Contacts of the helix formed by residues 201 - 221 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D GLU* 4.8 6.3 + - - +
98D GLU* 5.0 13.7 + - - +
98I GLU* 5.1 4.2 + - - -
131I LYS* 6.0 0.4 - - - +
170J PRO* 4.5 0.4 - - - +
196J SER* 2.8 37.5 + - - -
197J PRO* 3.6 12.2 - - - +
198J TRP* 3.6 32.8 + - - +
200J ASN* 1.3 72.1 + - - +
202J PHE* 1.3 66.5 + - - +
203J GLU* 3.6 20.2 - - - +
204J GLU* 2.9 50.8 + - + +
205J ARG* 3.2 12.9 + - - +
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Residues in contact with PHE 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195J THR 4.1 2.5 - - - +
196J SER* 2.8 27.0 + - - +
200J ASN 3.5 3.0 + - - -
201J ARG* 1.3 71.4 - - - +
203J GLU* 1.3 69.3 + - + +
205J ARG* 3.4 23.1 + - - +
206J ALA* 3.0 21.3 + - + +
226J TRP* 4.4 2.0 - + - -
228J ALA* 3.7 21.1 - - + -
229J ASN 3.4 30.7 - - - -
230J ILE* 4.0 4.3 - - + -
240J ARG* 3.5 49.1 - - + +
243J VAL* 4.1 11.7 - - + -
244J LEU* 3.7 34.8 - - + -
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Residues in contact with GLU 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J SER* 3.9 5.7 + - - -
201J ARG* 3.6 25.2 - - - +
202J PHE* 1.3 88.9 + - - +
204J GLU* 1.3 68.9 + - + +
206J ALA* 3.7 5.3 - - - +
207J GLU* 3.1 36.4 + - + +
240J ARG* 5.8 1.4 + - - +
243J VAL* 4.4 21.9 - - + +
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Residues in contact with GLU 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I ARG* 4.5 20.5 + - - +
170J PRO* 3.7 23.6 - - + +
171J GLU* 4.9 2.8 - - - +
198J TRP 5.7 1.1 - - - +
199J TYR 6.1 0.2 - - - -
201J ARG* 2.9 38.4 + - + +
203J GLU* 1.3 86.7 - - + +
205J ARG* 1.3 59.9 + - - +
207J GLU* 3.6 10.9 + - - +
208J ILE* 3.3 28.5 + - + +
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Residues in contact with ARG 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J TYR* 5.8 0.2 - - - -
170J PRO* 4.4 5.1 - - + +
173J PHE* 4.3 24.0 - - + -
190J ASP* 2.8 41.5 + - - -
194J LEU* 3.7 25.4 + - - +
195J THR 2.8 24.4 + - - -
200J ASN* 3.0 51.4 + - - +
201J ARG 3.2 1.8 + - - +
202J PHE* 3.6 26.4 - - - +
204J GLU* 1.3 76.7 - - - +
206J ALA* 1.3 62.7 + - - +
208J ILE* 3.7 9.9 - - - +
209J MET* 2.9 35.5 + - - +
226J TRP* 3.7 10.5 - - + -
229J ASN 4.1 1.2 + - - -
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Residues in contact with ALA 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202J PHE* 3.0 21.8 + - + +
203J GLU 3.7 6.1 - - - +
204J GLU 3.2 0.2 - - - -
205J ARG* 1.3 76.6 - - - +
207J GLU* 1.3 59.9 + - - +
209J MET* 3.3 1.4 + - - +
210J ALA* 2.9 30.3 + - - +
226J TRP* 3.5 24.9 - - + -
243J VAL* 3.9 14.4 - - + -
247J LEU* 3.6 18.4 - - + +
249J LEU* 3.9 5.4 - - + +
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Residues in contact with GLU 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J GLU* 3.1 22.8 + - + +
204J GLU* 3.9 9.6 - - - +
206J ALA* 1.3 77.1 - - - +
208J ILE* 1.3 62.9 + - + +
210J ALA* 3.4 4.5 + - - +
211J LYS* 3.3 22.3 + - - +
243J VAL* 6.1 0.4 - - + -
247J LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J PRO* 3.4 44.0 - - + +
171J GLU* 4.2 6.1 - - + +
173J PHE* 5.0 3.6 - - + -
174J GLU* 3.8 43.5 - - + +
204J GLU* 3.3 14.5 + - + +
205J ARG* 3.7 6.1 - - - +
206J ALA 3.2 0.6 - - - -
207J GLU* 1.3 80.1 - - + +
209J MET* 1.3 64.2 + - - +
211J LYS* 3.2 11.9 - - - +
212J ILE* 2.9 38.0 + - + +
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Residues in contact with MET 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J PHE* 3.4 34.3 - - + -
177J ALA* 3.8 11.9 - - - -
181J LEU* 4.0 26.9 - - + -
188J MET* 4.4 9.4 - - + -
205J ARG 2.9 22.0 + - - +
206J ALA 3.9 1.3 - - - +
208J ILE* 1.3 76.2 - - - +
210J ALA* 1.3 59.9 + - - +
212J ILE* 4.2 5.4 - - + -
213J ILE* 2.9 47.3 + - + +
225J THR 4.7 0.9 - - - +
226J TRP* 3.7 52.5 - - + -
249J LEU* 4.4 1.1 - - - -
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Residues in contact with ALA 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206J ALA 2.9 16.9 + - - +
207J GLU 3.6 7.4 - - - +
208J ILE 3.2 0.2 - - - -
209J MET* 1.3 77.8 - - - +
