Contacts of the helix formed by residues 201 - 221 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 5.1 3.8 + - - +
98B GLU* 5.9 1.4 + - - +
98F GLU* 6.3 0.8 - - - -
131F LYS* 6.0 0.4 - - - +
170G PRO* 4.4 4.8 - - - +
196G SER* 2.8 37.3 + - - +
197G PRO* 3.2 15.7 + - - +
198G TRP* 3.6 30.8 + - - +
200G ASN* 1.3 74.5 + - - +
202G PHE* 1.3 64.1 + - - +
203G GLU* 4.4 3.6 - - + +
204G GLU* 3.1 38.2 + - + +
205G ARG* 3.0 24.6 + - - +
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Residues in contact with PHE 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G THR 4.2 1.8 - - - +
196G SER* 3.0 25.6 + - - +
201G ARG* 1.3 71.8 - - - +
203G GLU* 1.3 62.9 + - + +
205G ARG* 3.4 25.8 + - - +
206G ALA* 2.9 31.5 + - + +
226G TRP* 4.4 2.2 - + - -
228G ALA* 3.7 20.0 - - + -
229G ASN 3.4 31.0 - - - -
230G ILE* 4.1 6.3 - - + -
240G ARG* 3.5 50.3 - - + +
243G VAL* 4.1 12.3 - - + -
244G LEU* 3.6 29.2 - - + -
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Residues in contact with GLU 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G SER* 4.9 0.2 + - - -
201G ARG* 3.3 3.2 - - + +
202G PHE* 1.3 84.9 - - + +
204G GLU* 1.3 60.6 + - + +
206G ALA* 3.3 7.4 + - - +
207G GLU* 3.0 36.0 + - + +
243G VAL* 4.4 19.0 - - + +
247G LEU* 5.0 0.2 - - - +
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Residues in contact with GLU 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ARG* 4.9 13.5 + - - +
170G PRO* 3.9 23.2 - - + +
171G GLU* 5.3 1.7 - - - +
198G TRP 5.7 0.2 - - - +
201G ARG* 3.1 37.4 + - + +
203G GLU* 1.3 79.6 - - + +
205G ARG* 1.3 60.1 + - - +
207G GLU* 3.6 7.3 + - - +
208G ILE* 3.3 28.6 + - + +
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Residues in contact with ARG 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G PRO* 4.6 4.7 - - + +
173G PHE* 4.1 23.7 - - + -
190G ASP* 2.8 40.8 + - - -
194G LEU* 3.5 25.0 + - - +
195G THR 2.7 29.7 + - - -
200G ASN* 3.2 45.0 + - - +
201G ARG 3.0 6.2 + - - +
202G PHE* 3.6 29.6 - - - +
204G GLU* 1.3 74.3 - - - +
206G ALA* 1.3 61.1 + - - +
208G ILE* 3.8 10.2 - - - +
209G MET* 3.1 32.7 + - - +
226G TRP* 3.7 10.3 - - + -
229G ASN 4.1 1.6 + - - -
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Residues in contact with ALA 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G PHE* 2.9 21.7 + - + +
203G GLU 3.4 6.7 - - - +
204G GLU 3.2 0.2 - - - -
205G ARG* 1.3 76.2 - - - +
207G GLU* 1.3 67.4 + - - +
209G MET* 3.3 1.7 + - - +
210G ALA* 2.9 25.1 + - - +
226G TRP* 3.6 23.3 - - + -
243G VAL* 4.0 13.2 - - + -
247G LEU* 3.6 19.3 - - + +
249G LEU* 4.1 4.7 - - + +
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Residues in contact with GLU 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G GLU* 3.0 23.6 + - + +
204G GLU* 3.8 7.9 - - - +
206G ALA* 1.3 76.1 - - - +
208G ILE* 1.3 65.5 + - + +
210G ALA* 3.3 10.1 + - - +
211G LYS* 3.3 15.5 + - - +
247G LEU* 3.4 29.9 - - + +
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Residues in contact with ILE 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G PRO* 3.3 42.2 - - + +
171G GLU* 4.4 3.4 - - + +
173G PHE* 4.5 9.0 - - + -
174G GLU* 3.5 47.6 - - + +
204G GLU* 3.3 17.4 + - + +
205G ARG* 3.8 7.6 - - + +
206G ALA 3.2 0.6 - - - -
207G GLU* 1.3 80.0 - - + +
209G MET* 1.3 61.4 + - - +
211G LYS* 3.0 17.1 + - - +
212G ILE* 2.8 30.2 + - + +
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Residues in contact with MET 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G PHE* 3.6 31.4 - - + -
177G ALA* 3.8 13.9 - - - -
181G LEU* 3.9 27.6 - - + -
188G MET* 4.0 10.3 - - + -
205G ARG 3.1 19.9 + - - +
206G ALA 3.3 1.1 + - - +
208G ILE* 1.3 79.5 - - - +
210G ALA* 1.3 56.5 + - - +
212G ILE* 4.2 6.7 - - + -
213G ILE* 2.8 50.3 + - + +
225G THR 4.4 1.1 - - - +
226G TRP* 3.6 52.0 - - + -
249G LEU* 4.8 0.4 - - + -
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Residues in contact with ALA 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G ALA 2.9 14.1 + - - +
207G GLU 3.4 11.2 - - - +
208G ILE 3.2 0.2 - - - -
209G MET* 1.3 79.3 - - - +
