Contacts of the helix formed by residues 201 - 217 (chain A) in PDB entry 2BAP
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASP* 3.4 26.6 - - + +
150A MET 3.8 5.1 + - - -
153A LEU* 4.9 6.6 - - - +
189A LEU* 4.7 11.1 - - + +
200A TYR* 1.3 106.8 - - + +
202A SER* 1.3 61.9 + - - +
203A ARG 3.2 2.9 - - - +
204A ASN* 2.5 46.9 + - + +
205A GLN* 3.8 10.2 + - - +
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Residues in contact with SER 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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200A TYR 3.8 3.4 + - - -
201A ASP* 1.3 72.7 - - - +
203A ARG* 1.3 64.8 + - - +
204A ASN 2.9 6.7 + - - -
205A GLN* 3.1 21.2 + - - +
206A HIS* 3.0 22.8 + - - +
243A VAL* 3.6 38.7 - - - +
246A MET* 4.6 2.1 - - - +
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Residues in contact with ARG 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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153A LEU* 4.1 30.0 - - + +
200A TYR* 3.2 25.9 + - - +
201A ASP* 4.9 0.2 - - - -
202A SER* 1.3 80.3 - - - +
204A ASN* 1.3 58.4 - - - +
206A HIS* 3.8 9.0 - - - +
207A GLU* 3.5 26.0 + - - +
166B ASN* 5.5 4.8 + - - -
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Residues in contact with ASN 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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149A ASP* 3.7 12.9 - - - +
152A LEU* 3.4 33.2 - - - +
153A LEU* 3.6 14.1 + - + +
156A LEU* 3.2 43.1 - - - +
189A LEU* 4.4 11.0 - - + +
201A ASP* 2.5 43.0 + - + +
202A SER 2.9 0.2 - - - -
203A ARG* 1.3 78.1 - - - +
205A GLN* 1.3 63.9 + - - +
207A GLU* 3.6 4.5 + - - +
208A ILE* 3.4 5.1 - - - +
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Residues in contact with GLN 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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186A LEU* 4.2 13.7 - - + +
189A LEU* 4.1 24.4 - - + +
190A HIS* 3.8 30.7 + - - -
201A ASP 3.8 10.2 + - - +
202A SER* 3.6 25.2 + - - +
204A ASN* 1.3 72.1 - - - +
206A HIS* 1.3 67.0 + - - +
208A ILE* 2.8 28.3 + - + +
209A ILE* 3.3 10.9 + - - +
243A VAL* 5.5 1.0 - - - +
246A MET* 3.8 26.7 - - - +
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Residues in contact with HIS 206 (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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202A SER 3.0 16.2 + - - +
203A ARG* 3.8 11.4 - - - +
205A GLN* 1.3 76.4 - - - +
207A GLU* 1.3 59.0 + - + +
209A ILE* 2.9 26.4 + - - +
210A ARG* 3.0 50.6 + - + +
243A VAL* 5.0 4.5 - - + -
245A ASN* 3.4 33.3 + - + +
246A MET* 3.7 27.6 - - + -
249A ASP* 3.9 24.7 + - + -
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Residues in contact with GLU 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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153A LEU* 4.4 8.7 - - + -
156A LEU* 3.7 22.8 - - + +
157A GLU* 3.3 41.5 + - + +
160A ARG* 2.9 37.5 + - - +
203A ARG 3.5 13.5 + - - +
204A ASN* 3.9 6.5 - - - +
205A GLN 3.1 0.8 - - - -
206A HIS* 1.3 79.0 - - + +
208A ILE* 1.3 57.0 + - - +
210A ARG* 3.3 25.4 + - - +
211A CYS* 2.8 35.2 + - - -
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Residues in contact with ILE 208 (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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156A LEU* 3.8 17.9 - - + -
182A LEU* 3.3 46.2 - - + +
185A ILE* 4.0 27.1 - - + -
186A LEU* 4.3 27.1 - - + +
189A LEU* 4.6 2.9 - - + -
204A ASN 3.4 18.4 - - - +
205A GLN* 2.8 18.8 + - - +
207A GLU* 1.3 73.4 - - - +
209A ILE* 1.3 59.6 + - - +
211A CYS* 3.4 7.6 - - - +
212A LEU* 3.0 36.5 + - + +
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Residues in contact with ILE 209 (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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186A LEU* 4.4 24.0 - - + -
205A GLN 3.3 10.5 + - - +
206A HIS* 2.9 14.9 + - - +
208A ILE* 1.3 74.1 - - - +
210A ARG* 1.3 58.9 + - - +
212A LEU* 2.9 12.3 + - + +
213A LYS* 2.9 27.5 + - - +
235A LEU* 5.0 7.2 - - + -
238A ALA* 3.6 25.8 - - + -
246A MET* 3.8 19.5 - - + +
249A ASP* 4.1 26.5 - - + -
250A ALA* 4.2 6.3 - - - +
253A LEU* 3.7 21.4 - - + +
