Contacts of the helix formed by residues 201 - 221 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 5.0 4.8 - - - +
98E GLU 5.9 0.6 - - - +
98H GLU* 5.5 4.9 + - - -
131H LYS* 6.0 0.2 - - - +
196I SER* 3.1 27.8 + - - +
197I PRO* 3.2 15.3 + - - +
198I TRP* 3.6 30.4 + - - +
200I ASN* 1.3 74.6 - - - +
202I PHE* 1.3 65.8 + - - +
203I GLU* 4.4 5.2 - - + +
204I GLU* 3.4 37.2 + - + +
205I ARG* 3.0 21.1 + - - +
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Residues in contact with PHE 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I THR 4.3 1.3 - - - +
196I SER* 3.0 26.1 + - - +
200I ASN 3.7 2.0 + - - -
201I ARG* 1.3 71.2 - - - +
203I GLU* 1.3 56.8 + - + +
205I ARG* 3.2 23.4 + - - +
206I ALA* 2.8 34.3 + - + +
226I TRP* 4.2 2.4 - + - -
228I ALA* 3.5 33.0 - - + -
229I ASN 3.3 32.1 - - - -
230I ILE* 4.0 5.6 - - + -
240I ARG* 3.5 51.1 - - + +
243I VAL* 4.2 13.7 - - + -
244I LEU* 3.7 18.6 - - + -
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Residues in contact with GLU 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I ARG* 3.3 4.1 - - + +
202I PHE* 1.3 77.2 - - + +
204I GLU* 1.3 63.3 - - + +
206I ALA* 3.1 7.6 + - - +
207I GLU* 2.8 47.3 + - + +
240I ARG* 6.3 0.9 - - + -
243I VAL* 3.9 31.6 - - + +
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Residues in contact with GLU 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H ARG* 5.2 5.5 + - - -
170I PRO* 3.2 31.4 - - + +
198I TRP 5.6 0.9 - - - +
199I TYR 5.7 0.2 - - - -
200I ASN* 5.0 0.2 - - - -
201I ARG* 3.4 33.7 + - + +
202I PHE 3.4 0.4 - - - -
203I GLU* 1.3 76.7 - - + +
205I ARG* 1.3 62.9 + - - +
207I GLU* 3.4 14.2 + - - +
208I ILE* 3.0 33.9 + - + +
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Residues in contact with ARG 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I PRO* 5.1 1.7 - - - +
173I PHE* 3.4 33.8 - - + -
190I ASP* 3.0 38.8 + - - -
194I LEU* 3.8 21.0 + - - +
195I THR* 2.6 25.0 + - - +
200I ASN* 2.7 54.5 + - - +
201I ARG 3.0 20.2 + - - +
202I PHE* 3.4 27.2 - - - +
204I GLU* 1.3 75.9 - - - +
206I ALA* 1.3 57.3 - - - +
208I ILE* 3.5 4.4 + - - +
209I MET* 3.0 33.6 + - - +
226I TRP* 3.6 11.5 - - + -
229I ASN 4.3 0.8 + - - -
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Residues in contact with ALA 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I PHE* 2.8 23.1 + - + +
203I GLU 3.1 4.7 + - - +
205I ARG* 1.3 71.3 - - - +
207I GLU* 1.3 66.7 + - - +
209I MET* 3.2 2.6 + - - +
210I ALA* 3.0 24.1 + - - +
226I TRP* 3.4 24.2 - - + -
243I VAL* 3.9 15.7 - - + -
247I LEU* 3.5 20.9 - - + +
249I LEU* 4.0 5.8 - - + +
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Residues in contact with GLU 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I GLU* 2.8 32.9 + - + +
204I GLU* 3.9 14.3 - - - +
206I ALA* 1.3 71.9 - - - +
208I ILE* 1.3 62.5 + - + +
210I ALA* 3.5 4.2 + - - +
211I LYS* 3.2 23.8 + - - +
247I LEU* 3.9 22.4 - - + -
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Residues in contact with ILE 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I PRO* 3.1 45.5 - - + +
171I GLU* 4.5 1.6 - - + +
173I PHE* 4.2 13.9 - - + -
174I GLU* 3.5 47.3 - - + +
204I GLU* 3.0 21.0 + - + +
205I ARG* 3.7 4.0 - - - +
207I GLU* 1.3 77.7 - - + +
209I MET* 1.3 58.3 + - - +
211I LYS* 3.4 10.3 + - - +
212I ILE* 2.9 38.7 + - + +
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Residues in contact with MET 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I PHE* 3.3 32.3 - - + -
177I ALA* 3.9 13.2 - - + -
181I LEU* 4.0 19.7 - - + -
188I MET* 4.1 9.6 - - + -
205I ARG 3.0 20.6 + - - +
206I ALA 3.2 1.5 + - - +
208I ILE* 1.3 76.2 - - - +
210I ALA* 1.3 59.6 + - - +
212I ILE* 4.5 3.6 - - + -
213I ILE* 2.6 62.2 + - + +
225I THR 4.6 1.1 - - - +
226I TRP* 3.4 51.6 - - + -
249I LEU* 4.6 0.4 - - + -
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Residues in contact with ALA 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I ALA 3.0 16.3 + - - +
207I GLU 3.7 5.2 - - - +
209I MET* 1.3 76.2 - - - +
211I LYS* 1.3 63.5 + - - +