211J LYS* 1.3 57.5 + - - +
213J ILE* 4.1 1.8 - - - +
214J ASP* 3.0 32.8 + - - +
247J LEU* 4.1 35.7 - - + +
249J LEU* 3.9 14.5 - - + +
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Residues in contact with LYS 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J GLU* 2.6 33.2 + - - -
207J GLU 3.3 9.4 + - - +
208J ILE* 3.2 18.9 - - - +
210J ALA* 1.3 78.3 - - - +
212J ILE* 1.3 72.7 + - + +
213J ILE 3.2 0.4 - - - -
214J ASP* 3.2 8.2 + - - +
215J LYS* 2.9 30.9 + - + +
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Residues in contact with ILE 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174J GLU* 3.8 31.6 - - + +
177J ALA* 4.4 4.0 - - + -
178J TYR* 4.0 42.8 - - + +
181J LEU* 4.2 13.5 - - + -
208J ILE* 2.9 35.3 + - + +
209J MET* 4.1 9.2 - - + +
211J LYS* 1.3 88.4 - - + +
213J ILE* 1.3 58.6 + - - +
215J LYS* 3.3 10.4 + - + +
216J VAL* 2.9 37.1 + - + +
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Residues in contact with ILE 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181J LEU* 4.7 2.5 - - + -
209J MET* 2.9 37.3 + - + +
210J ALA* 4.1 4.0 - - - +
212J ILE* 1.3 74.0 - - - +
214J ASP* 1.3 70.7 + - - +
216J VAL* 4.0 3.9 - - - +
217J GLU* 2.9 45.7 + - + +
224J LYS* 3.7 25.8 - - + +
225J THR* 3.7 31.6 - - - +
226J TRP* 4.2 8.1 - - + +
249J LEU* 4.1 19.3 - - + -
250J LYS* 4.4 10.1 - - + +
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Residues in contact with ASP 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J ALA* 3.0 17.8 + - - +
211J LYS* 3.2 10.1 + - - +
213J ILE* 1.3 82.5 - - - +
215J LYS* 1.3 58.0 + - - +
217J GLU* 3.7 10.2 - - - +
218J ASN* 3.0 31.6 + - - +
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Residues in contact with LYS 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J TYR* 3.4 35.6 + - + -
211J LYS* 2.9 19.4 + - + +
212J ILE* 3.6 13.7 - - + +
214J ASP* 1.3 78.0 - - - +
216J VAL* 1.3 57.8 + - - +
218J ASN* 3.2 5.9 + - - +
219J GLU* 2.7 62.8 + - - +
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Residues in contact with VAL 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178J TYR* 3.5 28.3 - - + +
181J LEU* 3.7 34.1 - - + +
182J SER* 3.7 9.9 - - - +
212J ILE* 2.9 30.6 + - + +
213J ILE* 4.1 2.9 - - - +
215J LYS* 1.3 73.2 - - - +
217J GLU* 1.3 57.3 + - - +
219J GLU* 4.5 6.7 - - - +
220J THR* 2.8 43.3 + - + +
224J LYS* 3.8 23.3 - - + -
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Residues in contact with GLU 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J ILE* 2.9 32.7 + - + +
214J ASP* 3.7 10.9 - - - +
216J VAL* 1.3 74.8 - - - +
218J ASN* 1.3 58.5 + - - +
221J GLY* 2.7 32.4 + - - -
222J GLU 3.2 21.8 - - - +
223J LYS* 3.3 19.8 + - - +
224J LYS* 3.0 18.2 + - + +
250J LYS* 2.7 33.8 + - - -
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Residues in contact with ASN 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J ASP 3.0 18.6 + - - +
215J LYS* 3.7 6.0 - - - +
217J GLU* 1.3 76.7 - - - +
219J GLU* 1.3 63.5 + - - +
221J GLY* 4.5 1.9 + - - -
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Residues in contact with GLU 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J TYR* 2.5 30.6 + - - -
182J SER* 4.8 2.1 + - - -
215J LYS* 2.7 52.0 + - + +
216J VAL* 4.1 4.2 - - - +
218J ASN* 1.3 85.5 - - + +
220J THR* 1.3 65.9 + - + +
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Residues in contact with THR 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J LEU 5.2 0.7 - - - +
182J SER* 4.6 20.6 - - - +
216J VAL* 2.8 36.0 + - + +
219J GLU* 1.3 85.6 - - + +
221J GLY* 1.3 59.0 + - - +
222J GLU* 3.1 41.4 + - - +
224J LYS* 4.4 1.4 - - - -
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Residues in contact with GLY 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J GLU* 4.9 7.1 - - - +
217J GLU* 2.7 22.2 + - - -
218J ASN 4.4 2.1 + - - -
219J GLU 3.7 0.6 - - - -
220J THR* 1.3 73.5 - - - +
222J GLU* 1.3 60.6 + - - +
223J LYS* 4.1 2.6 + - - +
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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