Contacts of the helix formed by residues 201 - 221 (chain B) in PDB entry 3KDO
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 ARG 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS* 6.0 0.4 - - - +
170B PRO* 4.6 0.8 - - - +
196B SER* 2.9 29.1 + - - +
197B PRO* 3.2 14.2 + - - +
198B TRP* 3.5 34.5 + - - +
200B ASN* 1.3 74.2 + - - +
202B PHE* 1.3 67.0 + - - +
203B GLU* 4.4 3.8 - - + +
204B GLU* 3.2 46.8 + - + +
205B ARG* 3.3 13.9 + - - +
97G GLU* 4.9 5.3 + - - +
98G GLU* 5.2 11.1 + - - +
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Residues in contact with PHE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B THR 4.4 1.6 - - - +
196B SER* 2.9 27.2 + - - +
200B ASN 3.7 0.4 + - - -
201B ARG* 1.3 72.3 - - - +
203B GLU* 1.3 68.1 + - + +
205B ARG* 3.5 23.4 + - - +
206B ALA* 3.0 25.6 + - + +
226B TRP* 4.6 1.8 - + - -
228B ALA* 3.7 18.4 - - + -
229B ASN 3.4 31.0 - - - -
230B ILE* 4.1 3.8 - - + -
240B ARG* 3.4 51.6 - - + +
243B VAL* 4.1 11.7 - - + -
244B LEU* 3.4 37.0 - - + -
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 3.3 3.2 - - + +
202B PHE* 1.3 82.7 - - - +
204B GLU* 1.3 65.8 + - + +
206B ALA* 3.4 7.3 - - - +
207B GLU* 3.1 35.7 + - - +
243B VAL* 4.5 17.9 - - + -
247B LEU* 5.1 0.2 - - - +
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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
----------------------------------------------------------
134A ARG* 4.6 16.0 + - - +
170B PRO* 3.6 24.2 - - + +
171B GLU* 4.7 3.5 - - - +
198B TRP 5.6 0.4 - - - +
201B ARG* 3.2 37.8 + - + +
202B PHE 3.2 1.0 - - - -
203B GLU* 1.3 75.7 - - + +
205B ARG* 1.3 66.5 + - - +
206B ALA 3.3 0.2 + - - -
207B GLU* 3.3 10.3 + - - +
208B ILE* 3.1 27.9 + - + +
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 6.0 0.7 - - - -
170B PRO* 4.4 4.4 - - + +
173B PHE* 4.0 24.2 - - + -
190B ASP* 3.0 38.6 + - - -
194B LEU* 3.5 23.4 + - - +
195B THR 2.8 30.5 + - - -
200B ASN* 3.0 44.4 + - - +
201B ARG 3.3 1.6 + - - +
202B PHE* 3.6 28.9 - - - +
204B GLU* 1.3 75.6 - - - +
206B ALA* 1.3 62.3 + - - +
208B ILE* 3.6 10.4 - - - +
209B MET* 2.8 36.8 + - - +
226B TRP* 3.6 11.4 - - + -
229B ASN 4.0 2.4 + - - -
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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
----------------------------------------------------------
202B PHE* 3.0 24.1 + - + +
203B GLU* 3.4 10.1 - - - +
205B ARG* 1.3 79.0 - - - +
207B GLU* 1.3 55.8 + - - +
209B MET* 3.3 3.3 + - - +
210B ALA* 2.9 28.2 + - - +
226B TRP* 3.5 23.3 - - + -
243B VAL* 4.1 9.6 - - + -
247B LEU* 3.8 18.1 - - + +
249B LEU* 4.1 5.5 - - + +
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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
----------------------------------------------------------
203B GLU* 3.1 24.8 + - - +
204B GLU* 3.3 7.4 + - - +
206B ALA* 1.3 76.2 - - - +
208B ILE* 1.3 65.3 + - + +
210B ALA* 3.4 5.0 + - - +
211B LYS* 3.2 22.0 + - - +
243B VAL* 6.1 0.7 - - + -
247B LEU* 3.8 29.6 - - + +
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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
----------------------------------------------------------
170B PRO* 3.3 45.8 - - + +
171B GLU* 4.2 3.4 - - + +
173B PHE* 5.0 5.2 - - + -
174B GLU* 3.3 52.3 - - + +
204B GLU* 3.1 12.7 + - + +
205B ARG* 3.6 9.6 - - - +
207B GLU* 1.3 77.7 - - + +
209B MET* 1.3 59.7 + - - +
211B LYS* 3.1 7.0 + - - +
212B ILE* 2.8 35.9 + - + +
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 3.3 35.0 - - + -
177B ALA* 3.9 12.1 - - + -
181B LEU* 4.0 19.3 - - + -
188B MET* 4.4 7.2 - - + -
205B ARG 2.8 28.4 + - - +
206B ALA 3.6 4.3 - - - +
208B ILE* 1.3 73.5 - - - +
210B ALA* 1.3 62.6 + - - +
212B ILE* 4.4 6.3 - - + -
213B ILE* 2.9 56.7 + - + +
225B THR 4.8 0.2 - - - +
