHE* 4.3 15.7 - - + -
195B VAL* 3.0 16.2 + - + +
196B VAL* 3.2 10.7 + - + +
198B CYS* 1.3 74.9 - - - +
200B CYS* 1.3 59.7 + - - +
202B HIS* 3.4 4.1 + - - +
203B LEU* 2.9 29.9 + - + +
234B LEU* 4.1 15.9 - - + -
237B LEU* 3.7 47.1 - - + +
238B THR* 3.8 19.1 + - - +
241B PHE* 4.4 11.4 - - + -
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Residues in contact with CYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 4.6 3.8 - - + -
174B SER* 3.7 22.3 + - - +
177B MET* 3.6 17.9 - - + +
178B ALA* 3.4 32.3 - - - +
181B SER* 4.2 12.1 - - - -
187B PHE* 6.4 0.2 - - - -
196B VAL* 3.0 23.0 + - - -
197B ALA* 3.6 9.6 - - - +
198B CYS 3.3 0.2 - - - -
199B VAL* 1.3 79.2 - - - +
201B ILE* 1.3 57.9 + - - +
203B LEU* 4.1 3.7 - - - +
204B ALA* 3.2 24.6 + - - +
241B PHE* 4.5 6.7 - - - -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B HIS 4.9 0.2 - - - +
157B VAL* 4.1 17.0 - - + +
160B CYS* 3.5 37.9 - - + -
161B THR* 4.4 8.1 - - + -
170B LEU* 5.5 2.7 - - + -
174B SER* 3.7 25.1 - - - +
197B ALA* 3.1 23.0 + - + +
198B CYS 3.7 3.6 - - - +
200B CYS* 1.3 74.2 - - - +
202B HIS* 1.3 55.9 + - - +
203B LEU 3.1 1.6 - - - -
204B ALA* 2.9 2.9 + - - +
205B CYS* 2.6 51.1 + - - +
212B ILE* 4.3 6.1 - - + -
221B TRP* 3.6 22.9 - - + -
225B VAL* 5.3 1.6 - - + -
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Residues in contact with HIS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B CYS 2.8 17.6 + - - +
199B VAL 3.6 4.3 - - - +
201B ILE* 1.3 76.6 - - - +
203B LEU* 1.3 62.4 + - - +
205B CYS* 3.2 8.1 + - - +
206B LYS* 3.1 49.8 + - - +
211B GLU* 5.9 2.7 - - - -
221B TRP* 3.9 17.6 + - + -
222B TRP* 5.8 0.9 - + - -
231B LEU* 3.7 25.8 - - + -
234B LEU* 3.6 31.2 - - + +
235B ASP* 3.1 20.8 + - - -
238B THR* 3.3 24.2 - - + +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B MET* 4.0 15.7 - - + -
199B VAL* 2.9 19.0 + - + +
200B CYS* 4.1 5.4 - - - +
202B HIS* 1.3 73.6 - - - +
204B ALA* 1.3 66.1 + - - +
206B LYS* 3.0 18.9 + - + +
207B TRP* 3.2 57.5 + - + +
238B THR* 3.8 26.4 + - + +
241B PHE* 4.1 25.1 - - + -
242B LEU* 4.1 19.3 - - + -
245B LEU* 5.3 0.2 - - + -
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.6 13.2 - - + +
173B THR* 3.9 27.7 - - + +
174B SER* 3.2 28.9 - - - +
177B MET* 5.2 0.4 - - + +
200B CYS 3.2 11.7 + - - +
201B ILE 2.9 3.0 + - - +
203B LEU* 1.3 79.2 - - - +
205B CYS* 1.3 59.6 + - - +
207B TRP* 3.4 9.1 + - - +
208B SER* 2.8 25.5 + - - -
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Residues in contact with CYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.0 4.9 - - - -
201B ILE* 2.6 27.1 + - - +
202B HIS* 3.5 11.0 - - - +
203B LEU 3.1 0.2 - - - -
204B ALA* 1.3 72.2 - - - +
206B LYS* 1.3 59.5 + - + +
208B SER* 3.4 5.8 + - - -
209B ASN* 3.0 6.4 + - - -
210B TRP* 2.8 75.6 + - - +
212B ILE* 3.7 22.0 - - - -
221B TRP* 5.7 1.6 - - + -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B HIS* 3.1 42.5 + - + +
203B LEU* 3.0 16.4 + - + +
205B CYS* 1.3 74.8 - - + +
207B TRP* 1.3 70.7 + - + +
209B ASN* 3.0 16.9 + - - +
211B GLU* 6.2 0.2 - - - -
235B ASP* 3.2 21.0 + - - -
238B THR* 5.0 9.6 - - + +
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Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B THR* 4.1 19.3 - - + -
177B MET* 3.4 39.3 - - + -
203B LEU* 3.2 41.2 + - + +
204B ALA* 3.4 6.5 + - - +
206B LYS* 1.3 80.2 - - + +
208B SER* 1.3 56.9 + - - +
209B ASN 3.4 0.6 + - - -
242B LEU* 3.8 28.5 - - + +
245B LEU* 4.4 10.5 - - + -
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASP* 6.0 1.6 - - - -
170B LEU* 3.4 20.2 - - - +
204B ALA 2.8 17.8 + - - -
205B CYS* 3.5 5.2 + - - -
206B LYS 3.1 0.6 - - - -
207B TRP* 1.3 76.8 - - - +
209B ASN* 1.3 72.1 + - - +
210B TRP* 2.8 12.5 + - - +
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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
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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