Contacts of the helix formed by residues 206 - 226 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G ARG* 6.0 1.8 - - - +
262G ARG* 5.1 2.2 + - - -
204H ASP 5.1 2.9 - - - +
205H ILE* 1.3 80.5 - - - +
207H ASP* 1.3 65.3 + - - +
208H ASP* 4.0 4.4 + - - +
209H ASP* 3.0 36.2 + - - +
210H LYS* 3.1 23.0 + - - +
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Residues in contact with ASP 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H ILE 4.5 4.2 - - - +
206H THR* 1.3 76.6 - - - +
208H ASP* 1.3 61.9 + - - +
210H LYS* 3.5 6.6 + - - +
211H GLN* 2.9 34.1 + - - +
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Residues in contact with ASP 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G ASP* 5.4 3.6 - - - +
144G GLU* 2.9 33.7 - - - +
262G ARG* 3.5 41.7 + - - +
265G THR* 4.0 13.5 - - + +
269G ASN* 4.3 3.6 + - - +
206H THR* 3.3 3.6 + - - +
207H ASP* 1.3 79.2 - - - +
209H ASP* 1.3 65.1 + - - +
211H GLN* 3.2 10.3 + - - +
212H GLU* 2.9 27.4 + - - +
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Residues in contact with ASP 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G ARG* 2.7 33.4 + - - +
205H ILE* 4.0 20.5 - - + +
206H THR* 3.0 29.5 + - - +
208H ASP* 1.3 77.1 - - - +
210H LYS* 1.3 58.0 + - - +
212H GLU* 3.3 4.1 + - - +
213H LEU* 2.8 39.2 + - + +
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Residues in contact with LYS 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H LEU* 3.3 49.1 + - + +
201H ASN* 4.8 8.0 - - - +
205H ILE* 4.6 14.5 - - + +
206H THR 3.1 17.9 + - - +
207H ASP* 3.8 6.7 - - - +
208H ASP 3.2 0.2 - - - -
209H ASP* 1.3 74.5 - - - +
211H GLN* 1.3 59.6 + - - +
213H LEU* 3.8 5.1 - - - +
214H ASP* 2.8 34.6 + - + +
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Residues in contact with GLN 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G THR* 3.7 22.2 - - + +
268G LYS* 4.4 13.7 - - - +
269G ASN* 3.9 25.2 + - - +
207H ASP* 2.9 21.9 + - - +
208H ASP* 3.2 11.0 + - - +
210H LYS* 1.3 75.0 - - - +
212H GLU* 1.3 57.5 + - - +
214H ASP* 3.5 6.8 + - - +
215H GLU* 3.1 47.4 + - - +
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Residues in contact with GLU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G LYS* 5.0 5.7 - - - +
261G ARG* 4.4 23.7 - - + +
262G ARG* 2.7 53.3 + - - +
265G THR* 2.6 31.3 + - + +
208H ASP 2.9 12.1 + - - +
209H ASP* 3.8 4.4 - - - +
211H GLN* 1.3 75.7 - - - +
213H LEU* 1.3 59.7 + - - +
215H GLU* 3.2 13.7 + - - +
216H ALA* 2.9 29.2 + - - +
219H ARG* 5.3 0.5 + - - -
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Residues in contact with LEU 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H CYS* 4.1 21.3 - - - +
199H GLN* 3.2 44.6 - - + +
200H LEU* 4.0 17.0 - - + +
205H ILE* 4.0 22.9 - - + -
209H ASP* 2.8 29.5 + - + +
210H LYS* 3.8 5.6 - - - +
212H GLU* 1.3 76.5 - - + +
214H ASP* 1.3 57.9 + - - +
216H ALA* 3.2 7.3 + - + +
217H LEU* 2.8 29.7 + - - +
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Residues in contact with ASP 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H ARG* 2.6 47.3 + - - -
200H LEU* 4.4 13.5 - - + +
210H LYS* 2.8 21.3 + - + +
211H GLN* 3.5 8.5 - - + +
213H LEU* 1.3 76.8 - - - +
215H GLU* 1.3 58.1 + - + +
217H LEU* 3.1 6.5 + - - +
218H GLN* 2.9 47.9 + - - +
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Residues in contact with GLU 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G ARG* 5.8 0.3 - - - +
265G THR* 5.3 3.1 + - - +
268G LYS* 5.9 1.7 - - - +
275G ARG* 3.7 27.0 + - - +
211H GLN* 3.1 39.2 + - - +
212H GLU* 3.2 13.7 + - - +
214H ASP* 1.3 76.7 - - + +
216H ALA* 1.3 61.4 + - - +
218H GLN* 3.7 16.8 + - - +
219H ARG* 3.1 39.2 + - - +
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Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H CYS* 4.0 16.2 - - - -
212H GLU 2.9 14.6 + - - +
213H LEU* 3.5 11.0 - - + +
215H GLU* 1.3 74.8 - - - +
217H LEU* 1.3 64.7 + - - +
219H ARG* 3.1 30.8 + - - +
220H GLU* 3.1 21.1 + - + +
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Residues in contact with LEU 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H LEU* 3.9 9.6 - - + -
41H LEU* 3.7 25.1 - - + -
44H ARG* 4.1 15.9 - - - +
193H ILE* 3.8 34.0 - - + +
196H CYS* 3.7 25.5 - - + -
197H LEU* 4.7 1.6 - - + +
200H LEU* 3.8 24.0 - - + -
213H LEU 2.8 17.6 + - - +
