Contacts of the helix formed by residues 215 - 227 (chain H) in PDB entry 6BCH
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 ASP 215 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105H ILE 4.8 1.2 - - - +
106H THR* 3.8 10.0 - - - +
107H GLN* 3.2 43.4 + - - +
166H VAL* 4.1 11.6 - - - +
211H GLN* 4.5 21.9 + - + +
212H ASP 3.8 3.4 + - - -
214H ARG* 1.3 80.1 - - - +
216H ILE* 1.3 57.5 + - - +
217H GLU* 3.2 3.8 - - - +
218H LEU* 3.0 29.8 + - + +
219H MET* 2.9 32.8 + - + +
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Residues in contact with ILE 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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213H THR* 3.6 14.6 - - - -
214H ARG* 3.3 29.0 + - - +
215H ASP* 1.3 77.9 - - - +
217H GLU* 1.3 63.4 + - - +
219H MET* 3.1 11.4 + - + +
220H LYS* 2.9 45.8 + - + +
231H ILE* 5.0 14.4 - - + -
233H ILE* 5.7 6.3 - - + -
247H VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 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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167H THR* 5.1 16.4 - - + -
168H GLY 5.5 4.3 - - - +
215H ASP* 3.2 1.5 - - - -
216H ILE* 1.3 77.5 - - - +
218H LEU* 1.3 58.5 + - - +
220H LYS* 3.3 12.0 + - - +
221H ASN* 3.0 26.2 + - - +
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Residues in contact with LEU 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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105H ILE* 3.8 34.8 - - + +
106H THR* 4.2 16.8 - - + -
169H GLN* 4.6 9.0 - - + +
171H ILE* 3.6 18.8 - - + -
176H TRP* 4.5 8.5 - - + -
180H PHE* 5.3 5.4 - - + -
215H ASP* 3.0 33.5 + - + +
217H GLU* 1.3 80.7 - - - +
219H MET* 1.3 58.8 + - - +
221H ASN* 2.9 23.0 + - + +
222H LEU* 2.9 37.3 + - + +
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Residues in contact with MET 219 (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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180H PHE* 5.3 6.5 - - - -
209H ILE* 3.6 38.1 - - + +
211H GLN* 4.4 18.4 - - + -
215H ASP* 2.9 23.6 + - + +
216H ILE* 3.1 14.3 + - - +
218H LEU* 1.3 78.8 - - - +
220H LYS* 1.3 62.8 + - - +
222H LEU* 3.0 14.3 + - - +
223H ILE* 3.0 27.1 + - - +
231H ILE* 5.0 8.5 - - + -
247H VAL* 4.4 22.2 - - + +
248H ASP 4.3 3.1 - - - -
249H LEU* 3.6 30.7 - - + +
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Residues in contact with LYS 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H ILE* 2.9 32.8 + - + +
217H GLU* 3.6 11.2 - - - +
219H MET* 1.3 75.7 - - - +
221H ASN* 1.3 58.6 + - - +
223H ILE* 3.2 10.9 + - - +
224H SER* 2.9 27.7 + - - -
231H ILE* 3.6 27.4 - - + -
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Residues in contact with ASN 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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169H GLN 4.7 9.0 - - - +
170H GLU* 5.9 0.7 - - - -
171H ILE* 4.4 18.0 - - + +
217H GLU 3.0 12.0 + - - +
218H LEU* 2.9 17.5 + - + +
220H LYS* 1.3 77.9 - - - +
222H LEU* 1.3 55.5 + - - +
224H SER* 3.4 7.7 + - - -
225H TYR* 2.9 29.1 + - - +
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Residues in contact with LEU 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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171H ILE* 3.8 15.7 - - + -
176H TRP* 4.3 17.5 - - + -
177H VAL* 4.3 24.9 - - + -
180H PHE* 5.3 9.0 - - + -
181H THR* 6.3 0.2 - - + -
209H ILE* 5.1 10.1 - - + -
218H LEU* 2.9 55.5 + - + +
219H MET* 3.0 15.0 + - - +
221H ASN* 1.3 73.0 - - - +
223H ILE* 1.3 60.7 + - - +
225H TYR* 3.8 5.3 - - + +
226H LEU* 2.9 41.9 + - + +
249H LEU* 3.7 16.6 - - + -
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Residues in contact with ILE 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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219H MET 3.0 15.0 + - - +
220H LYS* 3.2 9.6 + - - +
222H LEU* 1.3 77.8 - - - +
224H SER* 1.3 54.2 + - - +
227H ASN* 2.7 30.2 + - - -
228H CYS* 3.0 35.2 + - - +
229H GLY 3.5 25.6 - - - +
230H ASN* 4.1 4.3 - - - -
231H ILE* 3.5 37.2 - - + -
249H LEU* 3.6 16.6 - - + -
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Residues in contact with SER 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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220H LYS 2.9 16.5 + - - -
221H ASN* 3.7 8.1 - - - -
223H ILE* 1.3 79.1 - - - +
225H TYR* 1.3 62.2 + - - +
227H ASN* 3.3 13.8 + - - +
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Residues in contact with TYR 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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171H ILE* 3.9 35.9 - - + -
173H ASP* 4.8 1.3 - - - -
174H SER* 3.3 34.4 + - - -
177H VAL* 4.0 11.0 - - + -
221H ASN 2.9 18.4 + - - +
222H LEU* 3.8 7.9 - - + +
224H SER* 1.3 78.7 - - - +
226H LEU* 1.3 71.3 + - + +
227H ASN* 4.9 1.2 - - - +
264H PHE* 3.6 28.3 - + - -
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Residues in contact with LEU 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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177H VAL* 4.7 10.8 - - + -
207H PHE* 4.5 15.7 - - + -
209H ILE* 5.5 3.4 - - + -
222H LEU* 2.9 27.6 + - + +
223H ILE 4.4 0.9 - - - +
225H TYR* 1.3 84.1 - - + +
227H ASN* 1.3 79.0 + - - +
228H CYS* 3.4 20.7 + - - +
249H LEU* 5.3 8.5 - - + -
260H LYS* 4.1 8.2 - - - +
261H ILE* 4.2 21.8 - - + -
264H PHE* 4.1 45.3 - - + -
265H PHE* 5.4 2.2 - - + -
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Residues in contact with ASN 227 (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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223H ILE* 2.7 13.7 + - - -
224H SER* 3.7 10.8 - - - +
225H TYR 3.3 3.3 - - - +
226H LEU* 1.3 89.1 + - - +
228H CYS* 1.3 57.3 + - - +
256H ASP* 5.1 1.9 - - - +
260H LYS* 3.0 50.3 - - - +
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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