Contacts of the helix formed by residues 206 - 226 (chain B) in PDB entry 6V3O
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 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ARG* 5.3 1.6 + - - -
204B ASP 3.8 6.2 + - - +
205B ILE* 1.3 80.1 - - - +
207B ASP* 1.3 61.4 + - - +
208B ASP* 3.7 5.5 + - - +
209B ASP* 3.1 37.0 + - - +
210B LYS* 2.9 30.4 + - - +
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Residues in contact with ASP 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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205B ILE* 4.9 3.3 - - - +
206B THR* 1.3 75.9 - - - +
208B ASP* 1.3 62.6 + - - +
210B LYS* 3.3 13.5 + - - +
211B GLN* 2.8 30.4 + - - +
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP* 5.3 4.7 - - - +
144A GLU* 3.5 29.1 - - - +
262A ARG* 3.7 41.8 + - - +
265A THR* 4.5 6.8 + - - +
269A ASN* 3.7 9.5 + - - -
206B THR* 3.3 4.9 + - - +
207B ASP* 1.3 77.6 - - - +
209B ASP* 1.3 66.2 + - - +
211B GLN* 3.2 10.7 + - - +
212B GLU* 3.0 29.0 + - - +
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 5.4 5.8 + - - -
262A ARG* 2.9 25.8 + - - +
205B ILE* 3.9 16.5 - - + +
206B THR* 3.1 33.6 + - - +
208B ASP* 1.3 76.0 - - - +
210B LYS* 1.3 57.5 + - - +
212B GLU* 3.3 4.5 + - - +
213B LEU* 2.8 41.7 + - + +
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.7 25.8 - - + +
205B ILE* 4.0 24.8 - - + +
206B THR 2.9 17.9 + - - +
207B ASP* 3.5 14.2 + - - +
209B ASP* 1.3 74.5 - - - +
211B GLN* 1.3 60.4 + - - +
213B LEU* 3.4 0.8 + - - -
214B ASP* 2.8 35.7 + - + +
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Residues in contact with GLN 211 (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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265A THR* 4.4 12.4 - - + -
268A LYS* 3.4 32.9 - - - +
269A ASN* 3.5 30.1 + - - +
207B ASP 2.8 19.8 + - - +
208B ASP* 3.2 11.8 + - - +
210B LYS* 1.3 74.2 - - - +
212B GLU* 1.3 59.8 + - + +
214B ASP* 3.4 7.3 + - - +
215B GLU* 3.0 37.9 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 5.3 10.2 + - - +
261A ARG* 4.4 23.1 - - + +
262A ARG* 2.9 50.5 + - - +
265A THR* 3.2 34.7 + - + +
208B ASP 3.0 14.9 + - - +
209B ASP* 3.8 5.0 - - - +
211B GLN* 1.3 73.0 - - - +
213B LEU* 1.3 61.5 + - + +
215B GLU* 3.2 11.9 + - - +
216B ALA* 2.9 28.6 + - - +
219B ARG* 5.0 1.2 + - - -
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Residues in contact with LEU 213 (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 CYS* 4.2 19.5 - - - +
199B GLN* 3.2 49.8 - - + +
200B LEU* 3.9 19.6 - - + +
205B ILE* 3.9 25.8 - - + -
209B ASP* 2.8 28.3 + - + +
210B LYS* 4.6 0.7 - - - -
212B GLU* 1.3 69.2 - - - +
214B ASP* 1.3 59.8 + - - +
216B ALA* 3.7 6.3 - - + +
217B LEU* 3.0 28.9 + - - +
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Residues in contact with ASP 214 (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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44B ARG* 3.0 40.9 + - - -
200B LEU* 4.1 13.2 - - + +
210B LYS* 2.8 22.3 + - + +
211B GLN* 3.4 8.3 - - - +
213B LEU* 1.3 76.8 - - - +
215B GLU* 1.3 63.4 + - + +
217B LEU* 3.1 4.0 + - - +
218B GLN* 2.9 46.3 + - - +
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Residues in contact with GLU 215 (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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261A ARG* 5.3 0.5 + - - +
265A THR* 4.5 6.1 - - - +
268A LYS* 2.6 39.6 + - - +
275A ARG* 3.6 17.5 + - - +
211B GLN* 3.0 29.8 + - - +
212B GLU* 3.2 13.8 + - - +
214B ASP* 1.3 76.7 - - + +
216B ALA* 1.3 62.0 + - - +
218B GLN* 3.6 15.9 + - - +
219B ARG* 3.1 39.7 + - - +
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Residues in contact with ALA 216 (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 CYS* 3.9 17.0 - - - -
212B GLU 2.9 16.7 + - - +
213B LEU* 3.7 9.2 - - + +
215B GLU* 1.3 74.8 - - - +
217B LEU* 1.3 58.4 + - - +
219B ARG* 3.1 24.1 + - - +
220B GLU* 2.9 34.0 + - + +
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Residues in contact with LEU 217 (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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40B LEU* 5.3 2.0 - - + +
41B LEU* 4.0 19.3 - - + -
44B ARG* 3.7 24.7 - - - +
193B ILE* 3.8 42.8 - - + +
196B CYS* 3.9 16.0 - - + -
197B LEU* 4.4 9.4 - - + +
200B LEU* 4.0 21.8 - - + -
213B LEU 3.0 18.1 + - - +
214B ASP* 3.1 5.8 + - - +
216B ALA* 1.3 76.4 - - - +
218B GLN* 1.3 62.9 + - - +
220B GLU* 3.3 3.6 + - - +
221B ILE* 3.0 33.8 + - + +
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Residues in contact with GLN 218 (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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430A ALA* 6.0 0.9 - - - -
