Contacts of the helix formed by residues 192 - 209 (chain N) in PDB entry 3J7Y
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 192 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82N PHE* 3.4 44.7 + - + +
84N GLU* 4.7 9.3 - - - +
85N GLY 3.1 26.1 + - - -
86N ASN* 3.1 32.3 + - - +
191N SER* 1.3 77.0 + - - +
193N GLY* 1.3 60.0 + - - +
195N LEU* 3.2 5.2 + - - +
196N GLU* 2.9 50.3 + - + +
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Residues in contact with GLY 193 (chain N).
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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191N SER* 3.4 4.2 + - - -
192N ARG* 1.3 80.0 - - - +
194N THR* 1.3 55.7 + - - +
196N GLU* 3.2 16.7 + - - +
197N LYS* 2.9 29.4 + - - +
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Residues in contact with THR 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173N GLN* 6.0 4.3 - - - +
188N LYS* 6.5 0.7 - - - -
190N VAL* 3.7 6.6 - - - +
191N SER* 2.7 48.8 + - - +
193N GLY* 1.3 75.6 - - - +
195N LEU* 1.3 58.1 + - - +
197N LYS* 3.2 10.7 + - - +
198N MET* 2.9 31.8 + - - +
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Residues in contact with LEU 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N THR 4.7 8.3 - - - +
81N GLU* 5.6 3.4 - - + -
82N PHE* 4.3 22.4 - - + -
90N LEU* 3.5 33.7 - - + -
159N LEU* 5.3 5.6 - - + -
190N VAL* 3.7 9.9 - - + -
191N SER 3.1 14.5 + - - +
192N ARG* 3.2 4.9 + - - +
194N THR* 1.3 81.3 + - - +
196N GLU* 1.3 59.6 + - + +
198N MET* 3.2 20.2 + - + +
199N ARG* 2.9 69.1 + - - +
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Residues in contact with GLU 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N ARG* 2.9 36.9 + - + +
193N GLY* 3.2 14.7 + - - +
195N LEU* 1.3 79.9 - - + +
197N LYS* 1.3 56.0 + - - +
199N ARG* 3.2 10.0 + - - +
200N LYS* 2.9 37.8 + - + +
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Residues in contact with LYS 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193N GLY 2.9 12.8 + - - +
194N THR* 3.4 12.8 - - - +
196N GLU* 1.3 75.3 - - - +
198N MET* 1.3 59.7 + - - +
200N LYS* 3.2 9.6 + - + +
201N ASP* 2.8 66.5 + - - +
204N GLU* 5.3 3.0 + - - -
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Residues in contact with MET 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90N LEU* 4.2 21.3 - - + -
92N LEU* 5.3 6.1 - - + -
188N LYS* 3.7 39.0 - - + +
190N VAL* 4.5 5.8 - - + -
194N THR* 2.9 12.1 + - - +
195N LEU* 3.2 25.3 + - + +
197N LYS* 1.3 77.2 - - - +
199N ARG* 1.3 66.3 + - + +
201N ASP* 3.2 10.3 + - - +
202N GLN* 2.9 45.6 + - + +
248N PRO* 6.5 0.7 - - - -
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Residues in contact with ARG 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N THR* 4.0 23.0 + - - -
81N GLU* 3.9 27.1 + - - +
90N LEU* 5.8 1.2 - - - +
157N GLY* 5.4 3.0 + - - -
195N LEU* 2.9 52.2 + - - +
196N GLU* 3.5 10.3 - - - +
198N MET* 1.3 80.6 - - + +
200N LYS* 1.3 57.8 + - + +
202N GLN* 3.2 10.4 + - + +
203N GLU* 2.9 35.2 + - + +
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Residues in contact with LYS 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196N GLU* 2.9 21.4 + - - +
197N LYS* 3.2 12.8 + - + +
199N ARG* 1.3 75.8 - - + +
201N ASP* 1.3 59.2 + - - +
203N GLU* 3.2 11.3 + - - +
