Contacts of the helix formed by residues 202 - 216 (chain B) 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 SER 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LYS* 5.9 3.1 - - - -
201B ASP* 1.3 72.5 + - - +
203B ARG* 1.3 64.7 + - - +
204B ASN 3.2 2.0 - - - -
205B GLN* 3.4 29.5 - - - +
206B HIS* 3.1 26.2 + - - +
243B VAL* 4.0 28.6 - - - +
246B MET* 4.8 0.7 - - - +
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Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASN* 6.0 3.4 - - - +
153B LEU* 3.9 35.7 - - + +
201B ASP* 3.2 9.4 - - - +
202B SER* 1.3 81.2 + - - +
204B ASN* 1.3 64.9 + - - +
206B HIS* 3.8 6.4 + - - +
207B GLU* 3.4 26.7 + - - +
210B ARG* 5.7 0.2 + - - -
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Residues in contact with ASN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ASP* 4.0 5.5 - - - +
150B MET 3.8 17.0 + - - -
152B LEU* 3.3 32.4 - - + +
153B LEU* 3.8 15.6 + - - +
156B LEU* 3.5 13.4 - - - +
189B LEU* 4.6 13.7 - - + -
201B ASP* 2.6 45.8 + - - +
203B ARG* 1.3 77.6 - - - +
205B GLN* 1.3 67.1 + - - +
207B GLU* 3.1 18.5 + - - +
208B ILE* 3.5 4.7 + - - +
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Residues in contact with GLN 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LEU* 3.8 17.6 - - + +
189B LEU* 3.7 30.4 - - + +
190B HIS* 4.0 17.9 + - - -
193B LYS* 4.5 20.0 - - - +
201B ASP 4.8 1.1 - - - +
202B SER* 3.4 34.0 - - - +
204B ASN* 1.3 73.7 - - - +
206B HIS* 1.3 61.9 + - - +
207B GLU 3.0 1.8 - - - -
208B ILE* 2.7 29.8 + - - +
209B ILE* 3.3 11.3 + - - +
240B ASP* 5.9 0.8 + - - -
243B VAL* 5.5 2.4 - - - +
246B MET* 3.6 25.3 - - + +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B SER 3.1 19.9 + - - +
203B ARG* 3.8 8.1 - - - +
204B ASN 3.3 0.2 - - - -
205B GLN* 1.3 76.5 - - - +
207B GLU* 1.3 60.9 + - - +
209B ILE* 3.3 14.9 - - - +
210B ARG* 3.4 43.3 + - + +
243B VAL* 4.6 4.3 - - + -
245B ASN* 3.1 58.0 + - - +
246B MET* 3.7 32.8 - - + +
249B ASP* 3.6 11.7 - - + -
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.3 8.3 - - + -
156B LEU* 3.6 17.4 - - + +
157B GLU* 3.6 35.0 - - + +
160B ARG* 3.0 40.9 + - - +
203B ARG 3.4 12.5 + - - +
204B ASN* 3.1 12.0 + - - +
205B GLN 2.9 1.0 + - - -
206B HIS* 1.3 78.1 - - - +
208B ILE* 1.3 59.1 + - - +
210B ARG* 3.0 33.3 + - - +
211B CYS* 2.9 32.3 + - - -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 3.8 15.7 - - + -
182B LEU* 3.5 44.2 - - + +
183B LEU* 5.1 0.7 - - - +
185B ILE* 3.9 11.9 - - + -
186B LEU* 3.8 36.8 - - + -
189B LEU* 3.8 23.1 - - + -
204B ASN* 3.7 8.5 - - + +
205B GLN* 2.7 13.8 + - - +
207B GLU* 1.3 69.3 - - - +
209B ILE* 1.3 60.1 + - - +
211B CYS* 3.3 7.8 + - - +
212B LEU* 2.9 38.0 + - + +
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.1 20.0 - - + -
205B GLN 3.8 3.1 - - - +
206B HIS* 3.3 10.1 - - - +
208B ILE* 1.3 77.2 - - - +
210B ARG* 1.3 51.3 + - - +
212B LEU* 3.2 13.4 + - + +
213B LYS* 2.8 32.2 + - - +
234B LEU 5.1 1.6 - - - +
235B LEU* 5.0 8.3 - - + -
