Contacts of the helix formed by residues 215 - 227 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D ILE 4.8 1.2 - - - +
106D THR* 3.7 10.3 - - - +
107D GLN* 3.2 44.9 + - - +
166D VAL* 4.1 12.1 - - - +
211D GLN* 4.6 21.4 + - + +
212D ASP 3.8 3.2 + - - -
214D ARG* 1.3 80.5 - - - +
216D ILE* 1.3 56.9 + - - +
217D GLU* 3.1 4.3 - - - +
218D LEU* 3.0 28.8 + - + +
219D MET* 2.9 32.9 + - + +
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Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D THR* 3.6 14.6 - - - -
214D ARG* 3.3 29.2 + - - +
215D ASP* 1.3 77.4 - - - +
217D GLU* 1.3 63.2 + - - +
219D MET* 3.1 11.9 + - + +
220D LYS* 2.9 45.8 + - + +
231D ILE* 5.0 14.1 - - + -
233D ILE* 5.7 6.7 - - + -
247D VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D THR* 5.1 16.8 - - + -
168D GLY 5.5 4.3 - - - +
215D ASP* 3.1 1.5 - - - -
216D ILE* 1.3 76.7 - - - +
218D LEU* 1.3 58.7 + - - +
220D LYS* 3.3 11.2 + - - +
221D ASN* 3.0 26.0 + - - +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ILE* 3.8 35.0 - - + +
106D THR* 4.1 17.0 - - + -
169D GLN* 4.5 11.2 - - + +
171D ILE* 3.6 18.4 - - + -
176D TRP* 4.5 8.3 - - + -
180D PHE* 5.4 5.4 - - + -
215D ASP* 3.0 34.2 + - + +
217D GLU* 1.3 80.5 - - - +
219D MET* 1.3 57.8 + - - +
221D ASN* 2.9 21.0 + - + +
222D LEU* 2.9 37.4 + - + +
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Residues in contact with MET 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 5.3 6.1 - - - -
209D ILE* 3.6 38.6 - - + +
211D GLN* 4.4 18.4 - - + -
215D ASP* 2.9 23.4 + - + +
216D ILE* 3.1 13.9 + - - +
218D LEU* 1.3 79.6 - - - +
220D LYS* 1.3 62.8 + - - +
222D LEU* 3.0 14.8 + - - +
223D ILE* 3.0 26.6 + - - +
231D ILE* 5.0 8.3 - - + -
247D VAL* 4.3 22.7 - - + +
248D ASP 4.3 2.5 - - - -
249D LEU* 3.6 30.1 - - + +
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Residues in contact with LYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ILE* 2.9 32.3 + - + +
217D GLU* 3.6 10.8 - - - +
219D MET* 1.3 76.5 - - - +
221D ASN* 1.3 57.7 + - - +
223D ILE* 3.2 11.1 + - + +
224D SER* 2.8 32.1 + - - +
231D ILE* 3.6 28.0 - - + -
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Residues in contact with ASN 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D GLN 4.7 9.0 - - - +
170D GLU* 5.9 0.7 - - - -
171D ILE* 4.3 17.8 - - + +
217D GLU 3.0 12.4 + - - +
218D LEU* 2.9 18.0 + - + +
220D LYS* 1.3 77.2 - - - +
222D LEU* 1.3 55.9 + - - +
224D SER* 3.4 7.5 + - - -
225D TYR* 2.9 28.8 + - - +
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D ILE* 3.8 15.7 - - + -
176D TRP* 4.2 17.9 - - + -
177D VAL* 4.3 24.5 - - + -
180D PHE* 5.3 7.9 - - + -
181D THR* 6.3 0.2 - - + -
209D ILE* 5.1 11.9 - - + -
218D LEU* 2.9 55.7 + - + +
219D MET* 3.0 14.6 + - - +
221D ASN* 1.3 73.0 - - - +
223D ILE* 1.3 60.0 + - - +
225D TYR* 3.8 5.1 - - + +
226D LEU* 2.9 41.0 + - + +
249D LEU* 3.6 17.5 - - + -
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Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D MET 3.0 15.8 + - - +
220D LYS* 3.2 9.8 + - - +
222D LEU* 1.3 74.7 - - - +
224D SER* 1.3 62.5 + - - +
226D LEU* 5.1 0.2 - - - -
227D ASN* 2.7 25.2 + - - -
228D CYS* 3.1 34.8 + - - +
229D GLY 3.5 24.9 - - - +
230D ASN* 4.2 3.8 - - - -
231D ILE* 3.5 37.2 - - + -
249D LEU* 3.6 16.6 - - + -
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D LYS 2.8 18.2 + - - -
221D ASN* 3.8 7.0 - - - -
222D LEU 3.3 0.2 - - - -
223D ILE* 1.3 79.7 - - - +
225D TYR* 1.3 63.5 + - - +
227D ASN* 3.2 14.7 + - - +
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Residues in contact with TYR 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D ILE* 3.9 36.6 - - + -
173D ASP* 4.8 1.3 - - - -
174D SER* 3.3 34.4 + - - -
177D VAL* 4.0 11.0 - - + -
221D ASN 2.9 18.6 + - - +
222D LEU* 3.8 8.1 - - + +
224D SER* 1.3 79.7 - - - +
226D LEU* 1.3 70.1 + - + +
227D ASN* 4.9 1.2 - - - +
264D PHE* 3.6 28.3 - + - -
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D VAL* 4.8 11.4 - - + -
207D PHE* 4.4 16.6 - - + -
209D ILE* 5.4 2.9 - - + -
222D LEU* 2.9 26.8 + - + +
223D ILE 4.4 0.9 - - - +
225D TYR* 1.3 87.2 - - + +
227D ASN* 1.3 78.4 + - - +
228D CYS* 3.4 20.8 + - - +
249D LEU* 5.2 8.5 - - + -
260D LYS* 4.1 8.4 - - - +
261D ILE* 4.2 22.7 - - + -
264D PHE* 4.1 41.5 - - + -
265D PHE* 5.4 2.0 - - + -
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Residues in contact with ASN 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ILE* 2.7 13.7 + - - -
224D SER* 3.2 13.8 + - - +
225D TYR 4.9 1.3 + - - +
226D LEU* 1.3 88.8 + - - +
228D CYS* 1.3 57.1 + - - +
256D ASP* 5.1 1.9 - - - +
260D LYS* 3.1 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