Contacts of the helix formed by residues 185 - 201 (chain B) in PDB entry 3IO6
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 ASN 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLY 3.6 19.0 + - - -
166B GLY* 3.6 3.9 - - - -
167B TYR* 3.6 9.7 + - - -
182B GLY* 3.5 30.6 + - - -
183B VAL 3.6 0.6 - - - +
184B ASP* 1.3 82.0 + - - +
186B ALA* 1.3 58.8 + - - +
187B GLY 3.4 3.4 + - - -
188B ALA* 2.9 32.4 + - - +
189B LYS* 3.0 28.3 + - - +
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASP* 3.7 6.8 - - - +
185B ASN* 1.3 74.5 - - - +
187B GLY* 1.3 58.3 + - - +
189B LYS* 3.9 13.0 - - - +
190B ALA* 3.5 18.5 + - - +
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Residues in contact with GLY 187 (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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161B ILE 3.6 5.3 - - - +
164B ASP* 3.2 36.6 - - - +
165B GLY* 3.7 13.2 - - - -
185B ASN* 3.1 5.5 + - - +
186B ALA* 1.3 76.1 - - - +
188B ALA* 1.3 64.2 + - - +
189B LYS 3.2 1.3 - - - -
190B ALA 3.5 0.9 + - - -
191B GLY 3.0 18.4 + - - -
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 3.4 30.2 + - + +
166B GLY* 3.9 10.1 - - - +
182B GLY 4.2 0.7 - - - +
183B VAL* 3.2 29.4 - - - +
185B ASN* 2.9 18.4 + - - +
187B GLY* 1.3 74.4 - - - +
189B LYS* 1.3 63.0 + - - +
191B GLY* 3.7 0.3 - - - -
192B LEU* 3.0 26.9 + - - +
361B LEU* 3.7 3.2 - - + +
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Residues in contact with LYS 189 (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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74A GLY* 6.1 1.8 - - - -
184B ASP* 3.6 25.4 + - + +
185B ASN 3.0 14.5 + - - +
186B ALA* 3.9 11.7 - - - +
188B ALA* 1.3 78.9 - - - +
190B ALA* 1.3 55.5 + - - +
193B THR* 2.7 35.3 + - - +
357B VAL* 3.2 13.7 - - + +
358B ASP* 3.3 49.5 + - - +
361B LEU* 3.9 15.2 - - + +
362B ALA* 6.2 1.0 - - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASP* 4.3 8.7 - - - +
186B ALA 3.5 14.9 + - - +
187B GLY 3.5 2.4 + - - +
189B LYS* 1.3 76.5 - - - +
191B GLY* 1.3 67.5 + - - +
193B THR* 3.3 9.4 + - - -
194B PHE* 3.1 17.0 + - - +
250B PHE* 3.6 17.7 - - + -
251B LYS* 4.7 12.3 - - + -
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Residues in contact with GLY 191 (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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160B LEU* 3.7 29.1 - - - +
161B ILE* 4.3 4.9 - - - -
164B ASP* 5.3 0.2 - - - -
187B GLY 3.0 17.0 + - - -
188B ALA 3.7 1.8 - - - -
189B LYS 3.3 0.2 - - - -
190B ALA* 1.3 80.0 - - - +
192B LEU* 1.3 59.6 + - - +
194B PHE* 3.2 12.0 + - - +
195B LEU* 3.3 11.3 + - - +
250B PHE* 3.8 12.4 - - - -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 4.4 16.2 - - + +
188B ALA 3.0 17.4 + - - +
191B GLY* 1.3 72.5 - - - +
193B THR* 1.3 66.2 + - - +
195B LEU* 3.4 25.0 + - + +
196B VAL* 3.0 24.6 + - + +
346B ALA 4.6 5.2 - - - +
347B VAL* 4.2 22.9 - - + +
350B ALA* 3.6 31.6 - - + -
357B VAL* 3.8 18.4 - - + +
360B ALA* 5.2 0.9 - - + -
361B LEU* 3.8 29.6 - - + -
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Residues in contact with THR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LYS* 2.7 24.4 + - - +
190B ALA* 3.5 11.9 - - - -
191B GLY 3.3 0.4 - - - -
192B LEU* 1.3 75.3 - - - +
194B PHE* 1.3 54.1 + - - +
196B VAL* 3.2 2.9 + - - +
197B ASP* 2.8 57.3 + - - +
357B VAL* 3.4 28.5 - - + +
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Residues in contact with PHE 194 (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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129B TRP* 3.3 45.1 - + + -