214H ASP* 3.1 7.8 + - - +
216H ALA* 1.3 73.9 - - - +
218H GLN* 1.3 62.7 + - - +
219H ARG 3.3 0.2 + - - -
220H GLU* 3.3 3.3 + - - +
221H ILE* 3.1 33.0 + - + +
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Residues in contact with GLN 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430G ALA* 6.2 0.2 - - - -
44H ARG* 3.7 28.5 - - + +
48H ILE* 3.3 24.0 - - + +
214H ASP* 2.9 43.3 + - - +
215H GLU* 3.9 16.1 - - - +
217H LEU* 1.3 75.2 - - - +
219H ARG* 1.3 63.0 + - - +
221H ILE* 3.4 5.3 + - - -
222H GLN* 3.0 21.6 + - - +
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Residues in contact with ARG 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G ARG* 3.3 30.3 - - - +
275G ARG* 4.4 9.9 - - - +
430G ALA* 3.1 39.2 + - + +
431G ILE* 4.0 10.5 - - + +
433G ASP* 3.6 13.0 + - - +
434G GLY* 3.3 24.6 - - - -
212H GLU 5.3 0.6 + - - -
215H GLU* 3.1 38.0 + - - +
216H ALA* 3.1 32.4 + - - +
218H GLN* 1.3 79.1 - - - +
220H GLU* 1.3 63.2 + - + +
222H GLN* 3.4 5.8 + - - +
223H ALA* 3.0 25.6 + - - +
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Residues in contact with GLU 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLU* 3.5 17.2 - - - +
435G SER* 5.2 4.3 + - - -
189H LYS* 4.1 12.1 - - - +
192H ARG* 2.9 56.6 + - + +
193H ILE* 4.0 23.4 - - + +
196H CYS* 5.5 2.0 - - - -
216H ALA* 3.1 17.7 + - + +
217H LEU* 3.3 2.7 + - - +
219H ARG* 1.3 79.9 - - + +
221H ILE* 1.3 61.2 + - - +
223H ALA* 3.6 5.9 - - - +
224H ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LEU* 3.8 29.4 - - + +
44H ARG* 4.2 15.5 - - + -
45H PHE* 3.8 28.4 - - + -
48H ILE* 3.7 14.6 - - + -
108H LEU* 4.2 23.1 - - + -
193H ILE* 4.5 12.1 - - + +
217H LEU* 3.1 29.9 + - + +
218H GLN* 3.7 6.7 - - - +
220H GLU* 1.3 75.9 - - - +
222H GLN* 1.3 62.4 + - - +
224H ALA* 3.2 5.8 + - - +
225H PHE* 3.0 21.7 + - - +
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Residues in contact with GLN 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G GLY 3.6 14.8 + - - -
428G ASP* 3.2 30.8 + - - +
430G ALA* 3.4 25.7 - - - +
431G ILE* 4.0 9.6 - - + +
48H ILE* 3.9 33.6 - - + +
51H ASP* 5.8 0.4 + - - +
52H LEU* 3.8 16.9 - - + +
218H GLN 3.0 17.7 + - - +
219H ARG* 3.7 5.4 - - - +
221H ILE* 1.3 75.6 - - - +
223H ALA* 1.3 64.0 + - - +
225H PHE* 3.1 6.6 + - - +
226H ARG* 3.1 24.0 + - + +
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Residues in contact with ALA 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329G GLU* 3.8 16.2 - - - +
332G MET* 4.0 8.4 - - + +
431G ILE* 3.4 21.2 - - + +
189H LYS* 3.7 19.6 - - - -
219H ARG 3.0 15.1 + - - +
220H GLU* 3.2 10.5 + - - +
222H GLN* 1.3 76.4 - - - +
224H ALA* 1.3 61.7 + - - +
226H ARG* 3.4 3.2 + - - +
227H THR* 3.3 25.8 + - - -
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Residues in contact with ALA 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H HIS* 3.2 24.2 - - + +
108H LEU* 6.5 0.4 - - + -
186H LEU* 5.3 13.1 - - + +
189H LYS* 3.9 20.5 - - + +
193H ILE* 5.0 7.9 - - + -
220H GLU 2.9 16.7 + - - +
221H ILE* 3.2 6.9 + - - +
223H ALA* 1.3 78.4 - - - +
225H PHE* 1.3 61.2 + - - +
226H ARG 3.6 0.2 + - - -
227H THR* 3.7 15.4 + - - +
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Residues in contact with PHE 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G ARG* 5.0 7.0 + - - -
45H PHE* 3.8 23.1 - + + -
48H ILE* 5.0 5.4 - - + -
49H LEU* 3.9 13.9 - - + -
52H LEU* 4.0 29.6 - - + -
53H HIS* 4.1 12.6 - + - -
97H LEU* 3.8 26.2 - - + -
100H SER* 4.0 12.8 - - - -
101H SER* 3.5 22.0 - - - -
104H HIS* 3.5 27.0 + + + -
221H ILE 3.0 16.0 + - - +
222H GLN* 3.1 6.9 + - - +
224H ALA* 1.3 78.0 - - - +
226H ARG* 1.3 64.7 + - + +
227H THR 3.4 5.3 + - - +
229H GLU* 4.5 4.7 - - - +
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Residues in contact with ARG 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332G MET* 3.8 32.0 - - + +
333G TRP* 3.9 12.6 + - - -
334G ARG* 3.1 51.3 + - - +
426G CYS* 3.1 24.6 + - - +
428G ASP* 3.3 31.7 + - - +
431G ILE* 4.8 1.8 - - + -
52H LEU* 3.4 40.7 - - + +
53H HIS* 5.0 2.4 + - - -
222H GLN* 3.1 18.8 + - + +
223H ALA 3.4 2.9 + - - +
224H ALA 3.3 0.2 - - - -
225H PHE* 1.3 85.4 - - + +
227H THR* 1.3 61.5 - - - +
228H ASP 3.9 1.4 + - - -
928H GLU* 3.5 23.4 + - - -
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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