Contacts of the helix formed by residues 193 - 205 (chain B) in PDB entry 1JPP
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 GLN 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B PRO* 6.0 1.7 - - - +
157B THR* 4.3 23.5 + - + +
191B SER* 2.5 11.5 + - - +
192B PRO* 1.3 80.6 - - + +
194B MET* 1.3 69.1 + - - +
195B VAL 3.0 0.9 - - - -
196B SER* 2.6 20.1 + - - -
197B ALA* 3.1 9.8 + - - +
200B ARG* 5.4 0.3 + - - -
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Residues in contact with MET 194 (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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153B ILE* 3.3 49.1 - - + +
156B LEU* 4.1 17.7 - - + -
157B THR* 3.9 19.4 + - - +
160B LEU* 4.5 14.1 - - - -
175B VAL* 4.5 10.8 - - + -
188B ILE* 4.1 25.6 - - + +
191B SER* 3.1 24.8 + - - +
193B GLN* 1.3 78.4 - - - +
195B VAL* 1.3 60.7 + - - +
197B ALA* 3.5 4.2 + - - +
198B ILE* 2.8 45.9 + - + +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 3.8 22.0 - - + +
189B MET* 4.0 11.4 - - - +
191B SER 3.7 14.4 - - - +
192B PRO* 4.8 4.9 - - + +
193B GLN 2.8 4.2 + - - -
194B MET* 1.3 74.2 - - - +
196B SER* 1.3 61.0 + - - +
198B ILE* 3.4 11.8 + - + +
199B VAL* 3.2 24.1 + - + +
218B LEU* 5.3 4.7 - - + -
221B LEU* 5.2 6.5 - - + -
230B ALA* 3.9 24.0 - - + +
231B ILE* 4.4 9.4 - - + +
234B SER* 3.2 25.4 - - - +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO 2.6 27.7 + - - -
193B GLN* 2.6 13.3 + - - -
195B VAL* 1.3 70.7 - - - +
197B ALA* 1.3 66.2 + - - -
199B VAL* 3.0 15.7 + - - +
200B ARG* 3.3 31.4 + - - +
234B SER* 4.2 20.2 - - - -
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Residues in contact with ALA 197 (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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157B THR* 4.6 7.4 - - + +
160B LEU* 4.2 17.0 - - + -
161B ASN* 3.5 27.5 - - - +
193B GLN 3.1 6.0 + - - +
194B MET* 3.8 7.2 - - - +
196B SER* 1.3 78.9 - - - +
198B ILE* 1.3 58.0 + - - +
200B ARG* 3.4 22.7 + - - +
201B THR* 2.8 33.3 + - - -
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Residues in contact with ILE 198 (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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160B LEU* 4.3 16.4 - - + -
175B VAL* 4.1 11.7 - - + -
188B ILE* 5.1 6.5 - - + -
194B MET* 2.8 40.1 + - + +
195B VAL* 3.5 12.6 - - + +
196B SER 3.1 0.8 - - - -
197B ALA* 1.3 78.6 - - - +
199B VAL* 1.3 60.8 + - - +
201B THR* 3.6 5.7 + - - -
202B MET* 3.4 21.5 + - - +
214B THR* 4.4 17.2 - - + +
217B THR* 4.1 25.6 - - + -
218B LEU* 3.9 28.0 - - + +
221B LEU* 6.2 1.6 - - + -
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Residues in contact with VAL 199 (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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195B VAL* 3.2 17.3 - - + +
196B SER 3.0 5.9 + - - +
198B ILE* 1.3 73.3 - - - +
200B ARG* 1.3 61.0 + - - +
201B THR 3.1 2.0 - - - -
202B MET* 3.3 10.4 + - + +
203B GLN* 3.0 30.3 + - - +
218B LEU* 4.5 18.8 - - + -
231B ILE* 5.5 1.3 - - + +
234B SER* 4.0 24.2 - - - +
235B GLY 3.8 8.3 - - - +
236B GLY* 3.7 27.8 - - - -
239B ALA* 3.8 17.3 - - + -
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Residues in contact with ARG 200 (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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157B THR* 5.9 0.8 - - - +
161B ASN* 3.5 27.5 + - - +
193B GLN 5.4 0.4 + - - -
196B SER* 3.3 26.2 + - - +
197B ALA* 3.4 30.6 + - - +
199B VAL* 1.3 78.9 - - - +
201B THR* 1.3 57.3 + - - +
203B GLN* 3.8 14.8 - - - +
204B ASN* 2.8 38.2 + - - +
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Residues in contact with THR 201 (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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160B LEU* 4.3 25.7 + - + +
168B VAL* 5.1 16.4 - - + +
172B ALA* 5.4 0.2 - - + -
197B ALA 2.8 22.3 + - - -
198B ILE* 3.8 6.0 - - - -
199B VAL 3.1 0.8 - - - -
200B ARG* 1.3 76.4 - - - +
202B MET* 1.3 61.6 + - - +
203B GLN 2.9 1.3 - - - -
204B ASN* 5.2 0.7 - - - -
205B THR* 2.8 38.3 + - - +
210B THR* 4.1 24.0 - - + -
214B THR* 4.2 9.0 - - + -
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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
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198B ILE 3.4 10.5 + - - +
199B VAL* 3.3 6.0 + - + +
201B THR* 1.3 80.4 - - - +
203B GLN* 1.3 60.4 + - - +
205B THR* 4.0 13.6 - - - +
211B ALA* 5.0 4.1 - - + +
214B THR* 3.1 29.3 + - - +
215B ALA* 4.1 20.4 - - + +
218B LEU* 3.7 24.5 - - + -
236B GLY 4.8 0.2 - - - +
239B ALA* 3.7 37.9 - - + +
240B LEU* 3.8 23.3 - - + -
243B MET* 3.8 35.1 - - + +
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.0 18.1 + - - +
200B ARG* 3.8 13.5 - - - +
201B THR 2.9 0.6 - - - -
202B MET* 1.3 80.8 - - - +
204B ASN* 1.3 73.9 + - - +
205B THR 3.7 1.9 - - - +
235B GLY 5.8 1.2 + - - -
238B PRO* 5.2 3.8 - - - +
239B ALA* 4.3 28.3 + - + +
242B LYS* 3.0 50.4 + - + +
243B MET* 5.0 3.2 - - - +
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Residues in contact with ASN 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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165B GLN* 5.7 2.0 + - - -
200B ARG* 2.8 29.9 + - - +
201B THR* 4.6 0.7 - - - +
203B GLN* 1.3 95.4 + - - +
205B THR* 1.3 68.7 + - - +
206B ASN* 4.9 1.2 - - - +
242B LYS* 5.2 2.2 - - - +
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Residues in contact with THR 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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165B GLN* 5.5 8.2 + - - +
169B ASN* 4.7 3.1 + - - -
201B THR* 2.8 22.4 + - - +
202B MET* 4.0 13.5 - - - +
203B GLN 3.7 1.8 - - - +
204B ASN* 1.3 84.6 - - - +
206B ASN* 1.3 65.2 + - - +
207B ASP* 3.3 22.9 + - - +
210B THR* 3.5 23.6 + - + +
211B ALA* 4.3 20.0 - - + +
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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