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Residues in contact with ARG 210 (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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160A ARG* 3.2 40.8 - - - +
206A HIS* 3.0 55.2 + - + +
207A GLU* 3.3 27.5 + - - +
209A ILE* 1.3 75.6 - - - +
211A CYS* 1.3 61.7 + - - +
213A LYS* 3.4 9.1 + - - +
214A ALA* 3.0 24.8 + - - +
245A ASN* 5.3 6.1 - - - +
249A ASP* 4.8 11.2 + - - +
165B ASN* 5.9 2.2 - - - +
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Residues in contact with CYS 211 (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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156A LEU* 3.7 22.2 - - - -
159A LEU* 3.5 29.8 - - - -
160A ARG* 4.1 9.6 - - - -
163A LEU* 3.5 12.2 - - + +
182A LEU* 4.2 16.6 - - + -
207A GLU 2.8 28.6 + - - +
208A ILE* 3.4 8.7 - - - +
210A ARG* 1.3 75.7 - - - +
212A LEU* 1.3 53.7 + - - +
214A ALA* 3.5 4.9 + - - +
215A PHE* 2.8 34.9 + - - +
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Residues in contact with LEU 212 (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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179A LEU* 3.7 30.3 - - + -
182A LEU* 4.5 12.8 - - + -
183A LEU* 4.2 12.3 - - + -
186A LEU* 4.4 11.4 - - + -
208A ILE* 3.0 27.8 + - + +
209A ILE* 2.9 9.5 + - - +
211A CYS* 1.3 77.1 - - - +
213A LYS* 1.3 56.8 + - - +
215A PHE* 2.8 12.8 + - + +
216A MET* 2.5 53.5 + - + +
225A MET* 4.0 15.7 - - + -
235A LEU* 3.8 23.6 - - + -
253A LEU* 4.5 1.1 - - + -
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Residues in contact with LYS 213 (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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209A ILE 2.9 12.6 + - - +
210A ARG* 3.6 11.0 - - - +
212A LEU* 1.3 73.5 - - - +
214A ALA* 1.3 54.6 - - - +
216A MET* 3.4 3.6 + - - +
217A ASN* 2.9 32.9 + - + +
249A ASP* 3.5 23.9 + - - +
252A LYS* 5.8 6.9 - - + +
253A LEU* 3.8 28.4 - - + +
1182C MET* 4.7 8.4 - - + +
1183C ASP* 4.1 11.8 + - - -
1186C LEU* 3.7 29.8 - - + +
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Residues in contact with ALA 214 (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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160A ARG* 4.5 2.0 - - + +
163A LEU* 4.1 19.2 - - + +
164A ASN* 3.3 39.5 - - - +
171A VAL* 5.6 1.7 - - - +
210A ARG 3.0 16.9 + - - +
211A CYS* 3.5 6.7 - - - +
213A LYS* 1.3 77.2 - - - +
215A PHE* 1.3 61.9 + - - +
217A ASN* 3.4 20.2 + - - +
218A ASN* 5.6 0.2 - - - -
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Residues in contact with PHE 215 (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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163A LEU* 4.2 18.6 - - + -
171A VAL* 3.5 33.5 - - + +
174A PHE* 4.9 9.4 - + + -
175A GLY 4.2 11.4 - - - -
179A LEU* 3.2 45.5 - - + -
182A LEU* 5.7 4.3 - - + -
211A CYS 2.8 21.6 + - - +
212A LEU* 2.8 15.1 + - + +
214A ALA* 1.3 74.1 - - - +
216A MET* 1.3 69.0 + - + +
218A ASN* 3.0 20.1 - - - +
220A PHE* 4.4 5.8 - + - -
221A GLY* 3.5 29.6 - - - -
224A THR* 4.3 8.3 - - - -
225A MET* 4.6 1.8 - - + -
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Residues in contact with MET 216 (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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212A LEU* 2.5 45.3 + - + +
213A LYS* 3.7 3.8 - - - +
215A PHE* 1.3 76.2 - - + +
217A ASN* 1.3 50.6 + - - +
218A ASN* 2.4 33.1 + - - +
221A GLY 4.1 1.6 - - - -
222A ILE* 3.5 45.3 - - + +
225A MET* 3.6 32.8 - - + +
235A LEU* 4.5 11.2 - - + -
253A LEU* 3.6 33.9 - - + +
257A LEU* 5.2 9.0 - - - -
1181C VAL* 5.7 0.2 - - - +
1182C MET* 4.2 10.4 - - - +
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Residues in contact with ASN 217 (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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164A ASN* 5.2 5.7 + - - -
213A LYS* 2.9 19.4 + - + +
214A ALA* 3.4 14.1 - - - +
215A PHE 3.3 1.6 - - - -
216A MET* 1.3 72.4 - - - +
218A ASN* 1.3 64.4 + - - +
1180C GLY* 3.1 32.4 + - - -
1181C VAL 2.7 7.9 + - - -
1182C MET* 2.7 37.1 + - + -
1183C ASP* 3.0 30.8 + - - -
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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