211G LYS* 1.3 58.9 + - + +
213G ILE* 4.1 2.0 - - - +
214G ASP* 3.5 26.5 + - - +
247G LEU* 4.2 33.9 - - + +
249G LEU* 4.0 14.3 - - + +
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Residues in contact with LYS 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G GLU* 2.4 32.7 + - - -
207G GLU 3.3 8.4 + - - +
208G ILE* 3.0 21.7 + - - +
210G ALA* 1.3 77.5 - - + +
212G ILE* 1.3 69.9 + - + +
213G ILE 3.3 0.4 - - - -
214G ASP* 3.8 5.6 - - - +
215G LYS* 2.9 30.3 + - - +
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Residues in contact with ILE 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G GLU* 4.0 22.2 - - + +
177G ALA* 4.4 4.7 - - + -
178G TYR* 4.1 39.5 - - + +
181G LEU* 4.2 15.7 - - + -
208G ILE* 2.8 35.0 + - + +
209G MET* 4.0 9.4 - - - +
211G LYS* 1.3 86.9 - - + +
213G ILE* 1.3 60.1 + - - +
215G LYS* 3.7 8.4 - - + +
216G VAL* 2.9 42.6 + - + +
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Residues in contact with ILE 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G LEU* 4.8 1.3 - - + -
209G MET* 2.8 39.0 + - + +
210G ALA* 4.1 3.6 - - - +
212G ILE* 1.3 78.7 - - - +
214G ASP* 1.3 63.8 + - - +
216G VAL* 4.2 1.4 - - - +
217G GLU* 2.9 47.8 + - + +
224G LYS* 3.6 29.4 - - + +
225G THR* 3.9 29.2 - - - -
226G TRP* 4.2 9.0 - - + +
249G LEU* 4.0 21.3 - - + -
250G LYS* 4.6 9.6 - - - +
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Residues in contact with ASP 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ALA 3.5 18.1 + - - +
211G LYS* 3.4 7.9 + - - +
212G ILE 3.3 0.2 - - - -
213G ILE* 1.3 81.5 - - - +
215G LYS* 1.3 66.6 + - - +
217G GLU* 3.8 11.5 - - - +
218G ASN* 3.0 24.3 + - - +
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Residues in contact with LYS 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G TYR* 3.5 29.4 - - + -
211G LYS* 2.9 19.0 + - - +
212G ILE* 3.7 11.4 - - + +
214G ASP* 1.3 75.4 - - - +
216G VAL* 1.3 64.1 + - - +
218G ASN* 3.0 7.5 + - - +
219G GLU* 2.9 52.0 + - + +
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Residues in contact with VAL 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G TYR* 3.6 26.9 - - + +
181G LEU* 3.9 21.5 - - + +
182G SER* 3.7 9.2 - - - +
212G ILE* 2.9 32.9 + - + +
213G ILE* 4.2 2.5 - - - +
215G LYS* 1.3 72.5 - - - +
217G GLU* 1.3 53.8 + - - +
219G GLU* 3.1 8.1 + - - -
220G THR* 2.7 49.5 + - + +
224G LYS* 3.8 36.1 - - + -
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Residues in contact with GLU 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G ILE* 2.9 36.4 + - + +
214G ASP* 3.8 11.9 - - - +
216G VAL* 1.3 76.6 - - - +
218G ASN* 1.3 56.9 + - - +
221G GLY* 2.7 31.9 + - - -
222G GLU 3.3 22.4 - - - +
223G LYS* 3.3 24.4 + - + +
224G LYS* 2.9 28.3 + - + +
250G LYS* 3.3 17.6 + - - -
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Residues in contact with ASN 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G ASP 3.0 16.5 + - - +
215G LYS* 3.0 8.3 + - - +
217G GLU* 1.3 77.0 - - - +
219G GLU* 1.3 63.1 + - + +
221G GLY* 4.5 1.4 + - - -
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Residues in contact with GLU 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G TYR* 2.4 32.0 + - - -
182G SER* 4.7 2.6 + - - -
215G LYS* 2.9 51.5 + - + +
216G VAL* 3.7 4.8 - - - +
218G ASN* 1.3 83.2 - - + +
220G THR* 1.3 65.3 + - + +
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Residues in contact with THR 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G LEU 5.1 1.3 - - - +
182G SER* 4.5 21.5 - - - +
216G VAL* 2.7 43.1 + - + +
219G GLU* 1.3 81.3 - - + +
221G GLY* 1.3 60.5 + - - +
222G GLU* 3.1 41.7 + - - +
224G LYS* 4.3 1.0 - - - -
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Residues in contact with GLY 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G GLU* 4.8 8.1 - - - +
217G GLU* 2.7 23.8 + - - -
218G ASN 4.5 1.3 + - - -
219G GLU 3.7 0.6 - - - -
220G THR* 1.3 72.4 - - - +
222G GLU* 1.3 60.8 + - - +
223G LYS* 4.1 1.4 + - - +
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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