Contacts of the helix formed by residues 193 - 209 (chain B) in PDB entry 6R7H
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 GLN 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ASN* 2.9 44.6 - - - +
153B THR* 4.4 9.2 + - - +
156B GLY* 4.5 8.7 - - - -
168B LEU* 4.8 0.4 + - - +
171B ILE* 3.4 35.0 + - - +
172B LEU* 3.4 27.7 - - + +
175B LEU* 3.8 18.7 - - + +
181B THR* 4.0 4.8 + - - -
191B GLY 4.3 0.2 - - - -
192B THR* 1.3 73.8 - - - +
194B LEU* 1.3 67.6 + - - +
195B LEU 3.3 1.8 - - - -
196B GLU* 3.8 3.4 - - - +
197B ILE* 3.3 38.1 + - + +
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Residues in contact with LEU 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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172B LEU* 3.8 27.8 - - + +
175B LEU* 5.5 0.2 - - - +
176B HIS* 5.6 10.5 - - + -
181B THR* 4.1 20.7 + - + +
192B THR* 4.3 0.2 - - - +
193B GLN* 1.3 80.3 - - - +
195B LEU* 1.3 59.2 + - - +
197B ILE* 4.0 5.9 + - + +
198B TYR* 3.4 46.2 + - + +
224B ILE* 3.7 25.1 - - + -
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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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192B THR* 3.6 17.8 - - + +
193B GLN 3.3 0.2 - - - -
194B LEU* 1.3 76.8 - - - +
196B GLU* 1.3 61.0 + - - +
197B ILE 3.3 0.7 - - - -
198B TYR* 3.5 7.5 + - + +
199B ALA* 3.0 27.9 + - - +
221B SER* 3.3 31.4 - - - +
224B ILE* 3.7 28.9 - - + +
228B ILE* 3.8 29.8 - - + -
233B ILE* 3.7 23.6 - - + +
237B ILE* 3.8 24.2 - - + -
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Residues in contact with GLU 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 THR* 4.3 7.9 - - + +
157B LYS* 3.8 43.8 + - + -
192B THR* 3.4 18.8 + - - +
193B GLN* 3.4 6.9 + - - +
195B LEU* 1.3 77.1 - - - +
197B ILE* 1.3 64.8 + - + +
199B ALA* 3.9 7.0 - - - +
200B LEU* 3.2 30.0 + - + +
233B ILE* 3.3 39.3 - - + +
236B VAL* 5.7 2.1 - - - +
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Residues in contact with ILE 197 (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 GLY 4.7 12.8 - - - +
157B LYS* 6.0 1.6 - - + -
160B LEU* 4.3 25.6 - - + +
168B LEU* 4.1 28.3 - - + -
172B LEU* 5.0 10.8 - - + -
193B GLN* 3.3 33.1 + - + +
194B LEU* 4.4 6.3 - - + +
195B LEU 3.3 0.4 - - - -
196B GLU* 1.3 78.4 - - + +
198B TYR* 1.3 70.8 + - + +
200B LEU* 3.4 14.1 + - + +
201B GLU* 3.4 26.5 + - + +
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Residues in contact with TYR 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 LEU* 3.4 38.0 + - + +
195B LEU* 3.5 15.1 + - + +
196B GLU 3.4 0.2 - - - -
197B ILE* 1.3 85.2 - - + +
199B ALA* 1.3 61.1 + - - +
201B GLU* 3.4 17.8 + - - +
202B ILE* 3.3 27.1 + - + +
217B LEU* 3.9 28.3 - - + +
220B GLN* 3.3 40.9 + - + -
221B SER* 4.9 6.3 - - - +
224B ILE* 4.6 11.2 - - + -
237B ILE* 6.0 0.2 - - - -
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Residues in contact with ALA 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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195B LEU 3.0 18.4 + - - +
196B GLU* 3.9 13.0 - - - +
197B ILE 3.3 0.4 - - - -
198B TYR* 1.3 74.9 - - - +
200B LEU* 1.3 65.2 + - - +
202B ILE* 3.4 19.8 + - - +
203B GLN* 3.6 12.3 + - - +
233B ILE* 4.4 8.7 - - + -
236B VAL* 3.9 32.7 - - + +
237B ILE* 4.8 7.4 - - + +
272B ARG* 5.9 0.9 + - - -
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Residues in contact with LEU 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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157B LYS* 3.9 31.4 - - + +
160B LEU* 3.8 27.6 - - + -
196B GLU* 3.2 25.2 + - + +
197B ILE* 3.8 5.6 - - - +
198B TYR 3.3 0.6 - - - -
199B ALA* 1.3 78.5 - - + +
201B GLU* 1.3 62.4 + - + +
202B ILE 3.6 0.2 + - - -
203B GLN* 3.7 7.5 + - + +
204B MET* 3.6 19.0 + - - +
272B ARG* 4.8 16.4 - - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 6.4 1.6 - - + -
