Contacts of the helix formed by residues 189 - 209 (chain A) in PDB entry 2BU6
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 VAL 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A CYS* 3.3 4.1 + - - +
188A ASN* 1.3 70.0 - - - +
190A SER* 1.3 66.3 + - - +
192A VAL* 2.9 15.3 + - - +
193A VAL* 2.9 13.8 + - + +
228A ILE* 3.5 13.6 + - + +
230A MET* 3.9 34.3 - - + -
237A LEU* 4.1 16.2 - - + -
269A VAL* 3.9 24.0 - - + -
276A LEU* 4.1 15.0 - - + -
278A ILE* 3.5 31.0 - - + -
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 3.2 8.1 + - - -
189A VAL* 1.3 78.6 - - - +
191A GLU* 1.3 57.5 + - - +
193A VAL* 3.3 12.8 + - - +
194A LYS* 3.0 41.0 + - - +
216A ILE* 3.6 19.8 - - - +
218A GLU* 2.3 40.7 + - - +
228A ILE 4.9 0.6 + - - -
269A VAL* 4.1 5.2 - - - +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 2.9 30.7 + - + +
190A SER* 1.3 74.0 - - - +
192A VAL* 1.3 67.8 + - + +
194A LYS* 3.4 23.9 + - - +
195A ASP* 3.1 53.1 + - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A CYS* 3.9 24.0 - - - -
188A ASN 3.3 10.5 + - - +
189A VAL 2.9 6.9 + - - +
191A GLU* 1.3 75.4 - - + +
193A VAL* 1.3 67.1 + - - +
195A ASP* 3.3 9.1 + - - +
196A ALA* 3.1 22.3 + - - +
234A PRO* 4.1 14.4 - - + +
237A LEU* 3.9 17.3 - - + -
238A TYR* 3.8 40.6 - - + +
241A LEU* 4.1 2.2 - - + -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 2.9 26.0 + - + +
190A SER* 3.3 13.9 - - - +
191A GLU 3.1 0.2 - - - -
192A VAL* 1.3 78.1 - - - +
194A LYS* 1.3 63.1 + - - +
196A ALA 3.4 0.2 + - - -
197A TYR* 3.0 18.5 + - - +
214A LEU* 4.3 2.0 - - + -
216A ILE* 3.3 28.7 - - + -
241A LEU* 3.7 27.8 - - + +
245A PHE* 3.3 27.1 - - + -
267A VAL* 4.2 12.8 - - + -
269A VAL* 4.3 12.1 - - + -
278A ILE* 4.5 1.3 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER* 3.0 26.0 + - - +
191A GLU* 3.7 25.2 + - - +
192A VAL 3.3 0.2 - - - -
193A VAL* 1.3 75.1 - - - +
195A ASP* 1.3 59.5 + - - +
197A TYR* 3.3 7.4 + - + +
198A ASP* 2.8 41.6 + - - +
214A LEU* 4.4 8.1 - - + -
216A ILE* 3.9 19.7 - - + -
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.1 40.7 + - - +
192A VAL* 3.6 12.9 - - + +
193A VAL 3.2 0.2 - - - -
194A LYS* 1.3 77.4 - - - +
196A ALA* 1.3 63.6 + - - +
198A ASP* 3.2 11.9 + - - +
199A MET* 3.1 22.2 + - - +
238A TYR* 3.9 17.2 - - + -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL 3.1 10.3 + - - +
193A VAL 3.9 0.2 - - - +
195A ASP* 1.3 78.2 - - - +
197A TYR* 1.3 63.5 + - - +
199A MET 3.5 0.3 + - - -
200A ALA* 3.0 24.6 + - - +
238A TYR* 3.5 24.3 - - + +
241A LEU* 3.7 16.6 - - + -
242A PHE* 3.6 34.9 - - - +
245A PHE* 3.8 5.7 - - + -
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL 3.0 14.1 + - - +
194A LYS* 3.4 7.9 - - - +
196A ALA* 1.3 77.2 - - - +
198A ASP* 1.3 68.0 + - - +
200A ALA* 3.0 3.3 + - - +
201A LYS* 2.7 66.9 + - + +
212A PRO 2.6 25.7 + - - -
213A ASP* 3.2 14.7 + - - -
214A LEU* 3.7 40.2 - - + -
245A PHE* 3.6 29.7 - + + -
249A MET* 3.2 27.4 - - + -
265A ILE* 5.3 2.2 - - + -
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 2.8 32.7 + - - +
195A ASP* 3.5 11.7 - - - +
197A TYR* 1.3 88.3 - - - +
199A MET* 1.3 56.6 + - - +
201A LYS* 3.4 9.5 + - - +
202A LEU* 3.0 28.5 + - - +
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASP 3.1 12.0 + - - +
