Contacts of the helix formed by residues 194 - 208 (chain h) in PDB entry 5JPQ
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 194 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142h ARG 5.2 9.9 - - - +
143h LEU* 5.7 4.5 - - - +
150h THR* 6.0 5.6 - - - -
184h VAL* 5.4 9.9 - - + +
188h THR* 5.0 13.8 - - - -
192h ILE 3.4 4.6 - - - +
193h HIS* 1.3 69.4 - - - +
195h ILE* 1.3 57.7 + - - +
196h TYR 3.3 0.9 - - - -
197h LEU* 3.2 13.7 + - + +
198h ILE* 2.9 30.4 + - + +
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Residues in contact with ILE 195 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193h HIS* 3.1 10.3 + - + +
194h PRO* 1.3 76.4 - - - +
196h TYR* 1.3 56.7 + - - +
198h ILE* 3.3 6.7 + - - +
199h LYS* 2.9 32.7 + - - +
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Residues in contact with TYR 196 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193h HIS 3.7 9.9 + - - +
194h PRO 3.3 0.2 - - - -
195h ILE* 1.3 75.7 - - - +
197h LEU* 1.3 57.9 + - - +
199h LYS* 3.4 6.4 + - - +
200h GLU* 2.9 30.7 + - - +
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Residues in contact with LEU 197 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184h VAL* 4.7 21.3 - - + -
193h HIS 4.7 0.4 + - - -
194h PRO* 3.2 16.6 + - + +
196h TYR* 1.3 76.3 - - - +
198h ILE* 1.3 56.7 + - - +
200h GLU* 3.3 6.9 + - - +
201h LEU* 2.9 32.0 + - - +
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Residues in contact with ILE 198 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153h ALA* 5.7 9.4 - - + -
154h LEU 6.4 0.2 - - - +
157h LEU* 5.7 2.3 - - - +
194h PRO* 2.9 16.7 + - + +
195h ILE* 3.7 7.6 - - - +
197h LEU* 1.3 75.2 - - - +
199h LYS* 1.3 57.3 + - - +
201h LEU* 3.4 5.8 + - - +
202h MET* 2.9 29.9 + - - +
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Residues in contact with LYS 199 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195h ILE 2.9 17.7 + - - +
196h TYR* 3.7 6.3 - - - +
198h ILE* 1.3 73.9 - - - +
200h GLU* 1.3 57.6 + - - +
202h MET* 3.1 8.6 + - - +
203h ILE* 2.9 29.3 + - - +
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Residues in contact with GLU 200 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196h TYR 2.9 17.9 + - - +
197h LEU* 3.6 7.2 - - - +
199h LYS* 1.3 75.0 - - - +
201h LEU* 1.3 57.5 + - - +
203h ILE* 3.3 7.6 + - - +
204h LYS* 2.9 29.0 + - - +
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Residues in contact with LEU 201 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157h LEU* 4.0 29.1 - - + +
197h LEU 2.9 18.9 + - - +
198h ILE* 3.7 5.6 - - - +
200h GLU* 1.3 72.9 - - - +
202h MET* 1.3 58.7 + - - +
204h LYS* 3.3 8.5 + - - +
205h ARG* 2.9 30.2 + - - +
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Residues in contact with MET 202 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157h LEU* 5.4 1.3 - - - +
198h ILE 2.9 15.3 + - - +
199h LYS* 3.2 14.6 - - - +
201h LEU* 1.3 75.4 - - - +
203h ILE* 1.3 57.5 + - - +
205h ARG* 3.2 9.1 + - - +
206h GLU* 3.0 28.9 + - - +
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Residues in contact with ILE 203 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199h LYS 2.9 11.7 + - - +
200h GLU* 3.6 11.0 - - - +
202h MET* 1.3 76.7 - - - +
204h LYS* 1.3 56.2 + - - +
206h GLU* 3.1 8.8 + - - +
207h LEU* 2.9 30.5 + - - +
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Residues in contact with LYS 204 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200h GLU 2.9 14.1 + - - +
201h LEU* 3.3 12.3 + - - +
203h ILE* 1.3 74.3 - - - +
205h ARG* 1.3 62.6 + - - +
207h LEU* 3.3 9.3 + - - +
208h ALA* 3.2 22.7 + - - +
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Residues in contact with ARG 205 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157h LEU* 5.9 7.6 - - + +
201h LEU 2.9 14.1 + - - +
202h MET* 3.3 13.2 - - - +
204h LYS* 1.3 74.7 - - - +
206h GLU* 1.3 61.9 + - - +
208h ALA* 3.3 21.6 + - - +
209h LYS* 4.2 3.3 + - - +
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Residues in contact with GLU 206 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202h MET 3.0 12.9 + - - +
203h ILE* 3.1 11.2 + - - +
205h ARG* 1.3 74.6 - - - +
207h LEU* 1.3 65.6 + - - +
208h ALA 3.4 0.5 + - - -
209h LYS* 3.5 19.1 + - - +
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Residues in contact with LEU 207 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203h ILE 2.9 16.3 + - - +
204h LYS* 3.6 9.4 - - - +
206h GLU* 1.3 72.4 - - - +
208h ALA* 1.3 56.2 + - - +
209h LYS 3.1 16.5 + - - +
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Residues in contact with ALA 208 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204h LYS 3.2 11.5 + - - +
205h ARG* 3.6 14.8 - - - +
206h GLU 3.2 1.4 - - - -
207h LEU* 1.3 74.3 - - - +
209h LYS* 1.3 58.3 + - - +
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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