Contacts of the helix formed by residues 197 - 212 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334C ILE* 4.1 10.8 - - + -
336C VAL* 3.8 26.2 - - + -
9D SER* 3.9 31.6 - - - +
10D LEU 3.2 23.3 - - - +
11D ASP* 3.8 15.0 - - - +
189D ARG* 4.4 5.6 - - - +
196D TYR* 1.3 93.6 - - + +
198D GLN* 1.3 60.9 + - - +
199D LEU 3.4 1.1 - - - -
200D SER* 3.4 5.1 + - - +
201D ALA* 3.0 24.9 + - - +
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Residues in contact with GLN 198 (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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11D ASP* 3.2 14.2 + - - +
12D PHE* 3.8 29.2 - - + -
160D VAL* 5.2 0.2 - - - +
178D VAL* 2.9 26.0 + - - +
179D GLY* 3.3 21.0 - - - -
180D ILE 4.6 0.3 + - - -
182D PRO* 3.6 25.0 - - + +
189D ARG* 5.2 0.8 - - - +
196D TYR 3.3 4.2 + - - +
197D PRO* 1.3 71.9 - - - +
199D LEU* 1.3 58.9 + - - +
201D ALA* 3.3 7.4 + - - +
202D VAL* 2.9 34.4 + - + +
218D SER* 3.1 20.2 + - - +
219D ASP 3.6 6.5 + - - +
220D GLY 3.9 8.5 + - - +
221D GLY* 5.7 0.4 - - - -
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 3.2 28.9 + - + +
11D ASP* 3.9 13.5 - - - +
12D PHE* 3.8 25.9 - - + +
15D VAL* 3.6 40.4 - - + -
198D GLN* 1.3 78.0 - - - +
200D SER* 1.3 57.6 + - - +
202D VAL* 3.3 6.0 + - + +
203D MET* 3.0 37.7 + - - +
230D LYS* 3.9 9.0 - - + +
231D ALA* 4.9 0.2 - - - -
234D ALA* 3.5 30.3 - - + -
333D PHE* 4.2 11.2 - - + -
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Residues in contact with SER 200 (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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9D SER* 3.6 12.4 + - - -
10D LEU* 2.7 37.5 + - - +
196D TYR* 4.3 12.7 - - - -
197D PRO* 3.4 8.5 + - - -
199D LEU* 1.3 74.8 - - - +
201D ALA* 1.3 67.2 + - - +
203D MET* 3.7 17.0 - - - +
204D GLU* 3.0 27.4 + - - +
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Residues in contact with ALA 201 (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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160D VAL* 3.7 27.4 - - + +
178D VAL* 3.9 16.2 - - + -
196D TYR* 3.8 12.2 - - + -
197D PRO 3.0 14.6 + - - +
198D GLN* 3.4 16.6 - - - +
200D SER* 1.3 78.1 - - - +
202D VAL* 1.3 55.7 + - - +
204D GLU* 3.9 0.6 - - - +
205D CYS* 2.9 35.7 + - - +
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Residues in contact with VAL 202 (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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12D PHE* 5.2 3.4 - - + -
178D VAL* 4.5 4.7 - - + -
198D GLN* 2.9 28.3 + - + +
199D LEU* 3.3 10.3 + - + +
201D ALA* 1.3 72.8 - - - +
203D MET* 1.3 61.1 + - - +
206D ALA* 2.9 35.2 + - - +
216D ILE* 3.6 9.2 - - + +
218D SER* 3.2 32.8 - - - +
231D ALA* 3.7 14.4 - - + +
234D ALA* 3.7 26.5 - - + +
236D ALA* 3.9 14.4 - - + +
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Residues in contact with MET 203 (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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10D LEU* 4.1 19.7 - - + -
199D LEU* 3.0 24.4 + - - +
200D SER* 3.7 29.8 - - - +
202D VAL* 1.3 76.8 - - - +
204D GLU* 1.3 64.9 + - - +
206D ALA* 3.8 1.2 - - - +
207D ASP* 3.2 30.0 + - - +
234D ALA* 3.8 26.7 - - + +
333D PHE* 4.7 14.6 - - - -
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Residues in contact with GLU 204 (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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18C ARG* 4.7 2.8 + - - -
160D VAL 4.5 0.9 - - - -
161D THR* 3.5 17.4 - - - +
162D GLY* 3.0 31.2 + - - +
196D TYR* 2.9 27.9 + - - -
200D SER 3.0 16.6 + - - +
201D ALA* 3.9 2.9 - - - +
203D MET* 1.3 77.9 - - - +