213I ILE* 3.9 1.8 - - - +
214I ASP* 3.1 33.8 + - - +
247I LEU* 4.3 33.4 - - + +
249I LEU* 4.0 14.6 - - + +
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Residues in contact with LYS 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I GLU* 3.5 33.2 + - - +
207I GLU 3.2 12.2 + - - +
208I ILE* 3.7 11.1 - - - +
210I ALA* 1.3 78.9 - - - +
212I ILE* 1.3 66.6 + - + +
214I ASP* 3.4 6.8 + - - +
215I LYS* 3.1 30.6 + - + +
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Residues in contact with ILE 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I GLU* 3.8 34.8 - - + +
177I ALA* 4.4 5.2 - - + -
178I TYR* 4.0 32.3 - - + +
181I LEU* 4.3 12.3 - - + -
208I ILE* 2.9 35.4 + - + +
209I MET* 4.1 6.3 - - + +
211I LYS* 1.3 81.5 - - + +
213I ILE* 1.3 60.8 + - - +
215I LYS* 4.5 8.1 - - + -
216I VAL* 2.9 45.3 + - + +
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Residues in contact with ILE 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I LEU* 4.7 6.1 - - + -
209I MET* 2.6 49.7 + - + +
210I ALA* 3.9 3.6 - - - +
212I ILE* 1.3 72.9 - - - +
214I ASP* 1.3 62.9 + - - +
216I VAL* 4.4 1.3 - - - +
217I GLU* 2.8 45.5 + - - +
224I LYS* 3.5 28.9 - - + +
225I THR* 4.0 27.1 - - - -
226I TRP* 4.1 3.1 - - + +
249I LEU* 3.8 24.5 - - + -
250I LYS* 4.7 9.0 - - + +
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Residues in contact with ASP 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I ALA* 3.1 24.7 + - - +
211I LYS* 3.6 6.1 - - - +
213I ILE* 1.3 79.4 - - - +
215I LYS* 1.3 63.2 + - - +
217I GLU* 3.7 10.0 - - - +
218I ASN* 3.0 23.4 + - - +
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Residues in contact with LYS 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178I TYR* 3.7 32.0 + - + -
211I LYS* 3.1 18.3 + - + +
212I ILE* 3.3 12.0 + - + +
214I ASP* 1.3 78.9 - - - +
216I VAL* 1.3 58.1 + - + +
218I ASN* 2.9 10.2 + - - +
219I GLU* 2.6 59.5 + - + +
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Residues in contact with VAL 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178I TYR* 3.7 29.2 - - + +
181I LEU* 3.9 22.2 - - + +
182I SER* 3.7 30.1 - - - +
212I ILE* 2.9 32.8 + - + +
213I ILE* 4.4 2.5 - - - +
215I LYS* 1.3 72.3 - - - +
217I GLU* 1.3 53.0 + - - +
219I GLU* 4.5 5.6 - - - +
220I THR* 2.5 49.0 + - + +
224I LYS* 4.1 13.0 - - + -
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Residues in contact with GLU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213I ILE* 2.8 31.2 + - + +
214I ASP* 3.7 10.6 - - - +
216I VAL* 1.3 76.9 - - - +
218I ASN* 1.3 56.1 + - - +
221I GLY* 2.7 32.6 + - - -
222I GLU 3.2 22.2 - - - +
223I LYS* 3.5 16.5 + - + +
224I LYS* 3.0 28.4 + - + +
250I LYS* 3.0 24.1 + - - -
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Residues in contact with ASN 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214I ASP 3.0 12.8 + - - +
215I LYS* 2.9 12.0 + - - +
217I GLU* 1.3 78.2 - - - +
219I GLU* 1.3 64.4 + - + +
221I GLY* 4.3 2.4 + - - -
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Residues in contact with GLU 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178I TYR* 2.6 26.6 + - - -
182I SER* 4.7 3.1 + - - -
215I LYS* 2.6 54.0 + - + +
216I VAL* 4.1 3.5 - - - +
218I ASN* 1.3 81.3 - - + +
220I THR* 1.3 65.9 + - + +
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Residues in contact with THR 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181I LEU 5.3 1.3 - - - +
182I SER* 4.6 20.2 - - - +
216I VAL* 2.5 36.8 + - + +
219I GLU* 1.3 85.9 - - + +
221I GLY* 1.3 64.9 + - - +
222I GLU* 3.3 35.0 + - - +
224I LYS* 4.7 1.8 - - - -
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Residues in contact with GLY 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I GLU* 5.4 3.8 - - - +
217I GLU* 2.7 25.4 + - - -
218I ASN 4.3 2.3 + - - -
219I GLU 3.7 0.6 - - - -
220I THR* 1.3 73.9 - - - +
222I GLU* 1.3 60.4 + - - +
223I LYS* 5.8 2.4 - - - -
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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