197B ILE* 3.4 22.3 + - + +
198B TYR* 3.8 26.1 - - - +
199B ALA 3.3 0.8 - - - -
200B LEU* 1.3 77.2 - - + +
202B ILE* 1.3 61.0 + - - +
204B MET* 3.9 17.6 - - + +
205B TYR* 2.9 57.4 + - + -
213B LYS* 4.4 11.0 + - - -
217B LEU* 4.3 10.6 - - + +
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Residues in contact with ILE 202 (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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198B TYR* 3.3 17.5 - - + +
199B ALA* 3.4 13.9 + - - +
200B LEU 3.3 0.4 - - - -
201B GLU* 1.3 75.6 - - - +
203B GLN* 1.3 65.8 + - - +
206B THR* 2.9 35.2 + - + +
214B LEU* 3.8 17.8 - - + +
217B LEU* 4.1 28.9 - - + +
218B TYR* 5.6 1.1 - - - +
221B SER* 5.3 2.5 - - - +
236B VAL* 5.2 8.1 - - + +
237B ILE* 4.9 16.8 - - + +
239B GLU* 5.9 2.9 - - - +
240B CYS* 3.7 37.7 - - + +
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA 3.6 8.1 + - - +
200B LEU* 3.7 9.4 + - + +
201B GLU 3.4 0.6 - - - -
202B ILE* 1.3 82.3 - - - +
204B MET* 1.3 57.5 + - - +
206B THR* 3.2 17.3 + - - -
207B ALA* 4.4 6.8 + - - +
236B VAL* 4.9 6.6 - - - +
239B GLU* 4.4 23.5 + - - +
243B LYS* 5.6 2.4 - - - +
265B TYR* 4.5 8.0 + - - -
272B ARG* 4.2 31.5 + - - +
275B THR* 5.9 4.2 - - - +
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Residues in contact with MET 204 (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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200B LEU 3.6 11.5 + - - +
201B GLU* 3.4 26.4 + - + +
202B ILE 3.1 0.6 - - - -
203B GLN* 1.3 78.1 - - - +
205B TYR* 1.3 75.4 + - + +
206B THR 3.2 1.6 - - - -
207B ALA* 3.4 17.9 + - - +
208B GLN* 3.9 6.9 + - - +
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Residues in contact with TYR 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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201B GLU* 2.9 50.1 + - + +
204B MET* 1.3 84.2 - - + +
206B THR* 1.3 65.3 + - - +
208B GLN* 3.3 14.7 + - + +
209B LYS 3.3 9.0 + - - -
210B ASN* 3.6 44.2 + - + +
213B LYS* 3.6 41.9 - - + +
214B LEU* 4.0 20.4 - - + +
217B LEU* 4.5 3.8 - - + -
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Residues in contact with THR 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 ILE* 2.9 25.3 + - + +
203B GLN* 3.2 21.5 + - - -
205B TYR* 1.3 75.5 - - - +
207B ALA* 1.3 59.3 + - - +
208B GLN 3.5 0.2 + - - -
209B LYS* 3.5 10.4 + - - +
214B LEU* 4.0 25.6 - - + -
239B GLU* 5.7 0.9 - - - +
240B CYS* 5.7 0.9 - - - -
243B LYS* 4.1 27.5 + - + +
342B PHE* 3.5 36.3 - - + -
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Residues in contact with ALA 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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203B GLN 4.7 5.6 - - - +
204B MET* 3.4 12.2 + - - +
205B TYR 3.2 0.6 - - - -
206B THR* 1.3 81.5 + - - +
208B GLN* 1.3 64.5 + - - +
209B LYS* 3.4 6.0 - - - +
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Residues in contact with GLN 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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204B MET 3.9 6.7 + - - +
205B TYR* 3.3 11.9 + - + +
206B THR 3.3 0.4 - - - -
207B ALA* 1.3 81.3 - - - +
209B LYS* 1.3 73.3 + - - +
210B ASN* 3.5 23.2 - - - +
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Residues in contact with LYS 209 (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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321A GLU* 5.4 1.7 - - - +
205B TYR 3.3 4.9 + - - -
206B THR* 3.5 13.3 + - - +
207B ALA 3.4 6.2 - - - +
208B GLN* 1.3 80.7 - - - +
210B ASN* 1.3 66.3 + - - +
211B ASN* 3.9 7.6 + - - -
214B LEU* 6.0 0.4 - - - -
247B ARG* 4.1 18.6 - - - +
341B PRO* 3.9 32.5 + - + +
342B PHE* 4.9 7.4 - - + -
345B GLU* 2.4 33.6 + - - +
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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