44B ARG* 3.9 24.9 - - + +
48B ILE* 3.4 25.4 - - + +
214B ASP* 2.9 39.4 + - - +
215B GLU* 3.9 14.1 - - - +
217B LEU* 1.3 76.0 - - - +
219B ARG* 1.3 62.5 + - - +
221B ILE* 3.4 3.1 + - - -
222B GLN* 3.1 22.1 + - - +
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Residues in contact with ARG 219 (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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261A ARG* 3.2 35.5 - - - +
275A ARG* 4.6 4.9 - - - +
430A ALA* 3.0 40.6 + - + +
431A ILE* 4.1 8.5 - - - +
433A ASP* 3.7 6.8 + - - +
434A GLY* 3.4 22.2 - - - -
212B GLU 5.0 1.6 + - - -
215B GLU* 3.1 43.5 + - - +
216B ALA* 3.1 30.8 + - - +
218B GLN* 1.3 77.2 - - - +
220B GLU* 1.3 64.4 + - + +
222B GLN* 3.4 6.0 + - - +
223B ALA* 3.0 22.3 + - - +
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Residues in contact with GLU 220 (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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329A GLU* 5.6 1.9 - - - +
189B LYS* 4.1 13.3 - - - +
192B ARG* 2.9 64.5 + - + +
193B ILE* 3.8 18.8 - - + +
196B CYS* 5.3 3.1 - - - -
216B ALA* 2.9 20.5 + - + +
217B LEU* 3.8 6.1 - - - +
219B ARG* 1.3 75.6 - - + +
221B ILE* 1.3 66.3 + - - +
223B ALA* 3.2 8.5 + - - +
224B ALA* 3.0 23.6 + - - +
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Residues in contact with ILE 221 (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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41B LEU* 3.8 33.0 - - + +
44B ARG* 4.2 14.6 - - + -
45B PHE* 4.0 28.0 - - + -
48B ILE* 3.7 16.4 - - + -
108B LEU* 4.4 13.2 - - + -
193B ILE* 4.4 19.1 - - + -
217B LEU* 3.0 33.2 + - + +
218B GLN* 3.9 4.0 - - - +
220B GLU* 1.3 76.0 - - - +
222B GLN* 1.3 62.8 + - - +
224B ALA* 3.3 5.7 + - - +
225B PHE* 3.0 20.8 + - + +
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Residues in contact with GLN 222 (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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427A GLY 3.5 15.4 + - - -
428A ASP* 3.0 30.7 + - - +
430A ALA* 3.3 26.0 - - - +
431A ILE* 4.1 6.7 - - + -
48B ILE* 3.8 30.6 - - + +
52B LEU* 3.9 11.4 - - + +
218B GLN 3.1 17.0 + - - +
219B ARG* 3.9 4.0 - - - +
221B ILE* 1.3 75.1 - - - +
223B ALA* 1.3 65.0 + - - +
225B PHE* 3.2 6.4 + - - +
226B ARG* 3.0 39.0 + - + +
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Residues in contact with ALA 223 (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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329A GLU 5.4 2.0 - - - +
332A MET* 4.6 5.8 - - - +
431A ILE* 3.6 25.7 - - + +
189B LYS* 4.1 16.8 - - + -
219B ARG 3.0 14.6 + - - +
220B GLU* 3.2 14.6 + - - +
222B GLN* 1.3 77.7 - - - +
224B ALA* 1.3 60.3 + - - +
226B ARG* 3.4 1.6 + - - +
227B THR* 3.0 29.9 + - - -
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Residues in contact with ALA 224 (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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104B HIS* 3.6 18.8 - - + +
186B LEU* 4.9 14.9 - - + +
189B LYS* 4.0 20.5 - - + +
190B ASN* 6.0 1.6 - - - +
193B ILE* 4.5 15.7 - - + -
220B GLU 3.0 16.2 + - - +
221B ILE* 3.3 6.0 + - - +
223B ALA* 1.3 76.1 - - - +
225B PHE* 1.3 59.2 + - - +
226B ARG 3.6 0.2 + - - -
227B THR* 3.8 8.7 + - - -
228B ASP* 4.1 4.9 + - - -
229B GLU 5.3 1.0 + - - -
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Residues in contact with PHE 225 (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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45B PHE* 3.7 28.3 - + + -
48B ILE* 5.0 5.8 - - + -
49B LEU* 3.9 24.2 - - + -
52B LEU* 3.9 23.1 - - + -
53B HIS* 4.3 12.3 - + - -
97B LEU* 4.3 20.9 - - + -
100B SER* 5.0 2.7 - - - -
101B SER* 4.5 7.0 - - - -
104B HIS* 3.4 33.4 - + + +
221B ILE 3.0 15.8 + - - +
222B GLN* 3.2 6.2 + - - +
224B ALA* 1.3 79.6 - - - +
226B ARG* 1.3 73.9 + - + +
227B THR 3.4 0.2 - - - -
228B ASP* 3.3 20.4 - - - +
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Residues in contact with ARG 226 (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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332A MET* 3.4 33.6 - - + +
333A TRP* 4.2 10.5 + - - -
334A ARG* 3.0 51.0 + - - +
426A CYS 3.3 24.2 + - - -
428A ASP* 3.1 25.6 + - - +
431A ILE* 4.5 2.7 - - + -
52B LEU* 3.8 25.8 - - - +
53B HIS* 3.9 24.9 + - - -
222B GLN* 3.0 23.8 + - + +
223B ALA 3.4 1.7 + - - +
225B PHE* 1.3 85.7 - - + +
227B THR* 1.3 62.7 + - - +
228B ASP* 3.6 2.0 - - - -
928B GLU* 4.0 13.7 + - - -
929B PHE* 5.1 0.2 - - - -
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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