Contacts of the helix formed by residues 196 - 212 (chain E) in PDB entry 3JSX
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 PRO 196 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C GLY 5.8 1.3 - - - +
190C TYR* 3.4 38.8 - - + +
191C SER* 3.5 11.9 - - - +
195C THR* 3.6 18.8 - - + +
203C ILE* 6.1 1.3 - - + -
194E HIS 3.6 5.6 - - - +
195E THR* 1.3 98.6 - - + +
197E ALA* 1.3 66.2 + - - +
198E ASP* 3.3 6.3 - - + +
199E ALA* 3.1 12.8 + - + +
200E ARG* 3.0 20.6 + - - +
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Residues in contact with ALA 197 (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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196E PRO* 1.3 71.9 - - - +
198E ASP* 1.3 63.5 + - - +
200E ARG* 3.2 31.5 + - - +
201E ILE* 3.1 30.1 + - + +
601E FAD 4.7 1.7 - - + -
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Residues in contact with ASP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLN* 5.5 5.0 + - - -
188C LEU 4.9 12.3 - - - +
190C TYR* 6.5 0.4 - - + -
203C ILE* 6.0 0.7 - - - -
196E PRO* 3.3 4.1 - - + +
197E ALA* 1.3 80.8 - - - +
199E ALA* 1.3 58.2 + - - +
201E ILE* 3.6 16.7 + - - +
202E GLN* 3.0 34.0 + - - +
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Residues in contact with ALA 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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195C THR* 4.4 5.8 - - + -
199C ALA* 4.4 15.6 - - + +
203C ILE* 4.5 12.1 - - + +
195E THR* 3.5 22.4 - - + -
196E PRO* 3.1 16.5 + - + +
198E ASP* 1.3 78.9 - - - +
200E ARG* 1.3 58.5 + - - +
201E ILE 3.2 0.2 - - - -
202E GLN* 3.1 16.0 - - + +
203E ILE* 3.0 30.0 + - - +
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Residues in contact with ARG 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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17E PHE* 3.7 9.1 - - + -
192E ILE* 3.4 37.7 - - + -
193E GLY 4.9 2.2 + - - -
195E THR* 3.0 36.6 + - + -
196E PRO* 3.0 8.5 + - - +
197E ALA* 3.2 38.0 + - - +
199E ALA* 1.3 73.7 - - - +
201E ILE* 1.3 64.9 + - - +
203E ILE* 3.6 9.0 - - + +
204E LEU* 2.9 32.5 + - - +
601E FAD 3.1 58.3 + - + -
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Residues in contact with ILE 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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197E ALA* 3.1 16.9 + - + +
198E ASP* 3.7 20.9 - - - +
199E ALA 3.2 0.2 - - - -
200E ARG* 1.3 75.0 - - - +
202E GLN* 1.3 65.9 + - + +
204E LEU* 3.5 9.3 + - - +
205E GLU* 3.3 28.6 + - + +
601E FAD 4.6 12.6 - - + +
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Residues in contact with GLN 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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202C GLN* 3.2 59.6 + - + +
203C ILE* 4.3 11.7 - - + +
206C GLY* 4.5 14.0 - - - +
198E ASP* 3.0 27.8 - - - +
199E ALA* 3.1 15.9 + - + +
201E ILE* 1.3 78.8 - - - +
203E ILE* 1.3 57.7 + - - +
205E GLU* 3.3 5.4 + - - +
206E GLY 3.1 24.1 + - - -
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Residues in contact with ILE 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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196C PRO* 5.7 2.5 - - + -
198C ASP* 5.6 4.7 - - - +
199C ALA* 4.4 20.0 - - + +
202C GLN* 5.1 4.5 - - + -
17E PHE* 3.4 26.2 - - + -
21E MET* 4.4 5.5 - - + +
187E GLN* 5.7 3.5 + - - +
189E THR* 3.8 30.3 - - + +
190E TYR 5.8 0.2 - - - +
192E ILE* 4.9 0.2 - - + -
195E THR* 3.9 25.1 - - + +
199E ALA 3.0 17.2 + - - +
200E ARG* 3.6 12.8 - - + +
201E ILE 3.2 0.2 - - - -
202E GLN* 1.3 76.3 - - + +
204E LEU* 1.3 63.9 + - - +
206E GLY* 4.1 1.2 - - - -
207E TRP* 3.3 22.0 + - - +
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Residues in contact with LEU 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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17E PHE* 3.4 21.8 - - + -
20E ALA* 3.9 12.1 - - + +
21E MET* 3.8 34.3 - - - +
24E ALA* 4.3 11.9 - - + +