130B GLU* 3.8 20.2 - - + -
133B PRO* 4.3 14.8 - - + -
160B LEU* 4.1 11.7 - - + -
190B ALA 3.1 6.0 + - - +
191B GLY 3.4 9.6 - - - +
193B THR* 1.3 76.8 - - - +
195B LEU* 1.3 66.3 + - - +
197B ASP* 3.3 10.4 + - + +
198B LEU* 3.1 49.4 + - + +
250B PHE* 3.4 28.7 - + + -
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Residues in contact with LEU 195 (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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129B TRP* 5.3 0.2 - - + -
149B PHE* 3.7 29.4 - - + -
151B LEU* 4.1 5.6 - - + -
157B THR* 4.0 28.5 - - + +
160B LEU* 3.9 24.4 - - + +
161B ILE* 5.6 2.5 - - + -
191B GLY 3.3 6.9 + - - +
192B LEU* 3.7 27.6 - - + +
193B THR 3.4 0.2 - - - -
194B PHE* 1.3 79.5 - - - +
196B VAL* 1.3 62.5 + - + +
198B LEU* 3.3 10.1 + - - +
199B ILE* 3.2 35.0 + - + +
204B MET* 3.7 17.3 - - + +
347B VAL* 4.3 7.9 - - + -
351B ALA* 6.0 0.9 - - + -
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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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192B LEU* 3.0 25.3 + - + +
193B THR* 3.7 5.6 - - + +
195B LEU* 1.3 76.4 - - + +
197B ASP* 1.3 59.9 + - - +
199B ILE* 3.0 11.2 + - + +
200B LYS* 2.9 45.7 + - + +
347B VAL 5.7 0.2 - - - +
350B ALA* 3.3 46.0 - - + +
351B ALA* 4.1 7.6 - - - +
357B VAL* 5.1 10.3 - - + -
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 2.8 39.9 + - - +
194B PHE* 3.3 11.2 + - + +
196B VAL* 1.3 73.8 - - - +
198B LEU* 1.3 54.6 + - + +
200B LYS* 2.9 31.8 + - - +
201B ASN* 2.8 41.6 + - - +
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Residues in contact with LEU 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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129B TRP* 4.4 13.7 - - + -
132B ILE* 5.1 10.1 - - + -
133B PRO* 3.9 26.9 - - + -
147B LEU* 5.9 0.4 - - + -
194B PHE* 3.1 44.0 + - + +
195B LEU* 3.4 10.1 - - - +
197B ASP* 1.3 75.2 - - + +
199B ILE* 1.3 60.1 + - - +
202B LYS 3.5 1.4 + - - -
203B HIS* 2.8 60.7 + - + +
204B MET* 3.2 31.1 + - + -
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Residues in contact with ILE 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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151B LEU* 3.9 28.3 - - + -
195B LEU* 3.2 24.1 + - + +
196B VAL* 3.0 14.8 + - + +
198B LEU* 1.3 79.0 - - - +
200B LYS* 1.3 58.4 + - + +
202B LYS* 3.3 28.7 + - - +
204B MET* 3.8 15.6 - - + +
206B ALA* 3.9 19.5 - - + +
351B ALA* 3.6 47.3 - - + +
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Residues in contact with LYS 200 (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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196B VAL* 2.9 29.2 + - + +
197B ASP* 2.9 33.0 + - - +
199B ILE* 1.3 74.0 - - + +
201B ASN* 1.3 66.0 + - - +
202B LYS* 3.2 14.8 + - - +
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Residues in contact with ASN 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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197B ASP* 2.8 23.1 + - - +
198B LEU 4.3 0.4 - - - +
199B ILE 3.4 0.2 - - - -
200B LYS* 1.3 81.9 + - - +
202B LYS* 1.3 70.0 + - - +
203B HIS* 3.6 26.4 + - + +
450B ZN 3.0 22.8 - - - -
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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
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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