Contacts of the helix formed by residues 201 - 221 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 6.0 1.6 + - - -
170C PRO* 4.6 4.8 - - - +
196C SER* 2.7 36.9 + - - +
197C PRO* 3.5 8.4 - - - +
198C TRP* 3.5 36.1 + - - +
200C ASN* 1.3 74.3 + - - +
202C PHE* 1.3 66.0 + - - +
203C GLU* 4.4 4.5 - - + +
204C GLU* 3.0 44.5 + - + +
205C ARG* 3.2 12.9 + - - -
97F GLU* 4.8 5.1 - - - +
98F GLU* 5.6 7.1 + - - +
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Residues in contact with PHE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C THR 4.1 1.8 - - - +
196C SER* 2.9 26.1 + - - +
200C ASN 3.6 1.6 + - - -
201C ARG* 1.3 71.4 - - - +
203C GLU* 1.3 63.4 + - + +
205C ARG* 3.5 22.9 + - - +
206C ALA* 3.0 32.9 + - + +
226C TRP* 4.5 2.7 - + - -
228C ALA* 3.6 19.1 - - + -
229C ASN 3.5 29.6 - - - -
230C ILE* 4.0 5.8 - - + -
240C ARG* 3.4 56.5 - - + +
243C VAL* 4.1 17.0 - - + -
244C LEU* 3.7 22.0 - - + -
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ARG* 3.2 4.7 - - + +
202C PHE* 1.3 85.2 - - + +
204C GLU* 1.3 60.7 + - + +
206C ALA* 3.7 3.9 - - - +
207C GLU* 3.1 36.8 + - - +
243C VAL* 4.5 19.4 - - + +
247C LEU* 5.1 0.2 - - - +
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 4.4 11.2 + - - +
358B SER* 5.6 0.3 + - - -
170C PRO* 3.6 27.1 - - + +
171C GLU* 4.4 7.6 - - - +
198C TRP 5.5 0.2 - - - +
201C ARG* 3.0 35.9 + - + +
203C GLU* 1.3 79.7 - - + +
205C ARG* 1.3 58.1 + - - +
207C GLU* 3.3 9.6 + - - +
208C ILE* 3.0 32.7 + - + +
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PRO* 4.6 5.8 - - + +
173C PHE* 4.1 25.6 - - + -
190C ASP* 3.0 38.9 + - - -
194C LEU* 3.5 28.6 + - - +
195C THR* 2.7 24.9 + - - +
200C ASN* 2.9 51.7 + - - +
201C ARG 3.2 1.6 + - - -
202C PHE* 3.7 26.3 - - - +
204C GLU* 1.3 77.1 - - - +
206C ALA* 1.3 58.1 + - - +
208C ILE* 3.4 10.5 - - - +
209C MET* 2.7 38.5 + - - +
226C TRP* 3.8 9.7 - - + -
229C ASN 4.1 1.2 + - - -
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PHE* 3.0 24.4 + - + +
203C GLU 3.7 5.2 - - - +
205C ARG* 1.3 78.3 - - - +
207C GLU* 1.3 57.4 + - - +
209C MET* 3.2 2.8 + - - +
210C ALA* 2.9 29.5 + - - +
226C TRP* 3.2 27.6 - - + -
243C VAL* 4.2 12.3 - - + -
244C LEU* 4.6 0.2 - - + -
247C LEU* 3.8 17.3 - - + +
249C LEU* 3.9 4.2 - - + +
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Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C GLU* 3.1 24.1 + - - +
204C GLU* 3.6 7.2 - - - +
205C ARG 3.3 0.2 - - - -
206C ALA* 1.3 75.8 - - - +
208C ILE* 1.3 62.5 + - + +
210C ALA* 3.6 3.5 + - - +
211C LYS* 3.4 21.3 + - - +
247C LEU* 3.8 28.6 - - + +
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PRO* 3.2 44.9 - - + +
171C GLU* 4.2 3.6 - - + +
173C PHE* 4.6 8.1 - - + -
174C GLU* 3.6 48.0 - - + +
204C GLU* 3.0 15.5 + - + +
205C ARG* 3.4 11.2 - - + +
207C GLU* 1.3 75.8 - - + +
209C MET* 1.3 61.7 + - - +
211C LYS* 3.3 5.2 + - - +
212C ILE* 2.8 37.1 + - + +
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Residues in contact with MET 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 3.4 33.7 - - + -
177C ALA* 3.8 13.5 - - + -
181C LEU* 3.9 22.4 - - + -
188C MET* 4.2 6.5 - - + -
205C ARG 2.7 22.8 + - - +
206C ALA 3.7 0.9 - - - +
208C ILE* 1.3 73.4 - - - +
210C ALA* 1.3 58.5 + - - +
212C ILE* 4.3 4.9 - - + -
213C ILE* 2.7 59.0 + - + +
225C THR 4.6 0.4 - - - +
226C TRP* 3.5 54.3 - - + -
249C LEU* 4.8 0.2 - - + -
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA 2.9 17.0 + - - +
207C GLU 3.8 6.3 - - - +
209C MET* 1.3 77.5 - - - +
211C LYS* 1.3 60.4 + - - +
213C ILE* 4.0 1.3 - - - +
214C ASP* 3.2 32.2 + - - +
247C LEU* 4.1 32.1 - - + +
