Contacts of the helix formed by residues 196 - 212 (chain B) in PDB entry 1DXO
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B HIS 3.9 7.0 - - - +
195B THR* 1.3 92.8 - - + +
197B ALA* 1.3 66.5 + - - +
198B ASP* 3.8 19.3 - - - +
199B ALA* 2.9 21.1 + - + +
200B ARG* 3.0 12.1 + - - +
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Residues in contact with ALA 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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196B PRO* 1.3 71.6 - - - +
198B ASP* 1.3 62.8 + - - +
200B ARG* 3.6 35.1 + - - +
201B ILE* 3.1 30.8 + - + +
301B FAD 5.0 0.9 - - - -
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Residues in contact with ASP 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 PRO* 3.8 12.4 - - - +
197B ALA* 1.3 81.1 + - - +
199B ALA* 1.3 65.7 + - - +
201B ILE* 3.3 26.7 - - + +
202B GLN* 3.4 15.1 + - - +
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Residues in contact with ALA 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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195B THR* 3.5 21.3 - - + -
196B PRO* 2.9 15.2 + - + +
198B ASP* 1.3 76.4 + - - +
200B ARG* 1.3 68.8 + - - +
201B ILE 3.0 1.8 - - - -
202B GLN* 2.8 20.6 + - - +
203B ILE* 2.8 18.2 + - + +
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Residues in contact with ARG 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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17B PHE* 3.6 12.8 - - + -
192B ILE* 4.2 11.8 + - + -
195B THR* 2.8 32.2 + - + +
196B PRO* 3.0 10.3 + - - +
197B ALA* 3.6 38.7 - - - +
199B ALA* 1.3 76.5 - - - +
201B ILE* 1.3 61.5 + - - +
203B ILE* 3.2 23.4 + - - +
204B LEU* 3.2 11.3 + - - +
301B FAD 3.4 74.7 + - - +
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Residues in contact with ILE 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 ALA* 3.1 21.1 - - + +
198B ASP* 3.3 17.0 - - + +
199B ALA 3.0 0.2 - - - -
200B ARG* 1.3 73.8 - - - +
202B GLN* 1.3 79.4 + - - +
204B LEU* 3.5 11.5 + - + +
205B GLU* 3.1 30.3 + - + +
301B FAD 4.6 12.1 - - + +
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Residues in contact with GLN 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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198B ASP* 3.7 13.0 + - - +
199B ALA* 2.8 14.4 + - - +
201B ILE* 1.3 89.0 - - - +
203B ILE* 1.3 55.9 + - + +
205B GLU* 2.9 17.3 + - - +
206B GLY* 2.6 35.5 + - - -
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Residues in contact with ILE 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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17B PHE* 3.3 23.8 - - + -
21B MET* 4.4 4.0 - - + -
187B GLN* 5.3 3.3 + - - +
189B THR* 3.9 27.1 - - + -
190B TYR 6.0 1.6 - - - +
192B ILE* 4.0 15.9 - - + -
195B THR* 3.9 20.0 - - + +
199B ALA* 2.8 13.9 + - + +
200B ARG* 3.2 22.7 - - - +
202B GLN* 1.3 77.4 - - - +
204B LEU* 1.3 61.4 + - - +
206B GLY* 3.4 1.1 + - - -
207B TRP* 3.1 22.9 + - + +
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Residues in contact with LEU 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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17B PHE* 3.7 24.7 - - + -
20B ALA* 3.5 33.4 - - + +
21B MET* 3.9 10.5 - - - +
24B ALA* 4.1 11.5 - - + +
200B ARG 3.2 4.8 + - - +
201B ILE* 3.8 10.1 - - + +
202B GLN 3.2 0.2 - - - -
203B ILE* 1.3 80.1 - - - +
205B GLU* 1.3 68.8 + - - +
207B TRP* 3.4 6.6 + - - +
208B LYS* 3.1 29.7 + - + +
301B FAD 3.3 41.7 - - + +