200E ARG 2.9 29.5 + - - +
201E ILE* 3.8 8.3 - - - +
202E GLN 3.4 0.2 - - - -
203E ILE* 1.3 76.2 - - - +
205E GLU* 1.3 70.4 + - - +
207E TRP* 3.3 7.7 + - - +
208E LYS* 3.2 24.0 + - - +
601E FAD 3.4 33.7 - - + +
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Residues in contact with GLU 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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201E ILE* 3.3 23.4 + - + +
202E GLN* 3.3 5.8 + - - +
203E ILE 3.3 0.4 - - - -
204E LEU* 1.3 84.2 - - + +
206E GLY* 1.3 57.6 + - - +
208E LYS* 3.5 37.6 + - - +
209E LYS* 3.0 26.9 + - - +
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Residues in contact with GLY 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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202C GLN* 4.5 10.8 - - - -
187E GLN* 5.5 3.4 - - - -
202E GLN 3.1 15.1 + - - -
203E ILE* 3.5 2.0 + - - -
204E LEU 3.2 0.2 - - - -
205E GLU* 1.3 74.7 - - - +
207E TRP* 1.3 64.6 + - - +
209E LYS* 3.0 8.6 + - - +
210E ARG* 2.9 26.2 + - - +
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Residues in contact with TRP 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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21E MET* 3.4 53.8 + - + +
24E ALA* 4.6 3.4 - - + -
25E ALA* 3.5 23.7 - - + +
98E ILE* 4.2 15.7 - - + +
100E GLN* 4.3 2.4 + - - -
143E VAL* 4.3 17.3 - - + -
145E SER* 4.0 19.2 + - - -
187E GLN* 3.4 32.0 - - + +
203E ILE 3.3 6.2 + - - +
204E LEU 3.3 9.3 + - - +
206E GLY* 1.3 76.2 - - - +
208E LYS* 1.3 62.8 + - - +
209E LYS 3.1 0.9 + - - -
210E ARG* 3.3 35.3 + - - -
211E LEU* 3.1 54.3 + - + +
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Residues in contact with LYS 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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24E ALA* 3.4 42.8 - - + +
27E ALA* 4.9 7.8 - - - +
28E ALA* 3.6 35.5 - - + +
31E LYS* 6.2 2.6 - - - +
204E LEU* 3.2 6.7 + - + +
205E GLU* 3.6 39.2 + - - +
206E GLY 3.3 0.2 - - - -
207E TRP* 1.3 77.4 - - - +
209E LYS* 1.3 63.2 + - - +
211E LEU* 3.5 6.8 + - - +
212E GLU* 3.4 20.9 + - - +
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Residues in contact with LYS 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 GLU 3.0 14.5 + - - +
206E GLY* 3.0 14.5 + - - +
208E LYS* 1.3 74.4 - - - +
210E ARG* 1.3 67.1 + - - +
212E GLU* 2.8 57.9 + - - +
213E ASN 4.2 0.2 + - - -
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Residues in contact with ARG 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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143E VAL* 3.9 5.8 - - - +
184E LEU* 4.2 0.2 - - - +
185E GLU* 2.7 43.6 + - - +
186E PRO 4.2 0.6 - - - -
187E GLN* 2.8 44.8 + - - +
206E GLY 2.9 16.5 + - - +
207E TRP* 3.3 25.7 - - + +
209E LYS* 1.3 72.8 - - - +
211E LEU* 1.3 62.7 + - - +
212E GLU 3.0 1.2 + - - -
213E ASN* 3.1 5.7 + - - +
214E ILE* 3.1 31.6 + - + +
217E GLU* 2.8 42.8 + - - +
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Residues in contact with LEU 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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25E ALA* 3.5 40.6 - - + +
28E ALA* 4.8 4.9 - - + -
29E LEU* 3.7 38.4 - - + +
32E LYS* 5.9 0.5 - - - +
34E TRP* 4.6 4.2 + - - -
96E LEU* 6.0 0.7 - - + -
98E ILE* 4.3 4.5 - - + -
143E VAL* 5.9 0.4 - - + -
207E TRP* 3.1 59.9 + - + +
208E LYS* 3.6 8.3 - - - +
209E LYS 3.1 1.0 - - - -
210E ARG* 1.3 80.3 - - - +
212E GLU* 1.3 62.3 + - - +
213E ASN 3.1 1.3 + - - -
214E ILE* 3.6 29.6 + - + +
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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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28E ALA* 6.0 3.8 - - + +
32E LYS* 3.4 39.6 - - + +
34E TRP* 5.5 2.6 + - - -
208E LYS 3.4 11.6 + - - +
209E LYS* 2.8 54.9 + - - +
211E LEU* 1.3 78.2 - - - +
213E ASN* 1.3 77.9 + - - +
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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