Contacts of the helix formed by residues 197 - 212 (chain B) in PDB entry 2BZN
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 PRO 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 4.0 26.0 - - - +
10B LEU 3.2 26.7 - - - +
11B ASP* 3.6 14.4 - - - +
189B ARG* 3.9 5.6 - - - +
196B TYR* 1.3 98.4 - - + +
198B GLN* 1.3 64.9 + - - +
199B LEU 3.3 1.1 + - - -
200B SER* 3.5 2.6 + - - -
201B ALA* 3.0 19.2 + - - +
334D ILE* 4.2 13.7 - - + -
336D VAL* 4.0 21.3 - - + -
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.2 13.3 + - - +
12B PHE* 3.8 30.3 - - + -
160B VAL* 5.0 0.2 - - - +
178B VAL* 2.8 29.0 + - - +
179B GLY* 3.4 18.1 - - - -
182B PRO* 3.5 26.3 - - + +
189B ARG* 5.1 0.4 - - - +
196B TYR 3.2 5.2 + - - +
197B PRO* 1.3 71.7 - - - +
199B LEU* 1.3 63.8 + - - +
201B ALA* 3.5 7.8 + - - +
202B VAL* 3.0 29.3 + - - +
218B SER* 3.2 18.7 + - - +
219B ASP 3.6 5.9 + - - +
220B GLY 3.8 10.0 + - - +
221B GLY* 5.7 0.7 - - - -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 2.9 33.1 + - + +
11B ASP* 3.8 13.2 - - - +
12B PHE* 4.0 21.0 - - + +
15B VAL* 3.5 40.8 - - + -
198B GLN* 1.3 78.8 - - - +
200B SER* 1.3 55.8 + - - +
202B VAL* 3.2 6.1 + - + +
203B MET* 3.0 33.5 + - - +
230B LYS* 4.0 10.5 - - + +
231B ALA* 5.0 0.4 - - - +
234B ALA* 3.5 31.4 - - + -
333B PHE* 4.3 10.1 - - + -
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 3.5 11.1 + - - -
10B LEU* 2.7 37.5 + - - +
196B TYR* 4.2 14.6 - - - -
197B PRO* 3.8 8.3 - - - -
198B GLN 3.3 0.2 - - - -
199B LEU* 1.3 72.5 - - - +
201B ALA* 1.3 65.9 + - - +
203B MET* 3.3 17.6 + - - +
204B GLU* 3.0 26.9 + - - +
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Residues in contact with ALA 201 (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 VAL* 3.7 31.2 - - + +
178B VAL* 3.8 17.3 - - + -
196B TYR* 3.8 11.5 - - + -
197B PRO 3.0 19.2 + - - +
198B GLN* 3.6 11.2 - - - +
200B SER* 1.3 77.1 - - - +
202B VAL* 1.3 57.2 + - - +
204B GLU* 3.8 1.0 - - - -
205B CYS* 2.8 35.3 + - - +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.2 1.8 - - + -
178B VAL* 4.5 4.3 - - + -
198B GLN* 3.0 27.8 + - + +
199B LEU* 3.2 10.3 + - + +
201B ALA* 1.3 76.6 - - - +
203B MET* 1.3 57.8 + - - +
206B ALA* 2.8 34.5 + - - +
216B ILE* 3.7 12.7 - - + +
218B SER* 3.2 33.7 - - - +
231B ALA* 3.9 14.4 - - + +
234B ALA* 3.9 11.9 - - + +
236B ALA* 3.8 27.4 - - + +
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Residues in contact with MET 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.0 24.2 - - + -
199B LEU* 3.0 23.2 + - - +
200B SER* 3.7 26.7 - - - +
201B ALA 3.3 0.2 - - - -
202B VAL* 1.3 75.7 - - - +
204B GLU* 1.3 62.1 + - - +
206B ALA* 3.5 1.6 + - - +
207B ASP* 3.2 32.1 + - - +
234B ALA* 3.9 26.7 - - + +
333B PHE* 4.5 17.0 - - - -
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Residues in contact with GLU 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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160B VAL 4.5 1.8 - - - +
161B THR* 3.4 18.6 - - - +
162B GLY* 2.7 33.5 + - - +
163B GLU* 4.7 0.7 + - - +
196B TYR* 3.5 20.0 + - - -
200B SER 3.0 14.3 + - - +
201B ALA* 4.3 2.9 - - - +
203B MET* 1.3 76.8 - - - +
205B CYS* 1.3 66.1 + - - +
207B ASP* 3.3 9.7 + - - +
208B ALA* 3.1 21.1 + - - +
18D ARG* 4.9 1.9 + - - -
