Contacts of the helix formed by residues 204 - 216 (chain B) in PDB entry 2JRI
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 THR 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B SER 3.6 4.6 + - - -
203B ASP* 1.3 76.7 + - - +
205B ILE* 1.3 64.4 + - - +
206B GLU* 4.2 7.2 - - + +
207B ASN* 2.9 22.4 + - - +
208B VAL* 3.1 13.4 + - - +
234B ASP 3.2 26.0 - - - +
235B GLY* 4.1 8.5 - - - +
236B ARG 3.2 16.2 - - - +
237B THR* 4.1 7.4 - - + +
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Residues in contact with ILE 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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204B THR* 1.3 69.8 - - - +
206B GLU* 1.3 61.7 + - - +
208B VAL* 3.1 9.7 + - + +
209B LYS* 3.1 27.6 + - - +
225B LEU* 3.9 15.5 - - + -
232B LEU* 3.7 50.9 - - + +
233B GLU 3.2 25.8 - - - +
234B ASP* 4.2 2.5 - - - -
236B ARG* 2.8 21.7 + - + +
237B THR 4.1 11.2 - - - +
238B LEU* 3.7 28.7 - - + -
241B TYR* 4.6 0.7 - - + -
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Residues in contact with GLU 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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204B THR* 3.1 6.5 - - - +
205B ILE* 1.3 78.8 - - - +
207B ASN* 1.3 61.9 + - - +
209B LYS* 3.2 16.5 + - + +
210B ALA* 3.2 12.0 + - - +
220B PRO* 5.1 5.5 - - + +
234B ASP* 3.5 39.7 + - + +
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Residues in contact with ASN 207 (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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203B ASP* 3.3 27.3 + - - +
204B THR* 2.9 15.4 + - - +
206B GLU* 1.3 76.1 + - - +
208B VAL* 1.3 65.3 + - - +
210B ALA* 3.1 12.1 + - - +
211B LYS* 2.8 42.6 + - - +
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Residues in contact with VAL 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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185B ILE* 4.3 15.5 - - + -
187B VAL* 5.3 0.4 - - + -
197B LEU* 6.1 1.6 - - + -
199B VAL* 4.3 18.4 - - + -
203B ASP* 3.8 11.9 + - - +
204B THR 3.1 16.5 + - - +
205B ILE* 3.1 15.2 + - + +
207B ASN* 1.3 76.6 - - - +
209B LYS* 1.3 61.6 + - - +
211B LYS* 3.1 12.7 + - + +
212B ILE* 3.1 34.4 + - + +
225B LEU* 4.2 14.6 - - + -
238B LEU* 4.2 21.8 - - + -
249B LEU* 4.9 6.5 - - + -
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Residues in contact with LYS 209 (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 ILE* 3.1 24.3 + - - +
206B GLU* 3.3 9.2 - - + +
207B ASN 3.2 0.2 - - - -
208B VAL* 1.3 77.2 - - - +
210B ALA* 1.3 57.2 + - - +
212B ILE* 3.1 3.0 + - - -
213B GLN* 2.8 26.0 + - - +
220B PRO* 3.2 34.4 + - + +
221B ASP* 4.6 3.8 + - - +
223B GLN* 3.0 56.5 + - - +
224B ARG* 4.2 9.5 - - - +
225B LEU* 3.7 14.4 - - + +
232B LEU 5.2 2.4 + - - -
234B ASP* 2.7 42.3 + - - +
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Residues in contact with ALA 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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206B GLU 3.2 8.1 + - - +
207B ASN* 3.1 17.4 + - - +
209B LYS* 1.3 79.2 - - - +
211B LYS* 1.3 63.4 + - + +
213B GLN* 3.3 18.8 + - - +
214B ASP* 3.0 22.7 + - - +
220B PRO* 4.4 5.8 - - + +
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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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197B LEU* 3.7 15.7 - - + -
198B GLU 3.7 18.4 - - - +
199B VAL* 3.7 25.6 - - + +
203B ASP* 2.6 29.6 + - - +
207B ASN* 2.8 36.1 + - - +
208B VAL* 3.1 8.0 + - + +
210B ALA* 1.3 77.7 - - + +
212B ILE* 1.3 60.3 + - - +
214B ASP* 3.2 12.9 + - - +
215B LYS* 3.3 27.5 - - - +
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Residues in contact with ILE 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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187B VAL* 4.0 26.7 - - + -
195B ILE* 3.9 23.8 - - + -
197B LEU* 3.8 18.4 - - + -
208B VAL* 3.1 21.5 + - + +
209B LYS 3.5 5.2 - - - +
211B LYS* 1.3 73.6 - - - +
213B GLN* 1.3 57.4 + - - +
215B LYS* 3.0 3.7 + - - +
216B GLU* 2.8 39.9 + - + -
217B GLY 3.7 0.3 + - - -
218B ILE* 5.0 2.0 - - + -
223B GLN* 3.4 23.8 - - - +
225B LEU* 4.1 20.6 - - + -
251B LEU* 4.1 14.4 - - + -
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Residues in contact with GLN 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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209B LYS 2.8 14.4 + - - +
210B ALA* 3.5 14.0 - - - +
211B LYS 3.3 0.2 - - - -
212B ILE* 1.3 77.0 - - - +
214B ASP* 1.3 59.8 + - - +
217B GLY* 2.9 33.1 + - - +
218B ILE 3.4 28.9 - - - +
219B PRO* 4.9 1.4 - - - +
220B PRO* 3.6 26.2 - - + +
223B GLN* 3.7 0.9 - - - +
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Residues in contact with ASP 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 ALA 3.0 12.8 + - - +
211B LYS* 3.4 13.2 - - - +
212B ILE 3.1 0.2 - - - -
213B GLN* 1.3 76.9 + - - +
215B LYS* 1.3 87.2 + - + +
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Residues in contact with LYS 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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195B ILE* 4.7 10.3 - - + -
197B LEU* 3.7 27.5 - - + +
211B LYS* 3.3 19.2 + - - +
212B ILE 3.0 6.3 + - - +
214B ASP* 1.3 104.9 + - - +
216B GLU* 1.3 76.0 + - + +
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Residues in contact with GLU 216 (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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117A LYS* 2.7 38.8 + - - +
189B THR* 5.0 3.1 - - + +
193B LYS* 2.7 32.4 + - - +
195B ILE* 3.6 29.0 - - + +
212B ILE* 2.8 15.9 + - + +
215B LYS* 1.3 85.9 - - + +
217B GLY* 1.3 62.2 + - - +
218B ILE* 3.7 27.4 + - + +
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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