226B TRP* 3.6 47.1 - - + -
249B LEU* 4.5 0.9 - - + -
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA 2.9 14.0 + - - +
207B GLU* 3.5 13.9 - - - +
208B ILE 3.2 0.4 - - - -
209B MET* 1.3 79.1 - - - +
211B LYS* 1.3 60.2 + - - +
213B ILE* 4.0 2.9 - - - +
214B ASP* 3.2 29.3 + - - +
247B LEU* 4.3 30.3 - - + +
249B LEU* 4.0 13.4 - - + +
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Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLU* 5.8 2.5 - - - +
207B GLU 3.2 8.6 + - - +
208B ILE* 3.1 9.0 + - - +
210B ALA* 1.3 76.9 - - - +
212B ILE* 1.3 70.8 + - + +
214B ASP* 3.0 10.1 + - - +
215B LYS* 2.9 23.6 + - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLU* 3.7 35.0 - - + +
177B ALA* 4.4 5.2 - - + -
178B TYR* 3.8 32.8 - - + +
181B LEU* 4.2 12.3 - - + -
208B ILE* 2.8 37.7 + - + +
209B MET* 4.0 7.9 - - + +
211B LYS* 1.3 74.2 - - + +
213B ILE* 1.3 59.4 + - - +
215B LYS* 3.3 7.6 + - + +
216B VAL* 2.8 52.1 + - + +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.3 9.6 - - + -
209B MET* 2.9 49.2 + - + +
210B ALA* 4.0 3.4 - - - +
212B ILE* 1.3 75.6 - - - +
214B ASP* 1.3 63.2 + - - +
216B VAL* 4.0 4.1 - - - +
217B GLU* 2.9 45.8 + - - +
224B LYS* 3.5 24.9 - - + +
225B THR* 3.9 24.2 - - - -
226B TRP* 4.1 3.1 - - + +
249B LEU* 4.1 21.5 - - + -
250B LYS* 4.8 6.5 - - + +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 3.2 16.3 + - - +
211B LYS* 3.0 11.2 + - - +
213B ILE* 1.3 81.7 - - - +
215B LYS* 1.3 60.9 + - - +
217B GLU* 3.4 12.0 + - - +
218B ASN* 3.1 24.1 + - - +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 3.9 23.6 + - + -
211B LYS 2.9 13.9 + - - +
212B ILE* 3.8 8.3 - - + +
214B ASP* 1.3 72.7 - - - +
216B VAL* 1.3 65.9 + - - +
217B GLU 3.0 1.7 + - - -
218B ASN* 3.1 5.7 + - - +
219B GLU* 2.5 62.0 + - + +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 3.7 28.9 - - + +
181B LEU* 3.8 30.5 - - + +
182B SER* 4.1 6.7 - - - +
212B ILE* 2.8 35.4 + - + +
213B ILE* 4.2 3.8 - - - +
215B LYS* 1.3 71.5 - - - +
217B GLU* 1.3 51.6 + - - +
219B GLU* 4.5 7.4 - - - -
220B THR* 2.6 46.6 + - + +
224B LYS* 3.8 26.5 - - + -
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Residues in contact with GLU 217 (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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213B ILE* 2.9 34.0 + - + +
214B ASP* 3.7 11.3 - - - +
215B LYS 3.0 0.8 - - - -
216B VAL* 1.3 76.9 - - - +
218B ASN* 1.3 58.7 + - - +
219B GLU 3.2 0.2 - - - -
221B GLY* 2.5 35.6 + - - -
222B GLU 3.3 20.2 - - - +
223B LYS* 3.2 20.3 + - - +
224B LYS* 2.8 29.4 + - + +
250B LYS* 3.1 19.9 + - - -
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Residues in contact with ASN 218 (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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214B ASP 3.1 16.8 + - - +
215B LYS* 3.1 5.6 + - - +
217B GLU* 1.3 77.9 - - - +
219B GLU* 1.3 65.7 + - + +
221B GLY* 4.3 3.0 + - - -
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 2.6 29.7 + - - -
182B SER* 5.3 0.5 + - - -
215B LYS* 2.5 57.7 + - + +
216B VAL* 4.3 3.5 - - - +
218B ASN* 1.3 85.2 - - + +
220B THR* 1.3 66.3 + - + +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU 5.2 1.3 - - - +
182B SER* 4.6 19.7 - - - +
216B VAL* 2.6 37.6 + - + +
219B GLU* 1.3 83.9 - - + +
221B GLY* 1.3 61.8 + - - +
222B GLU* 3.2 33.3 + - - +
224B LYS* 4.5 2.2 - - - -
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Residues in contact with GLY 221 (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 GLU* 5.4 3.3 - - - +
217B GLU* 2.5 24.4 + - - -
218B ASN 4.2 2.8 + - - -
219B GLU 3.5 1.4 - - - -
220B THR* 1.3 73.8 - - - +
222B GLU* 1.3 60.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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