Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 1GQF
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B ASP 4.0 1.0 + - - -
206B CYS* 1.3 77.8 - - - +
208B CYS* 1.3 59.8 + - - +
209B ALA* 3.6 8.3 + - - +
210B LYS* 2.9 26.6 + - - +
211B MET* 2.8 27.7 + - - +
245B GLY* 4.3 1.8 - - - -
246B LYS* 3.9 5.6 - - - +
247B ASP* 3.7 23.3 - - - -
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Residues in contact with CYS 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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207B SER* 1.3 75.4 - - - +
209B ALA* 1.3 53.5 + - - +
211B MET* 3.3 6.4 + - - +
212B GLN* 2.8 37.5 + - - +
245B GLY* 3.8 11.0 - - - -
247B ASP* 3.1 18.6 + - - +
254B GLY* 3.4 36.6 - - - -
255B VAL 3.5 16.2 - - - +
256B THR* 4.0 17.6 - - + +
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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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207B SER* 3.2 8.2 - - - +
208B CYS* 1.3 78.7 - - - +
210B LYS* 1.3 52.4 + - - +
212B GLN* 3.3 5.0 + - - +
213B ASP* 2.6 38.8 + - - +
247B ASP* 5.1 2.8 + - - +
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TYR* 4.2 19.5 - - - -
206B CYS* 3.7 18.4 - - + -
207B SER* 2.9 25.5 + - - +
209B ALA* 1.3 72.6 - - - +
211B MET* 1.3 69.4 + - - +
213B ASP* 4.0 11.9 - - + +
214B LEU* 2.9 50.3 + - + +
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Residues in contact with MET 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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168B ILE* 3.8 28.7 - - + -
170B ASN* 3.4 24.7 - - - +
206B CYS* 3.7 15.5 - - + +
207B SER 2.8 19.8 + - - +
208B CYS* 3.7 5.8 - - - +
210B LYS* 1.3 75.5 - - - +
212B GLN* 1.3 63.2 + - - +
214B LEU* 4.0 3.4 - - - +
215B LEU* 3.3 25.5 + - - +
234B LEU* 5.1 3.6 - - + -
243B ILE* 3.5 38.8 - - + -
244B TYR 3.9 1.1 - - - +
245B GLY* 3.8 18.2 - - - -
256B THR* 4.1 8.3 - - + -
261B LEU* 3.6 17.3 - - + +
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Residues in contact with GLN 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 CYS 2.8 22.7 + - - +
209B ALA* 3.7 5.2 - - - +
211B MET* 1.3 74.1 - - - +
213B ASP* 1.3 62.3 + - - +
216B LYS* 3.3 8.3 + - - +
256B THR* 2.9 27.9 + - - +
260B ASP* 3.3 26.0 + - - +
261B LEU* 3.1 31.5 - - - +
264B HIS* 3.1 50.3 - - + +
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Residues in contact with ASP 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 2.6 22.6 + - - +
210B LYS* 3.1 16.1 + - - +
212B GLN* 1.3 70.5 - - - +
214B LEU* 1.3 68.1 + - - +
216B LYS* 3.0 18.9 + - - +
217B LYS* 3.0 41.0 + - - +
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Residues in contact with LEU 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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166B ILE* 3.5 35.3 - - + +
168B ILE* 4.3 6.1 - - + -
203B TYR* 3.6 43.1 - - + +
206B CYS* 4.5 2.2 - - - -
210B LYS* 2.9 48.8 + - + +
211B MET* 4.0 7.0 - - - +
213B ASP* 1.3 77.0 - - - +
215B LEU* 1.3 75.5 + - + +
217B LYS* 4.0 7.4 - - - +
218B ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 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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166B ILE* 4.0 15.9 - - + -
168B ILE* 4.5 8.3 - - + -
211B MET 3.3 13.3 + - - +
212B GLN 4.0 0.9 - - - +
213B ASP 3.1 0.6 - - - -
214B LEU* 1.3 96.9 - - + +
216B LYS* 1.3 61.3 + - - +
218B ALA* 3.2 16.0 - - - +
219B SER* 3.2 2.4 + - - -
232B CYS* 4.1 27.6 - - + -
234B LEU* 4.9 3.1 - - + -
261B LEU* 3.4 49.6 - - + +
264B HIS* 3.9 13.5 - - - +
265B PHE* 3.2 28.8 - - + -
280B PHE* 5.3 2.5 - - + -
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Residues in contact with LYS 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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212B GLN 3.3 12.1 + - - +
213B ASP* 3.0 13.6 + - - +
215B LEU* 1.3 74.6 - - - +
217B LYS* 1.3 74.4 + - + +
218B ALA 3.0 1.6 - - - -
219B SER* 2.5 27.3 + - - +
220B GLU* 3.0 34.3 + - + +
264B HIS* 3.4 26.4 + - + +
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Residues in contact with LYS 217 (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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213B ASP* 3.0 35.8 + - - +
214B LEU* 4.0 7.0 - - - +
216B LYS* 1.3 83.7 - - + +
218B ALA* 1.3 54.2 - - - +
220B GLU* 2.7 49.7 + - - +
221B GLU* 3.1 15.6 + - + +
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Residues in contact with ALA 218 (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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164B LYS* 6.4 0.4 - - + -
166B ILE* 3.7 25.1 - - + -
214B LEU 3.1 14.6 + - - +
215B LEU 3.2 11.4 - - - +
216B LYS 3.0 0.4 - - - -
217B LYS* 1.3 78.0 - - - +
219B SER* 1.3 59.4 + - - +
221B GLU* 3.2 24.6 + - - +
224B HIS* 2.8 27.2 + - + +
230B PHE* 4.8 3.6 - - + -
265B PHE* 4.1 10.1 - - + -
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Residues in contact with SER 219 (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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215B LEU 3.2 3.4 + - - -
216B LYS* 2.5 32.7 + - - +
218B ALA* 1.3 74.4 - - - +
220B GLU* 1.3 63.1 + - - +
221B GLU 3.3 4.0 + - - +
264B HIS* 3.2 30.6 + - - +
265B PHE* 3.7 23.1 - - - -
269B ARG 3.6 11.9 + - - +
270B CYS* 3.4 26.5 - - - -
272B THR* 4.9 0.3 + - - -
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Residues in contact with GLU 220 (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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216B LYS* 3.0 48.0 + - + +
217B LYS* 2.7 38.9 + - - +
219B SER* 1.3 80.8 - - - +
221B GLU* 1.3 64.2 + - - +
269B ARG 5.4 1.6 - - - +
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Residues in contact with GLU 221 (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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164B LYS* 4.6 20.4 + - - +
217B LYS* 3.1 13.5 + - + +
218B ALA* 3.2 29.9 + - - +
219B SER 3.8 3.1 - - - +
220B GLU* 1.3 83.2 - - - +
222B ASP* 1.3 61.9 + - - +
224B HIS* 3.5 18.5 + - + +
272B THR* 3.3 14.7 + - - +
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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