Contacts of the helix formed by residues 202 - 214 (chain B) in PDB entry 3C9G
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 SER 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A THR 3.2 6.6 + - - -
202A SER* 4.4 14.5 - - - +
205A LYS* 5.0 5.6 - - - +
197B ILE* 4.5 0.9 - - - -
200B THR 4.2 0.4 + - - -
201B GLU* 1.3 74.0 - - - +
203B GLU* 1.3 66.7 + - - +
204B ASP* 3.2 17.3 + - - +
205B LYS* 3.3 35.7 + - - +
206B VAL* 3.1 24.7 + - - +
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Residues in contact with GLU 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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197B ILE* 4.4 18.1 - - + +
201B GLU 4.0 2.0 + - - -
202B SER* 1.3 72.3 + - - +
204B ASP* 1.3 65.4 + - - +
206B VAL* 3.3 1.7 + - - -
207B LEU* 3.0 37.5 + - + +
221B ILE* 3.2 42.6 - - + +
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Residues in contact with ASP 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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202B SER* 3.2 8.4 + - - +
203B GLU* 1.3 79.7 - - - +
205B LYS* 1.3 59.7 + - + +
207B LEU* 3.4 6.5 + - - +
208B LYS* 3.0 48.9 + - + +
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Residues in contact with LYS 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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199A PRO 3.5 19.3 + - - +
200A THR* 4.2 17.7 - - + +
201A GLU 3.3 20.0 + - - +
202A SER* 4.6 5.1 - - - +
203A GLU 5.3 1.4 - - - +
202B SER* 3.3 27.2 + - - +
203B GLU 3.4 0.2 - - - -
204B ASP* 1.3 78.3 - - + +
206B VAL* 1.3 58.5 + - - +
208B LYS* 4.0 7.9 - - + +
209B ALA* 3.1 27.2 + - - +
273B THR* 4.4 9.1 - - + +
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Residues in contact with VAL 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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200A THR* 4.3 19.3 - - - -
195B THR* 4.3 6.5 - - + -
196B LYS 4.5 0.4 - - - +
197B ILE* 3.3 34.5 - - + -
201B GLU* 4.3 15.5 - - + +
202B SER 3.1 17.5 - - - +
203B GLU 3.3 1.1 + - - +
204B ASP 3.3 0.6 - - - -
205B LYS* 1.3 75.1 - - - +
207B LEU* 1.3 66.3 + - + +
209B ALA* 3.5 4.9 + - - +
210B ILE* 3.2 35.9 + - + +
227B VAL* 4.9 0.4 - - + -
269B LYS* 3.8 22.4 - - + -
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 4.8 4.0 - - + -
203B GLU* 3.0 43.3 + - + +
204B ASP* 3.8 6.1 - - - +
206B VAL* 1.3 85.3 - - + +
208B LYS* 1.3 60.1 + - + +
210B ILE* 3.5 7.4 + - + +
211B ARG* 2.9 53.9 + - - +
219B ILE* 4.1 25.7 - - + +
221B ILE* 3.8 23.8 - - + -
227B VAL* 5.0 3.6 - - + -
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Residues in contact with LYS 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 ASP* 3.0 35.2 + - + +
205B LYS* 4.0 6.7 - - - +
206B VAL 3.2 0.2 - - - -
207B LEU* 1.3 76.1 - - + +
209B ALA* 1.3 56.5 + - - +
210B ILE 3.1 1.6 - - - -
211B ARG* 3.5 6.9 - - + +
212B ASN* 2.7 48.0 + - - +
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Residues in contact with ALA 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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200A THR* 5.0 0.2 - - + -
205B LYS 3.1 18.6 + - - +
206B VAL* 3.9 5.4 - - - +
207B LEU 3.4 0.2 - - - -
208B LYS* 1.3 77.3 - - - +
210B ILE* 1.3 63.6 + - - +
212B ASN* 3.4 13.6 + - - +
213B ILE* 3.7 5.9 + - - +
269B LYS* 3.7 32.8 - - + +
272B ALA* 3.5 34.0 - - + +
273B THR* 3.9 8.0 - - + +
289B ILE* 4.6 0.9 - - + -
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Residues in contact with ILE 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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193B ILE* 4.2 31.9 - - + -
195B THR* 3.9 26.0 - - + -
206B VAL* 3.2 21.2 + - + +
207B LEU* 3.6 9.2 - - + +
208B LYS 3.1 0.4 - - - -
209B ALA* 1.3 77.6 - - - +
211B ARG* 1.3 60.8 + - - +
213B ILE* 3.0 8.5 + - - +
214B PHE* 2.9 25.3 + - + +
217B ALA* 4.4 12.6 - - + -
219B ILE* 4.5 14.4 - - + -
227B VAL* 3.9 16.6 - - + -
289B ILE* 4.0 26.9 - - + -
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Residues in contact with ARG 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 LEU* 2.9 40.2 + - - +
208B LYS* 3.2 6.7 + - - +
210B ILE* 1.3 73.9 - - - +
212B ASN* 1.3 64.9 + - - +
214B PHE 3.4 15.3 - - - +
215B PRO* 3.1 42.5 + - + +
217B ALA* 2.8 31.7 + - + +
218B GLU* 4.1 8.1 + - - +
219B ILE* 3.2 29.5 + - + +
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Residues in contact with ASN 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 LYS* 2.7 36.0 + - - +
209B ALA* 3.5 4.9 - - - +
210B ILE 3.2 0.4 - - - -
211B ARG* 1.3 72.9 - - - +
213B ILE* 1.3 60.0 + - + +
236B ARG* 3.0 33.7 + - - +
240B LEU* 4.0 3.1 - - - +
272B ALA 2.8 27.4 + - - +
273B THR* 3.1 22.0 + - - +
275B SER* 3.2 23.6 + - - +
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Residues in contact with ILE 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 ALA 3.7 13.7 - - - +
210B ILE* 3.0 4.5 + - - +
212B ASN* 1.3 82.4 - - - +
214B PHE* 1.3 87.6 + - + +
215B PRO* 3.6 7.6 - - - +
233B SER 5.2 1.0 - - - +
236B ARG* 3.6 15.4 - - - +
237B PHE* 3.7 33.0 + - + -
240B LEU* 3.9 12.1 - - + -
267B LEU* 4.2 13.5 - - + -
272B ALA* 4.3 17.9 - - + -
275B SER* 4.5 11.9 - - - -
276B ARG 4.6 0.9 - - - +
277B ILE* 3.8 24.9 - - + -
289B ILE* 5.6 2.7 - - + -
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Residues in contact with PHE 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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191B ILE* 4.0 32.3 - - + -
193B ILE* 3.7 22.0 - - + -
210B ILE* 2.9 13.0 + - + +
211B ARG* 3.3 14.3 - - - -
213B ILE* 1.3 102.0 - - + +
215B PRO* 1.3 66.3 - - - +
216B ASP* 3.3 4.4 + - - +
217B ALA* 3.4 12.9 + - + +
231B ALA* 3.8 16.6 - - + -
233B SER 4.2 8.5 - - - -
234B LEU* 5.0 0.7 - - + -
237B PHE* 4.2 22.4 - + + -
267B LEU* 4.5 4.9 - - + -
289B ILE* 5.4 3.1 - - + -
291B VAL* 3.9 38.6 - - + -
293B PHE* 4.4 11.7 - + - -
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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