Contacts of the helix formed by residues 197 - 212 (chain B) in PDB entry 5AJI
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 ASP 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B ASP 3.8 1.0 + - - -
196B SER* 1.3 72.7 - - - +
198B ILE* 1.3 68.1 + - - +
199B ASP* 3.0 19.9 + - - +
200B GLN* 3.7 32.2 + - + +
201B VAL* 3.0 27.2 + - - +
266B ILE* 6.1 0.2 - - - +
259C ARG* 5.3 3.1 + - - -
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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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196B SER 3.9 8.1 - - - +
197B ASP* 1.3 75.2 + - - +
199B ASP* 1.3 63.8 + - - +
201B VAL* 3.6 1.4 + - - +
202B LYS* 3.2 39.8 + - + +
225B LEU* 4.5 18.2 - - + -
233B ILE* 5.8 4.0 - - + -
235B PHE* 4.2 24.0 - - + -
255C GLU* 4.0 17.7 - - + -
258C LYS* 3.9 33.7 - - + +
259C ARG* 3.8 33.2 - - + +
262C ASP* 5.4 0.9 - - - +
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Residues in contact with ASP 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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197B ASP* 3.0 14.2 + - - +
198B ILE* 1.3 75.8 - - - +
200B GLN* 1.3 60.3 + - - +
202B LYS* 3.5 10.9 + - - +
203B GLN* 2.9 29.9 + - - +
255C GLU* 4.5 1.6 - - - +
259C ARG* 2.7 33.5 + - - -
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Residues in contact with GLN 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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197B ASP* 3.2 31.0 + - + +
199B ASP* 1.3 75.3 - - - +
201B VAL* 1.3 66.6 + - - +
203B GLN* 3.1 7.1 + - + +
204B ILE* 2.9 35.6 + - + +
264B ALA* 3.9 26.9 + - - +
266B ILE* 4.0 20.3 - - + +
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Residues in contact with VAL 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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192B VAL* 4.3 5.6 - - + -
196B SER* 3.8 21.5 - - - -
197B ASP 3.0 21.1 + - - +
198B ILE 3.8 4.5 - - - +
200B GLN* 1.3 77.2 - - - +
202B LYS* 1.3 63.3 - - - +
204B ILE* 3.4 2.5 + - - +
205B LEU* 3.0 33.6 + - + +
235B PHE* 3.4 41.3 - - + -
261B PHE* 4.0 12.7 - - + -
266B ILE* 3.8 27.4 - - + -
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Residues in contact with LYS 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* 3.2 28.8 + - + +
199B ASP* 3.7 10.2 + - - +
201B VAL* 1.3 78.8 - - - +
203B GLN* 1.3 58.0 + - - +
205B LEU* 3.8 1.0 - - - +
206B THR* 2.8 37.4 + - - +
223B VAL* 4.0 35.2 - - + +
224B ARG* 4.5 18.2 - - - +
225B LEU 4.5 3.4 - - - +
235B PHE* 4.1 11.7 - - + -
255C GLU* 3.0 32.9 + - - -
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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
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199B ASP 2.9 19.1 + - - +
200B GLN* 3.1 8.5 + - + +
202B LYS* 1.3 75.4 - - - +
204B ILE* 1.3 59.8 + - + +
206B THR* 3.2 10.9 + - - +
207B ASN* 2.8 56.0 + - - +
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Residues in contact with ILE 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 GLN* 2.9 26.6 + - + +
201B VAL 3.7 3.8 - - - +
203B GLN* 1.3 76.1 - - + +
205B LEU* 1.3 65.0 + - - +
207B ASN* 3.1 13.4 + - - +
208B ILE* 3.0 27.7 + - + +
260B GLU* 3.8 26.9 - - + +
261B PHE* 3.6 19.3 - - + -
264B ALA* 3.6 23.6 - - + -
266B ILE* 3.4 32.1 - - + -