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Residues in contact with CYS 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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160B VAL* 3.3 33.0 - - - -
161B THR* 3.5 6.5 - - - -
165B VAL* 3.4 30.6 - - + +
178B VAL* 3.6 27.6 - - + -
201B ALA 2.8 24.8 + - - +
202B VAL 4.3 0.9 - - - +
204B GLU* 1.3 75.5 - - - +
206B ALA* 1.3 57.3 + - - +
208B ALA* 3.3 3.8 + - - +
209B ALA* 2.9 31.4 + - - +
216B ILE* 3.7 4.4 - - + +
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Residues in contact with ALA 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 VAL 2.8 19.4 + - - +
203B MET 3.7 4.3 - - - +
205B CYS* 1.3 75.3 - - - +
207B ASP* 1.3 67.7 + - - +
210B HIS* 3.0 38.2 + - + +
216B ILE* 3.7 15.8 - - + +
234B ALA 4.1 6.7 - - - +
235B GLY* 3.7 29.4 - - - +
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Residues in contact with ASP 207 (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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203B MET* 3.2 17.6 + - - +
204B GLU* 3.7 9.4 - - - +
205B CYS 3.3 0.2 - - - -
206B ALA* 1.3 78.8 - - - +
208B ALA* 1.3 61.8 + - - +
210B HIS* 4.0 4.8 + - - +
211B GLY* 3.1 20.1 + - - -
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLY* 3.6 38.8 - - - +
165B VAL* 4.2 6.3 - - + -
166B GLU* 4.2 25.7 - - + +
204B GLU 3.1 9.4 + - - +
205B CYS 3.6 7.2 - - - +
207B ASP* 1.3 75.5 - - - +
209B ALA* 1.3 66.1 + - - +
211B GLY* 3.5 6.2 + - - -
212B LEU* 3.7 9.5 + - - +
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Residues in contact with ALA 209 (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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165B VAL* 3.8 2.0 - - + +
169B ILE* 3.6 26.0 - - + -
205B CYS 2.9 17.5 + - - +
206B ALA 4.1 2.0 - - - +
208B ALA* 1.3 76.5 - - - +
210B HIS* 1.3 66.6 + - + +
212B LEU* 3.0 10.9 + - - +
214B GLY* 2.9 23.2 + - - -
215B HIS* 3.8 15.7 - - - +
216B ILE* 3.6 22.2 - - + -
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Residues in contact with HIS 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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34B ARG* 6.3 0.4 - - - -
206B ALA* 3.0 31.8 + - + +
207B ASP* 4.2 5.2 + - - +
209B ALA* 1.3 79.6 - - + +
211B GLY* 1.3 57.8 + - - +
213B LYS* 3.0 20.8 + - - +
214B GLY 3.5 20.6 - - - -
215B HIS* 5.6 0.2 - + - -
235B GLY* 3.2 27.1 + - - -
237B ASP* 2.8 30.5 + - - -
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Residues in contact with GLY 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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207B ASP 3.1 16.4 + - - -
208B ALA 3.5 3.8 + - - -
209B ALA 3.2 0.6 - - - -
210B HIS* 1.3 76.8 - - - +
212B LEU* 1.3 61.8 + - - +
213B LYS* 3.8 3.0 + - - +
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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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39B ARG* 2.9 42.7 + - - +
166B GLU* 3.8 46.7 - - + +
169B ILE* 4.1 19.3 - - + -
170B LEU* 4.1 15.5 - - + -
208B ALA 3.7 6.4 + - - +
209B ALA 3.0 8.8 + - - +
211B GLY* 1.3 78.4 - - - +
213B LYS* 1.3 72.9 + - - +
214B GLY 3.2 0.2 - - - -
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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