Contacts of the helix formed by residues 196 - 211 (chain B) in PDB entry 4XJO
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B PRO* 5.3 4.3 - - + -
194B ASP 4.3 2.5 - - - +
195B TYR* 1.3 76.4 - - - +
197B PRO* 1.3 66.3 - - - +
198B ALA* 3.1 27.2 + - - +
199B TYR* 2.9 30.4 + - + +
200B SER 3.7 0.5 + - - -
236B TYR* 2.8 21.2 + - - +
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Residues in contact with PRO 197 (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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195B TYR* 3.7 35.8 - - + +
196B ASP* 1.3 90.3 - - - +
198B ALA* 1.3 55.4 + - - +
200B SER* 3.3 6.6 + - - +
201B ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 198 (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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196B ASP* 3.0 19.9 + - - +
197B PRO* 1.3 75.8 - - - +
199B TYR* 1.3 63.5 - - - +
201B ALA* 3.8 8.3 - - - +
202B ALA* 3.0 24.6 + - - +
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Residues in contact with TYR 199 (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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153B TRP* 3.3 36.8 - + - +
188B ALA* 4.0 2.7 - - + +
189B PRO* 2.7 45.6 + - + -
190B GLN 3.6 11.4 - - - -
191B VAL* 3.7 12.3 + - + -
192B PRO* 3.6 18.8 - - + -
196B ASP* 2.9 18.2 + - + +
198B ALA* 1.3 79.4 - - - +
200B SER* 1.3 59.5 + - - +
202B ALA* 3.3 8.0 + - + +
203B PHE* 2.9 42.9 + + + +
236B TYR* 3.6 24.9 - + + +
240B LEU* 6.3 0.2 - - + -
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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
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195B TYR* 4.0 1.9 - - - -
196B ASP 3.7 0.7 + - - -
197B PRO 3.3 9.5 + - - -
199B TYR* 1.3 77.2 - - - +
201B ALA* 1.3 59.9 + - - +
203B PHE* 3.3 6.7 + - - +
204B GLU* 2.9 30.5 + - - +
236B TYR* 3.4 22.0 - - - -
239B ASP* 2.6 42.5 + - - +
243B ILE* 3.7 7.0 - - - +
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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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197B PRO 2.9 17.4 + - - +
198B ALA* 3.8 8.7 - - - +
199B TYR 3.3 0.2 - - - -
200B SER* 1.3 76.0 - - - +
202B ALA* 1.3 57.3 + - - +
204B GLU* 3.4 10.0 + - - +
205B ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 202 (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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189B PRO* 6.1 6.3 - - + -
198B ALA 3.0 18.3 + - - +
199B TYR* 3.6 7.4 - - + +
201B ALA* 1.3 73.7 - - - +
203B PHE* 1.3 65.0 + - - +
205B ALA* 3.3 6.5 + - - +
206B GLN* 3.0 24.5 + - - +
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Residues in contact with PHE 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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151B MET* 3.7 26.8 - - + +
152B THR 4.5 4.7 - - - -
153B TRP* 4.2 16.8 - + + -
188B ALA* 3.5 31.9 - - + -
189B PRO* 6.3 1.3 - - - +
199B TYR* 2.9 31.5 + + + +
200B SER* 3.5 13.0 - - - +
202B ALA* 1.3 74.7 - - - +
204B GLU* 1.3 58.5 - - - +
206B GLN* 3.3 9.5 + - - +
207B LEU* 2.9 40.1 + - + +
217B VAL* 4.1 18.4 - - + -
219B VAL* 5.5 0.4 - - + -
240B LEU* 3.5 34.8 - - + -
243B ILE* 4.2 9.2 - - + -
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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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200B SER 2.9 16.6 + - - +
201B ALA* 3.5 10.2 - - - +
203B PHE* 1.3 77.5 - - - +
205B ALA* 1.3 53.2 + - - +
207B LEU* 3.3 2.3 + - - +
208B ALA* 2.8 34.1 + - - +
243B ILE* 3.7 22.6 - - + +
246B ARG* 2.8 46.1 + - - -
247B TYR* 3.4 26.3 + - + +
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Residues in contact with ALA 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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201B ALA 3.0 17.2 + - - +
202B ALA* 3.7 7.2 - - - +
204B GLU* 1.3 75.8 - - - +
206B GLN* 1.3 63.4 + - - +
208B ALA* 3.4 8.1 + - - +
209B GLN* 3.4 21.1 + - - +
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Residues in contact with GLN 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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151B MET* 3.6 10.7 - - + +
186B VAL* 3.6 14.5 - - - +
187B PHE 3.0 23.2 + - - +
188B ALA* 3.3 27.2 - - - +
189B PRO* 4.1 6.4 - - - +
202B ALA 3.0 17.4 + - - +
203B PHE* 3.6 4.5 - - - +
205B ALA* 1.3 73.9 - - - +
207B LEU* 1.3 64.3 + - - +
209B GLN* 3.4 12.2 + - - +
210B HIS* 3.1 36.5 + - + +
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Residues in contact with LEU 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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151B MET* 3.7 18.3 - - + +
203B PHE* 2.9 21.8 + - + +
204B GLU 3.7 3.4 - - - +
206B GLN* 1.3 76.2 - - - +
208B ALA* 1.3 54.3 + - - +
210B HIS* 2.9 4.9 + - - +
211B ALA* 2.8 32.3 + - + -
214B LEU* 3.9 13.0 - - + -
217B VAL* 3.5 32.1 - - + -
243B ILE* 4.0 21.8 - - + -
244B CYS* 4.7 2.9 - - - -
247B TYR* 3.5 35.4 - - + -
249B VAL* 4.2 17.7 - - + -
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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
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204B GLU 2.8 21.0 + - - +
205B ALA* 3.6 10.1 - - - +
207B LEU* 1.3 74.7 - - - +
209B GLN* 1.3 62.1 + - - +
210B HIS 3.3 0.5 + - - -
211B ALA* 3.4 11.7 + - - +
247B TYR* 3.5 39.4 - - + +
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Residues in contact with GLN 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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205B ALA 3.4 9.5 + - - +
206B GLN* 3.4 13.1 + - - +
207B LEU 3.2 0.4 - - - -
208B ALA* 1.3 79.4 - - - +
210B HIS* 1.3 81.9 + - + +
211B ALA 3.5 0.4 + - - -
212B GLY 5.3 0.3 + - - -
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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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149B ARG* 3.8 12.5 + - - -
186B VAL* 3.8 29.3 - - + +
206B GLN* 3.1 29.7 + - + +
207B LEU 2.9 3.4 + - - +
209B GLN* 1.3 101.9 + - + +
211B ALA* 1.3 65.0 + - - +
212B GLY 3.2 3.1 - - - -
213B GLU* 2.8 45.0 + - + +
214B LEU* 3.2 30.3 + - + +
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Residues in contact with ALA 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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147B LYS* 2.8 29.7 + - - -
207B LEU* 2.8 23.0 + - + +
208B ALA* 3.4 14.9 + - - +
209B GLN 3.5 0.4 - - - -
210B HIS* 1.3 76.0 - - - +
212B GLY* 1.3 57.6 + - - +
213B GLU 3.2 0.7 + - - -
214B LEU* 3.2 13.9 + - - +
247B TYR* 4.1 25.4 - - + +
249B VAL* 4.5 2.7 - - + -
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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