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Residues in contact with GLU 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 ILE* 3.1 23.5 + - + +
202B GLN* 2.9 27.5 + - - +
204B LEU* 1.3 82.5 - - - +
206B GLY* 1.3 57.3 + - - +
208B LYS* 3.4 21.3 + - - +
209B LYS* 3.0 27.7 + - - +
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Residues in contact with GLY 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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187B GLN* 5.2 3.1 - - - -
202B GLN 2.6 18.1 + - - -
203B ILE* 3.9 2.0 - - - -
205B GLU* 1.3 70.3 - - - +
207B TRP* 1.3 59.5 + - - +
209B LYS* 3.3 7.8 + - - +
210B ARG* 3.0 28.1 + - - +
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Residues in contact with TRP 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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21B MET* 3.3 49.2 + - + +
24B ALA* 4.7 4.7 - - + -
25B ALA* 3.6 12.5 - - + +
98B ILE* 4.1 21.1 - - + +
100B GLN* 4.4 1.4 + - - -
143B VAL* 4.5 13.9 - - + -
145B SER* 4.0 20.3 + - - -
187B GLN* 3.3 53.5 - - + +
203B ILE 3.1 17.1 + - - +
204B LEU 3.6 3.6 - - - +
206B GLY* 1.3 72.9 - - - +
208B LYS* 1.3 65.8 + - - +
210B ARG* 3.2 25.5 + - - +
211B LEU* 3.1 59.2 + - + +
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Residues in contact with LYS 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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24B ALA* 3.4 40.0 - - + +
27B ALA* 4.1 10.5 - - - +
28B ALA* 3.7 19.3 - - + +
31B LYS* 2.7 35.5 - - - +
204B LEU* 3.1 18.8 + - + +
205B GLU* 3.7 26.1 + - - +
207B TRP* 1.3 75.8 - - - +
209B LYS* 1.3 65.2 + - - +
211B LEU* 3.2 14.5 + - - +
212B GLU* 3.4 16.8 + - - +
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Residues in contact with LYS 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 GLU 3.0 16.6 + - - +
206B GLY* 3.6 7.6 - - - +
207B TRP 3.3 0.2 - - - -
208B LYS* 1.3 77.7 - - - +
210B ARG* 1.3 61.6 + - - +
212B GLU* 3.3 51.3 + - - +
213B ASN* 4.4 15.8 + - - +
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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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143B VAL* 3.9 9.4 - - - +
184B LEU* 4.0 2.6 - - - +
185B GLU* 2.6 44.6 + - - +
186B PRO 4.0 1.0 + - - -
187B GLN* 2.8 42.7 + - - +
206B GLY 3.0 13.9 + - - +
207B TRP* 3.5 21.3 - - - +
208B LYS 3.1 0.4 - - - -
209B LYS* 1.3 78.4 - - - +
211B LEU* 1.3 60.8 + - - +
212B GLU 3.1 1.8 + - - -
213B ASN* 3.3 5.7 + - - +
214B ILE* 3.2 27.5 + - + +
217B GLU* 2.8 39.2 + - - +
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Residues in contact with LEU 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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25B ALA* 3.6 39.0 - - + +
28B ALA* 4.4 5.8 - - + -
29B LEU* 3.7 28.1 - - + +
32B LYS* 5.2 1.6 - - - +
34B TRP* 4.8 4.3 + - - -
96B LEU* 4.8 0.4 - - + -
98B ILE* 3.9 17.0 - - + -
207B TRP* 3.1 44.3 + - + +
208B LYS* 3.2 10.7 + - - +
210B ARG* 1.3 70.5 - - - +
212B GLU* 1.3 63.2 + - - +
213B ASN 3.1 3.2 + - - -
214B ILE* 3.6 43.3 - - + +
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Residues in contact with GLU 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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28B ALA* 5.8 4.7 - - + +
32B LYS* 3.8 50.6 + - + +
34B TRP* 5.9 0.3 + - - -
208B LYS* 3.4 13.8 + - - +
209B LYS* 3.3 49.1 + - - +
210B ARG 3.1 0.6 - - - -
211B LEU* 1.3 78.9 - - - +
213B ASN* 1.3 71.9 + - - +
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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