204N GLU* 2.9 45.2 + - - +
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Residues in contact with ASP 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N LYS* 2.8 53.9 + - - +
198N MET* 3.4 12.3 - - - +
200N LYS* 1.3 77.3 - - - +
202N GLN* 1.3 56.7 + - + +
204N GLU* 3.2 21.6 + - - +
205N ARG* 2.9 33.6 + - + +
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Residues in contact with GLN 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198N MET* 2.9 31.3 + - + +
199N ARG* 3.4 12.1 - - - +
201N ASP* 1.3 76.3 - - + +
203N GLU* 1.3 56.7 + - + +
205N ARG* 3.2 10.3 + - - +
206N GLU* 2.9 32.2 + - - +
240N LYS* 4.0 19.4 + - - +
246N TYR* 3.1 26.2 + - - -
248N PRO* 3.6 29.8 + - - +
251N VAL* 5.0 4.1 - - + +
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Residues in contact with GLU 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199N ARG* 2.9 19.0 + - + +
200N LYS* 3.2 13.4 + - - +
202N GLN* 1.3 76.4 - - + +
204N GLU* 1.3 57.9 - - - +
206N GLU* 3.2 9.4 + - - +
207N ARG* 2.9 61.4 + - - +
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Residues in contact with GLU 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197N LYS* 5.3 2.3 + - - -
200N LYS* 2.9 37.3 + - - +
201N ASP* 3.4 21.1 + - - +
203N GLU* 1.3 74.9 - - - +
205N ARG* 1.3 54.3 + - + +
207N ARG* 3.2 16.5 + - - +
208N ASN* 2.6 48.9 + - - +
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Residues in contact with ARG 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I TYR* 3.6 60.6 - - + +
201N ASP* 2.9 18.1 + - + +
202N GLN* 3.4 12.6 - - - +
204N GLU* 1.3 77.3 - - + +
206N GLU* 1.3 63.7 + - - +
208N ASN* 4.4 0.7 - - - -
209N ASN* 3.2 23.9 + - - +
248N PRO 5.7 0.9 - - - -
249N LYS* 2.7 57.4 + - - +
251N VAL* 3.9 13.6 - - + +
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Residues in contact with GLU 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N GLN 2.9 12.9 + - - +
203N GLU* 3.3 12.6 - - - +
205N ARG* 1.3 74.8 - - - +
207N ARG* 1.3 63.9 + - + +
209N ASN* 3.3 15.2 - - - +
216N GLU* 3.3 26.5 - - - +
238N LYS* 4.4 12.9 + - - -
240N LYS* 5.1 4.8 + - - +
251N VAL* 3.5 30.5 - - + +
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Residues in contact with ARG 207 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203N GLU* 2.9 57.5 + - - +
204N GLU* 3.5 21.2 - - - +
206N GLU* 1.3 81.1 - - + +
208N ASN* 1.3 67.9 + - - +
209N ASN* 3.9 2.8 - - - +
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Residues in contact with ASN 208 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I TYR* 3.7 16.7 + - - +
56I PRO* 3.2 33.4 - - + +
204N GLU* 2.6 29.7 + - - +
205N ARG 4.0 1.6 - - - +
207N ARG* 1.3 77.9 - - - +
209N ASN* 1.3 70.0 + - - +
210N GLN* 3.3 15.1 + - - +
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Residues in contact with ASN 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I GLU 4.9 2.2 + - - -
53I TYR* 3.7 24.5 - - + -
54I ILE 3.5 17.3 - - - +
205N ARG 3.2 7.7 + - - +
206N GLU* 3.3 17.2 - - - +
207N ARG 3.9 2.9 - - - +
208N ASN* 1.3 77.4 - - - +
210N GLN* 1.3 61.4 + - - +
211N ASN* 3.2 24.8 + - - +
213N TRP 5.0 0.8 + - - -
214N THR* 3.8 25.1 - - - +
251N VAL 4.2 14.9 + - - -
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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