238B ALA* 3.8 22.9 - - + -
246B MET* 3.5 33.7 - - + +
249B ASP* 3.7 34.1 - - + -
250B ALA* 4.1 4.5 - - - +
253B LEU* 3.7 16.1 - - + +
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Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLU* 5.7 1.0 + - - -
160B ARG* 3.5 43.0 + - - +
203B ARG 5.7 0.2 + - - -
206B HIS* 3.4 46.8 + - + +
207B GLU* 3.0 35.4 + - - +
209B ILE* 1.3 75.2 - - - +
211B CYS* 1.3 58.7 + - - +
213B LYS* 3.2 10.4 + - + +
214B ALA* 2.9 28.6 + - - +
245B ASN* 4.7 7.9 - - - +
249B ASP* 4.5 13.0 + - - +
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Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.1 24.0 - - - -
159B LEU* 4.1 13.9 - - + -
160B ARG* 4.2 11.7 - - - -
163B LEU* 4.0 14.2 - - + +
182B LEU* 4.3 21.9 - - + +
207B GLU* 2.9 27.5 + - - -
208B ILE* 3.3 8.9 + - - +
210B ARG* 1.3 76.2 - - - +
212B LEU* 1.3 57.1 + - - +
214B ALA* 3.6 7.0 + - - +
215B PHE* 2.8 30.4 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LEU* 3.7 31.0 - - + -
182B LEU* 5.2 7.4 - - + -
183B LEU* 4.3 10.3 - - + -
186B LEU* 4.6 3.8 - - + -
208B ILE* 2.9 38.4 + - + +
209B ILE* 3.4 18.2 - - + +
211B CYS* 1.3 76.5 - - + +
213B LYS* 1.3 66.1 + - - +
215B PHE* 2.9 7.6 + - + -
216B MET* 2.9 52.0 + - + +
225B MET* 4.0 16.6 - - + -
234B LEU* 6.3 0.7 - - + -
235B LEU* 4.9 7.0 - - + +
253B LEU* 4.8 3.6 - - + -
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ASN* 6.3 0.2 - - - +
209B ILE 2.8 17.8 + - - +
210B ARG* 3.2 15.3 - - + +
212B LEU* 1.3 72.9 - - - +
214B ALA* 1.3 62.7 + - - +
216B MET* 3.8 3.1 + - - +
217B ASN* 3.6 19.6 + - - +
249B ASP* 4.3 15.9 - - - +
252B LYS* 6.6 0.4 - - - +
253B LEU* 3.6 29.8 - - + +
1182D MET* 4.4 7.1 - - + +
1183D ASP* 2.8 29.3 + - - -
1186D LEU* 3.8 26.9 - - - +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 4.5 1.8 - - + +
163B LEU* 4.3 20.1 - - + +
164B ASN* 3.3 36.5 + - - +
171B VAL* 5.6 1.4 - - - +
210B ARG 2.9 16.2 + - - +
211B CYS* 3.6 6.7 - - - +
213B LYS* 1.3 77.1 - - - +
215B PHE* 1.3 64.3 - - - +
217B ASN* 3.0 21.6 + - - +
218B ASN* 4.5 1.7 + - - -
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU* 4.7 9.2 - - + +
171B VAL* 3.5 38.5 - - + +
174B PHE* 4.5 16.8 - + - -
175B GLY 3.4 28.9 - - - -
179B LEU* 3.7 37.0 - - + -
182B LEU* 6.1 3.4 - - + -
211B CYS 2.8 22.4 + - - +
212B LEU* 2.9 10.0 + - + +
214B ALA* 1.3 73.8 - - - +
216B MET* 1.3 59.1 + - + +
218B ASN* 2.7 29.5 + - - -
220B PHE* 4.4 4.9 - + - -
221B GLY* 3.3 32.2 - - - -
224B THR* 4.2 10.1 - - - -
225B MET* 4.7 1.1 - - + -
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU* 2.9 42.6 + - + +
213B LYS 4.2 3.4 - - - +
215B PHE* 1.3 76.5 - - + +
217B ASN* 1.3 49.9 + - - +
218B ASN 2.5 20.8 + - - +
221B GLY 3.7 20.6 - - - +
222B ILE* 3.0 31.7 - - + +
225B MET* 3.3 44.9 - - + -
235B LEU* 4.3 13.9 - - + -
253B LEU* 4.0 18.8 - - + +
257B LEU* 5.4 10.8 - - - -
1182D MET* 4.0 14.2 - - - +
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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