Contacts of the helix formed by residues 198 - 215 (chain B) in PDB entry 1JZO
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LYS* 4.7 4.3 - - - +
107B GLN* 4.7 2.9 - - - +
111B TYR* 3.7 0.4 - - - -
196B TYR* 3.3 31.2 - - + +
197B GLN* 1.3 88.3 - - + +
199B PRO* 1.3 71.3 - - + +
200B LYS 3.5 0.9 - - - +
201B GLU* 3.2 35.9 + - + +
202B MET* 2.8 26.3 + - - +
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Residues in contact with PRO 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLN* 3.6 30.7 - - + +
110B ASP* 3.6 29.6 - - + +
111B TYR* 3.4 32.7 - - + +
114B LEU* 3.4 19.1 - - + +
116B ILE* 4.2 2.3 - - - +
198B PRO* 1.3 86.2 - - + +
200B LYS* 1.3 60.2 + - + +
202B MET* 3.6 2.1 - - - +
203B LYS* 2.9 30.5 + - - +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.9 17.2 - - + +
198B PRO* 3.5 0.6 - - - +
199B PRO* 1.3 78.7 - - + +
201B GLU* 1.3 67.2 + - - +
203B LYS* 3.3 3.4 + - - +
204B GLU* 3.0 28.8 + - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLN* 3.7 9.1 - - + +
198B PRO* 3.2 43.8 + - + +
200B LYS* 1.3 83.1 - - - +
202B MET* 1.3 57.5 + - - +
204B GLU* 3.3 14.6 + - - +
205B PHE* 2.8 31.5 + - - +
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 4.4 17.9 - - + -
104B LEU* 5.3 8.5 - - + -
111B TYR* 4.0 16.2 - - + +
116B ILE* 3.8 15.0 - - + -
185B VAL* 4.0 27.6 - - + -
195B GLY 5.0 0.4 - - - +
197B GLN* 3.7 51.7 + - + +
198B PRO 2.8 18.2 + - - +
199B PRO 3.6 4.0 - - - +
201B GLU* 1.3 76.8 - - - +
203B LYS* 1.3 58.5 + - - +
205B PHE* 3.4 4.4 + - - +
206B LEU* 2.9 49.5 + - + +
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 4.6 11.7 - - - +
88B HIS* 4.0 16.6 - - + -
114B LEU* 2.9 43.7 - - + +
116B ILE* 3.8 11.4 - - + +
199B PRO 2.9 17.6 + - - +
200B LYS* 3.6 5.2 - - - +
202B MET* 1.3 74.7 - - - +
204B GLU* 1.3 66.0 + - - +
206B LEU* 3.4 1.5 + - - -
207B ASP* 2.7 62.0 + - - +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LYS 3.0 16.5 + - - +
201B GLU* 3.7 12.7 - - - +
203B LYS* 1.3 76.9 - - - +
205B PHE* 1.3 58.2 + - - +
207B ASP* 3.2 6.5 + - - +
208B GLU* 2.9 50.8 + - + +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B VAL* 6.1 1.1 - - + -
187B LEU* 4.5 10.3 - - + -
193B VAL* 3.8 37.0 - - + -
197B GLN* 3.3 30.1 - - - +
201B GLU 2.8 18.1 + - - +
202B MET* 3.5 4.5 - - - +
204B GLU* 1.3 78.5 - - - +
206B LEU* 1.3 79.7 + - + +
208B GLU* 3.4 5.6 + - + +
209B HIS* 2.8 40.9 + - + +
212B MET* 5.9 5.2 - - + -
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B HIS* 3.5 44.4 - - + +
90B ILE* 3.8 20.0 - - + -
116B ILE* 3.9 22.2 - - + -
185B VAL* 5.6 0.2 - - + -
187B LEU* 3.8 30.7 - - + -
202B MET* 2.9 33.8 + - + +
203B LYS 3.9 1.1 - - - +
205B PHE* 1.3 81.1 - - + +
207B ASP* 1.3 62.1 + - - +
209B HIS* 3.7 6.1 - - + +
210B GLN* 2.9 31.9 + - - +
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Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 5.6 0.3 - - - +
88B HIS* 2.7 31.5 + - - -
203B LYS* 2.7 50.2 + - - +
204B GLU* 3.6 6.1 - - + +
206B LEU* 1.3 77.7 - - - +
208B GLU* 1.3 59.2 + - - +
210B GLN* 3.3 4.6 + - - +
211B LYS* 2.9 45.9 + - - +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLU* 2.9 35.8 + - + +
205B PHE* 3.8 5.8 - - + +
207B ASP* 1.3 78.5 - - - +
209B HIS* 1.3 57.4 + - - +
211B LYS* 3.1 37.8 + - - +
212B MET* 2.9 50.7 + - + +
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Residues in contact with HIS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.4 37.4 - - + +
189B ASN* 3.9 16.9 + - - -
191B THR* 4.5 8.1 - - + -
205B PHE* 2.8 31.1 + - + +
206B LEU* 3.7 9.4 - - + +
208B GLU* 1.3 74.6 - - - +
210B GLN* 1.3 62.8 + - + +
212B MET* 3.3 15.8 + - + +
213B THR* 2.9 60.0 + - + +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS 4.1 8.2 + - - +
88B HIS* 3.6 26.2 + - + +
206B LEU 2.9 18.1 + - - +
207B ASP* 3.7 5.4 + - - +
209B HIS* 1.3 78.4 - - + +
211B LYS* 1.3 57.6 + - + +
213B THR* 3.1 17.6 + - - +
214B SER* 2.8 28.0 + - - +
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Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ASP* 2.9 29.2 + - + +
208B GLU* 3.1 37.7 + - - +
209B HIS 3.2 0.2 - - - -
210B GLN* 1.3 77.7 - - + +
212B MET* 1.3 58.6 + - + +
214B SER* 3.1 5.8 + - - -
215B GLY 2.8 10.0 + - - -
216B LYS* 2.7 56.3 + - + +
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Residues in contact with MET 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B PHE* 5.1 5.6 - - + +
208B GLU* 2.9 51.9 + - + +
209B HIS* 3.5 19.1 - - + +
211B LYS* 1.3 78.6 - - + +
213B THR* 1.3 62.1 + - + +
215B GLY* 3.4 11.7 + - - -
216B LYS 4.9 2.2 - - - +
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ASN* 4.5 9.9 - - - +
209B HIS* 2.9 52.4 + - + +
210B GLN* 3.1 18.4 + - - +
212B MET* 1.3 78.6 - - + +
214B SER* 1.3 56.8 + - - +
215B GLY 3.4 0.4 - - - -
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLN* 2.8 24.8 + - - +
211B LYS* 3.1 9.0 + - - -
213B THR* 1.3 77.4 - - - +
215B GLY* 1.3 61.4 + - - +
216B LYS* 3.6 27.9 - - - +
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LYS 2.8 7.3 + - - -
212B MET* 3.4 11.1 + - - -
213B THR 3.4 0.8 + - - -
214B SER* 1.3 78.8 - - - +
216B LYS* 1.3 71.1 + - - +
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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