Contacts of the helix formed by residues 197 - 212 (chain E) in PDB entry 5AJI
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 ASP 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195E ASP 3.8 1.2 + - - -
196E SER* 1.3 70.5 - - - +
198E ILE* 1.3 68.9 + - - +
199E ASP* 3.0 20.5 + - - +
200E GLN* 3.7 32.0 + - + +
201E VAL* 3.0 27.4 + - - +
266E ILE* 6.1 0.2 - - - +
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Residues in contact with ILE 198 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194E TYR 6.0 1.1 - - - +
196E SER 3.3 11.6 + - - +
197E ASP* 1.3 74.4 + - - +
199E ASP* 1.3 67.8 + - - +
201E VAL* 3.8 1.7 - - - +
202E LYS* 3.2 45.9 + - + +
225E LEU* 4.5 24.5 - - + -
233E ILE* 5.8 4.9 - - + -
235E PHE* 4.2 22.9 - - + -
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Residues in contact with ASP 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E ASP* 3.0 13.7 + - - +
198E ILE* 1.3 82.8 - - - +
200E GLN* 1.3 60.0 + - - +
202E LYS* 3.7 11.8 + - - +
203E GLN* 2.9 29.3 + - - +
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Residues in contact with GLN 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E ASP* 3.2 30.7 + - + +
199E ASP* 1.3 77.0 - - - +
201E VAL* 1.3 68.1 + - - +
203E GLN* 3.1 7.5 + - + +
204E ILE* 2.9 35.9 + - + +
264E ALA* 3.9 27.1 + - - +
266E ILE* 4.0 19.4 - - - +
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Residues in contact with VAL 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E VAL* 4.3 5.2 - - + -
196E SER* 3.8 21.1 - - - -
197E ASP 3.0 21.1 + - - +
198E ILE 3.8 4.0 - - - +
200E GLN* 1.3 75.7 - - - +
202E LYS* 1.3 63.1 + - - +
204E ILE* 3.7 2.0 - - - +
205E LEU* 3.0 33.6 + - + +
235E PHE* 3.3 41.5 - - + -
261E PHE* 4.0 13.5 - - + -
266E ILE* 3.8 26.0 - - + -
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Residues in contact with LYS 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ILE* 3.2 34.9 + - + +
199E ASP* 3.7 12.6 + - - +
201E VAL* 1.3 76.6 - - - +
203E GLN* 1.3 59.5 + - - +
205E LEU* 3.4 1.4 + - - +
206E THR* 2.8 37.1 + - - +
223E VAL* 4.0 35.3 - - + +
224E ARG* 4.5 13.9 - - - +
225E LEU* 4.5 13.0 - - - +
235E PHE* 4.1 12.1 - - + -
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Residues in contact with GLN 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ASP 2.9 19.0 + - - +
200E GLN* 3.5 7.6 - - - +
202E LYS* 1.3 75.9 - - - +
204E ILE* 1.3 59.7 + - + +
206E THR* 3.2 10.8 + - - +
207E ASN* 2.8 56.8 + - - +
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Residues in contact with ILE 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E GLN* 2.9 26.2 + - + +
201E VAL 3.7 3.4 - - - +
203E GLN* 1.3 77.7 - - + +
205E LEU* 1.3 64.4 + - - +
207E ASN* 3.1 13.5 + - - +
208E ILE* 3.0 27.2 + - + +
260E GLU* 3.8 26.7 - - + +
261E PHE* 3.6 18.6 - - + -
264E ALA* 3.6 22.7 - - + -
266E ILE* 3.4 32.3 - - + -
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Residues in contact with LEU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ILE* 4.8 5.2 - - + -
201E VAL* 3.0 35.9 + - + +
202E LYS 3.8 3.8 - - - +
204E ILE* 1.3 76.5 - - - +
206E THR* 1.3 62.9 + - - +
208E ILE* 3.2 8.3 + - + +
209E ILE* 3.1 28.0 + - + +
223E VAL* 3.8 19.1 - - + -
235E PHE* 4.2 13.2 - - + -
237E VAL* 3.8 27.8 - - + -
257E ILE* 3.7 37.9 - - + -
261E PHE* 3.8 19.7 - - + -
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Residues in contact with THR 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E LYS* 2.8 24.8 + - - +
203E GLN* 3.6 12.8 - - - +
205E LEU* 1.3 73.0 - - - +
207E ASN* 1.3 57.8 + - - +
209E ILE* 3.3 12.5 + - + +
210E GLN* 2.8 55.8 + - + +
223E VAL* 3.8 17.4 - - - +
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Residues in contact with ASN 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E GLN* 2.8 49.1 + - - +
204E ILE* 3.5 12.2 - - - +
206E THR* 1.3 77.2 - - - +
208E ILE* 1.3 64.8 + - + +
210E GLN* 3.4 7.9 + - - +
211E SER* 3.1 26.5 + - - -
256E ARG* 4.4 1.7 + - - +
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Residues in contact with ILE 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E ILE* 3.0 29.3 + - + +
205E LEU* 3.2 10.7 + - + +
207E ASN* 1.3 76.6 - - + +
209E ILE* 1.3 62.1 + - + +
211E SER* 3.1 15.9 + - - -
212E GLU* 3.3 10.4 + - - +
253E VAL* 4.0 28.5 - - + -
256E ARG* 3.3 40.4 + - + +
257E ILE* 3.9 28.0 - - + +
260E GLU* 3.7 30.5 - - + +
261E PHE* 5.1 0.2 - - + -
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Residues in contact with ILE 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LEU* 3.1 12.2 + - + +
206E THR* 3.3 18.2 - - + +
208E ILE* 1.3 79.0 - - + +
210E GLN* 1.3 66.6 + - + +
212E GLU* 3.7 7.3 - - - +
215E ILE* 3.8 31.3 - - + +
217E LYS* 3.3 16.5 - - - -
221E MET* 4.1 23.9 - - + +
223E VAL* 3.6 27.8 - - + -
237E VAL* 4.1 18.6 - - + -
239E VAL* 3.7 21.1 - - + -
253E VAL* 4.7 9.2 - - + -
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E THR* 2.8 42.2 + - + +
207E ASN* 3.7 8.7 - - - +
209E ILE* 1.3 79.7 - - + +
211E SER* 1.3 56.3 + - - +
217E LYS* 3.0 38.4 + - - +
221E MET* 3.7 25.9 - - - +
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Residues in contact with SER 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ASN 3.1 11.0 + - - -
208E ILE 3.1 2.3 + - - -
210E GLN* 1.3 74.8 - - - +
212E GLU* 1.3 61.5 - - - +
213E ASP* 3.4 5.9 + - - +
256E ARG* 2.7 43.3 + - - -
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Residues in contact with GLU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E ILE 3.3 14.4 + - - +
209E ILE 4.1 0.2 - - - +
210E GLN 3.3 1.2 - - - -
211E SER* 1.3 76.1 - - - +
213E ASP* 1.3 65.5 + - - +
214E ARG* 2.9 53.3 + - + +
215E ILE* 3.3 40.3 + - + +
217E LYS* 3.1 19.4 + - - -
249E VAL* 4.3 9.9 - - + -
252E ASP* 4.6 8.5 - - - +
253E VAL* 4.4 9.5 - - + +
256E ARG* 4.5 12.3 + - - +
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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
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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