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Residues in contact with LEU 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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190B ILE* 4.8 6.1 - - + -
201B VAL* 3.0 36.1 + - + +
202B LYS* 3.8 3.8 - - - +
204B ILE* 1.3 76.6 - - - +
206B THR* 1.3 62.8 + - - +
208B ILE* 3.2 8.1 + - + +
209B ILE* 3.1 28.3 + - + +
223B VAL* 3.8 19.1 - - + -
235B PHE* 4.2 13.7 - - + -
237B VAL* 3.8 27.1 - - + -
257B ILE* 3.7 37.2 - - + -
261B PHE* 3.8 18.6 - - + -
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Residues in contact with THR 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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202B LYS* 2.8 21.9 + - - +
203B GLN* 3.6 12.3 - - - +
205B LEU* 1.3 77.4 - - - +
207B ASN* 1.3 59.1 + - - +
209B ILE* 3.3 12.0 + - + +
210B GLN* 2.9 55.7 + - + +
223B VAL* 3.8 16.5 - - - +
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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 GLN* 2.8 48.9 + - - +
204B ILE* 3.1 12.2 + - - +
206B THR* 1.3 76.8 - - - +
208B ILE* 1.3 64.2 + - + +
210B GLN* 3.4 7.3 + - - +
211B SER* 3.1 26.0 + - - -
256B ARG* 4.4 2.2 + - - +
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Residues in contact with ILE 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 ILE* 3.0 29.4 + - + +
205B LEU* 3.2 10.3 + - + +
207B ASN* 1.3 78.1 - - + +
209B ILE* 1.3 62.7 + - + +
211B SER* 3.1 15.9 + - - -
212B GLU* 3.3 7.8 + - - +
253B VAL* 4.0 29.2 - - + +
256B ARG* 3.3 46.1 + - + +
257B ILE* 3.9 28.9 - - + +
260B GLU* 3.7 30.5 - - + +
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Residues in contact with ILE 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 LEU* 3.1 10.7 + - + +
206B THR* 3.3 18.2 - - + +
208B ILE* 1.3 80.6 - - + +
210B GLN* 1.3 65.4 + - + +
212B GLU* 3.7 7.1 - - - +
215B ILE* 3.8 31.8 - - + +
217B LYS* 3.3 16.3 - - - -
221B MET* 4.1 23.8 - - + +
223B VAL* 3.6 28.3 - - + -
237B VAL* 4.1 18.8 - - + -
239B VAL* 3.7 21.3 - - + -
253B VAL* 4.7 9.0 - - + -
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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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206B THR* 2.9 41.3 + - + +
207B ASN* 3.7 8.5 - - - +
208B ILE 3.3 0.2 - - - -
209B ILE* 1.3 79.3 - - + +
211B SER* 1.3 58.2 - - - +
213B ASP* 4.9 0.7 - - - +
217B LYS* 3.0 38.0 + - - +
221B MET* 3.7 26.3 - - - +
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Residues in contact with SER 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 ASN 3.1 10.9 + - - -
208B ILE 3.1 2.1 + - - -
209B ILE 3.4 0.2 - - - -
210B GLN* 1.3 75.3 - - - +
212B GLU* 1.3 59.1 + - - +
213B ASP* 3.2 16.9 + - - +
256B ARG* 2.7 44.3 + - - -
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Residues in contact with GLU 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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208B ILE 3.3 16.0 + - - +
209B ILE 4.1 0.2 - - - +
210B GLN 3.3 1.2 - - - -
211B SER* 1.3 76.0 - - - +
213B ASP* 1.3 63.0 + - - +
214B ARG* 2.9 52.0 + - + +
215B ILE* 3.3 40.2 + - + +
217B LYS* 3.1 19.7 + - - -
249B VAL* 4.3 9.6 - - + -
252B ASP* 4.6 8.1 - - - +
253B VAL* 4.4 9.8 - - + +
256B ARG* 4.5 13.1 + - - +
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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