196A ALA 3.8 3.1 - - - +
197A TYR 3.2 0.2 - - - -
198A ASP* 1.3 74.3 - - - +
200A ALA* 1.3 65.0 + - - +
202A LEU* 3.3 28.2 + - + +
203A LEU* 3.2 41.3 + - + +
238A TYR* 3.1 28.0 - - - +
242A PHE* 3.6 16.2 - - + -
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ALA 3.0 16.4 + - - +
197A TYR 3.0 3.6 + - - +
199A MET* 1.3 76.5 - - - +
201A LYS* 1.3 52.7 + - - +
203A LEU* 3.1 6.8 + - - +
204A CYS* 2.7 35.3 + - - +
242A PHE* 3.5 17.4 - - + -
245A PHE* 3.8 18.2 - - + -
246A LYS* 4.2 12.0 - - + +
249A MET* 3.5 20.3 - - - +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 2.7 45.1 + - + +
198A ASP* 3.5 10.1 - - - +
200A ALA* 1.3 73.8 - - - +
202A LEU* 1.3 57.7 + - - +
204A CYS* 3.1 2.5 + - - +
205A ASP* 2.7 62.4 + - - +
211A SER* 3.5 20.8 + - - +
212A PRO 5.1 0.2 - - - -
213A ASP* 5.3 5.6 - - - -
249A MET* 3.6 16.5 - - + -
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP 3.0 13.9 + - - +
199A MET* 3.5 30.7 - - + +
201A LYS* 1.3 78.4 - - - +
203A LEU* 1.3 67.7 + - + +
205A ASP* 3.3 7.0 + - - +
206A LYS* 3.1 35.8 + - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A MET* 3.2 27.6 + - + +
200A ALA* 3.1 6.6 + - - +
202A LEU* 1.3 79.9 - - + +
204A CYS* 1.3 66.8 + - - +
206A LYS* 3.2 12.0 + - + +
207A TYR* 3.1 25.3 + - - +
242A PHE* 3.6 31.6 - - + -
246A LYS* 4.9 9.4 - - + -
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Residues in contact with CYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA 2.7 19.7 + - - +
201A LYS 3.5 4.5 - - - +
203A LEU* 1.3 74.2 - - - +
205A ASP* 1.3 57.1 + - - +
207A TYR* 5.0 0.4 - - - -
208A TYR* 2.9 52.1 + - - +
209A MET 3.6 0.2 + - - -
210A ALA 3.4 19.0 - - - +
211A SER* 3.9 10.5 - - - -
249A MET* 3.8 34.5 - - + -
253A VAL* 3.9 10.3 - - - -
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LYS* 2.7 52.3 + - - +
202A LEU* 3.7 6.8 - - - +
204A CYS* 1.3 72.9 - - - +
206A LYS* 1.3 57.6 + - - +
209A MET* 2.6 37.7 + - - +
210A ALA* 3.5 11.3 + - - -
211A SER* 3.1 23.0 + - - -
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.1 29.4 + - + +
203A LEU* 3.2 12.7 + - + +
205A ASP* 1.3 76.9 - - - +
207A TYR* 1.3 60.3 + - + +
209A MET* 4.5 8.4 - - - +
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Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU 3.1 15.1 + - - +
204A CYS* 4.2 1.6 - - - +
206A LYS* 1.3 80.7 - - + +
208A TYR* 1.3 100.0 + + + +
209A MET* 3.7 12.3 - - - +
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Residues in contact with TYR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A CYS* 2.9 32.5 + - - +
207A TYR* 1.3 113.1 - + + +
209A MET* 1.3 78.3 + - - +
210A ALA* 3.2 11.1 + - + +
250A ARG* 3.6 31.4 + - + +
253A VAL* 3.5 25.4 - - + -
254A GLU* 2.8 40.3 + - + -
257A GLU* 5.5 5.4 - - - -
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Residues in contact with MET 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ASP* 2.6 34.3 + - - +
206A LYS* 4.5 8.1 - - - +
207A TYR 3.9 18.6 - - - +
208A TYR* 1.3 78.7 - - - +
210A ALA* 1.3 60.0 + - - +
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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
------------------------------------------------------------
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