249C LEU* 3.8 20.1 - - + +
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C GLU 3.4 10.3 + - - +
208C ILE* 3.3 8.4 + - - +
209C MET 3.2 0.6 - - - -
210C ALA* 1.3 77.2 - - - +
212C ILE* 1.3 68.9 + - + +
214C ASP* 3.3 6.3 + - - +
215C LYS* 3.0 25.0 + - - +
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLU* 3.7 39.5 - - + +
177C ALA* 4.4 5.8 - - + -
178C TYR* 3.9 43.3 - - + +
181C LEU* 4.3 12.8 - - + -
208C ILE* 2.8 25.8 + - + +
209C MET* 3.9 7.0 - - + +
211C LYS* 1.3 80.4 - - + +
213C ILE* 1.3 61.8 + - - +
215C LYS* 3.5 10.0 + - + +
216C VAL* 3.1 30.0 + - + +
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Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C LEU* 4.7 2.0 - - + -
209C MET* 2.7 40.8 + - + +
210C ALA* 4.0 3.6 - - - +
212C ILE* 1.3 74.6 - - - +
214C ASP* 1.3 69.0 + - - +
216C VAL* 4.1 1.4 - - - +
217C GLU* 3.0 54.7 + - + +
224C LYS* 3.7 18.8 - - + +
225C THR* 3.7 30.3 - - - +
226C TRP* 4.1 8.7 - - + +
249C LEU* 3.9 22.0 - - + -
250C LYS* 4.9 8.3 - - + +
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Residues in contact with ASP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ALA* 3.2 18.5 + - - +
211C LYS* 3.8 5.3 - - - +
213C ILE* 1.3 84.7 - - - +
215C LYS* 1.3 61.3 + - - +
217C GLU* 3.8 9.1 + - - +
218C ASN* 3.1 36.7 + - - +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C TYR* 3.9 29.9 + - + -
211C LYS 3.0 17.5 + - - +
212C ILE* 3.8 12.6 - - + +
213C ILE 3.2 0.2 - - - -
214C ASP* 1.3 75.5 - - - +
216C VAL* 1.3 65.7 + - - +
218C ASN* 3.2 8.6 + - - +
219C GLU* 3.0 54.4 + - + +
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.7 22.2 - - + +
181C LEU* 3.9 17.0 - - + +
182C SER* 3.6 18.8 - - - +
212C ILE* 3.1 25.0 + - + +
213C ILE 4.1 2.0 - - - +
215C LYS* 1.3 75.7 - - - +
217C GLU* 1.3 58.6 + - - +
219C GLU* 3.1 6.9 + - - +
220C THR* 2.9 47.0 + - + +
224C LYS* 3.8 34.5 - - + -
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Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ILE* 3.0 32.1 + - - +
214C ASP* 4.1 9.1 - - - +
216C VAL* 1.3 76.0 - - - +
218C ASN* 1.3 57.6 + - - +
221C GLY* 2.7 32.6 + - - -
222C GLU 3.2 21.5 - - - +
223C LYS* 3.5 20.9 + - + +
224C LYS* 2.6 33.9 + - + +
250C LYS* 2.9 21.8 + - - -
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Residues in contact with ASN 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ASP* 3.1 24.9 + - - +
215C LYS* 3.2 7.5 + - - +
216C VAL 3.2 0.4 - - - -
217C GLU* 1.3 81.8 - - - +
219C GLU* 1.3 61.6 + - + +
220C THR 3.6 0.3 + - - -
221C GLY* 4.2 2.8 + - - -
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 2.8 31.3 + - - -
182C SER* 4.7 2.3 + - - -
215C LYS* 3.0 47.0 + - + +
216C VAL* 3.9 4.8 - - - +
218C ASN* 1.3 78.8 - - + +
220C THR* 1.3 65.8 + - + +
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Residues in contact with THR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LEU 5.3 1.3 - - - +
182C SER* 4.8 18.8 - - - +
216C VAL* 2.9 37.4 + - + +
219C GLU* 1.3 85.4 - - + +
221C GLY* 1.3 58.8 + - - +
222C GLU* 3.0 41.2 + - - +
224C LYS* 4.6 0.7 - - - -
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Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLU* 4.9 7.6 - - - +
217C GLU 2.7 17.1 + - - -
218C ASN 4.2 2.9 + - - -
219C GLU 3.8 0.6 - - - -
220C THR* 1.3 77.7 - - - +
222C GLU* 1.3 60.0 + - - +
223C LYS* 4.2 3.0 + - - +
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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
------------------------------------------------------------
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