205D CYS* 1.3 61.5 + - - +
207D ASP* 3.4 7.1 + - - +
208D ALA* 3.2 20.3 + - - +
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Residues in contact with CYS 205 (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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160D VAL* 3.3 42.0 - - - -
161D THR* 3.5 8.7 - - - -
162D GLY* 4.9 0.2 - - - -
165D VAL* 3.5 27.6 - - + +
178D VAL* 3.7 23.3 - - + -
201D ALA 2.9 18.2 + - - +
202D VAL 4.1 1.1 - - - +
204D GLU* 1.3 74.7 - - - +
206D ALA* 1.3 60.9 + - - +
208D ALA* 3.4 3.9 + - - +
209D ALA* 2.9 31.0 + - - +
216D ILE* 3.7 3.3 - - + +
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Residues in contact with ALA 206 (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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202D VAL 2.9 19.4 + - - +
203D MET 3.8 3.4 - - - +
205D CYS* 1.3 77.5 - - - +
207D ASP* 1.3 59.6 + - - +
210D HIS* 2.8 44.7 + - + -
216D ILE* 3.6 17.6 - - + +
234D ALA 4.2 4.7 - - - +
235D GLY* 3.6 29.4 - - - +
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Residues in contact with ASP 207 (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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203D MET* 3.2 16.5 + - - +
204D GLU* 3.6 9.2 - - - +
206D ALA* 1.3 79.4 - - - +
208D ALA* 1.3 62.4 + - - +
210D HIS* 4.2 5.9 + - - +
211D GLY* 3.1 19.8 + - - -
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Residues in contact with ALA 208 (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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162D GLY* 3.7 37.9 - - - +
165D VAL* 4.3 4.9 - - + -
166D GLU* 4.1 20.5 - - + +
204D GLU 3.2 7.1 + - - +
205D CYS 3.7 7.2 - - - +
206D ALA 3.3 0.2 - - - -
207D ASP* 1.3 78.8 - - - +
209D ALA* 1.3 66.4 + - - +
210D HIS 3.3 0.3 + - - -
211D GLY* 3.4 6.9 + - - -
212D LEU* 3.6 15.6 + - - +
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Residues in contact with ALA 209 (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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165D VAL* 3.7 7.8 - - + +
169D ILE* 3.7 19.3 - - + -
205D CYS 2.9 21.6 + - - +
206D ALA 3.8 2.7 - - - +
208D ALA* 1.3 73.9 - - - +
210D HIS* 1.3 58.9 + - + +
212D LEU* 3.1 8.5 + - - +
214D GLY* 2.6 31.3 + - - +
215D HIS 3.9 13.2 - - - +
216D ILE* 3.6 22.4 - - + -
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Residues in contact with HIS 210 (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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206D ALA* 2.8 36.5 + - + +
207D ASP* 4.2 5.7 + - - +
209D ALA* 1.3 75.0 - - + +
211D GLY* 1.3 66.2 + - - +
213D LYS* 3.1 17.1 + - - +
214D GLY 3.4 20.6 - - - -
215D HIS* 5.4 0.7 - + - -
235D GLY* 3.1 27.8 + - - -
237D ASP* 2.8 31.7 + - - -
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Residues in contact with GLY 211 (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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207D ASP 3.1 15.9 + - - -
208D ALA 3.4 3.3 + - - -
209D ALA 3.2 0.4 - - - -
210D HIS* 1.3 77.8 - - - +
212D LEU* 1.3 61.5 + - - +
213D LYS* 3.3 3.9 + - - +
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Residues in contact with LEU 212 (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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39D ARG* 2.9 42.2 + - - +
166D GLU* 3.7 48.9 - - + +
169D ILE* 4.2 20.2 - - + -
170D LEU* 4.4 14.8 - - + -
208D ALA 3.6 5.8 + - - +
209D ALA 3.1 8.6 + - - +
211D GLY* 1.3 78.2 - - - +
213D LYS* 1.3 70.7 + - - +
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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