Contacts of the helix formed by residues 203 - 215 (chain B) in PDB entry 1GQT
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 GLU 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ASN* 3.0 11.9 + - - +
202B ASP* 1.3 84.3 + - - +
204B ASP* 1.3 70.3 + - - +
206B ALA* 3.1 17.3 + - - +
207B LYS* 3.3 24.1 + - + +
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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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197B ILE* 4.2 4.4 - - + +
198B ARG* 3.2 27.1 - - - +
199B VAL* 3.6 9.6 - - - -
200B GLU* 3.2 19.1 + - - +
201B ASN* 2.7 33.6 + - - +
203B GLU* 1.3 74.9 - - - +
205B ALA* 1.3 65.9 + - - +
207B LYS* 3.1 13.6 + - - +
208B ALA* 2.9 23.6 + - - +
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Residues in contact with ALA 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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199B VAL* 4.0 18.2 - - + -
201B ASN 3.0 13.0 + - - +
202B ASP* 3.0 12.0 + - - +
204B ASP* 1.3 75.3 - - - +
206B ALA* 1.3 59.4 + - - +
208B ALA* 3.0 2.8 + - - +
209B ALA* 2.7 31.2 + - - +
222B ILE* 3.7 10.7 - - + +
224B LEU* 4.7 5.6 - - + -
230B TRP* 3.8 30.7 - - + -
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Residues in contact with ALA 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 ASP 2.9 12.0 + - - +
203B GLU* 3.1 13.0 + - - +
205B ALA* 1.3 77.6 - - - +
207B LYS* 1.3 61.9 + - + +
209B ALA* 3.5 3.9 + - - +
210B GLN* 3.0 23.7 + - - +
230B TRP* 4.1 21.7 - - + +
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Residues in contact with LYS 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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197B ILE* 3.8 30.2 - - + +
203B GLU* 3.7 21.8 - - + +
204B ASP* 3.1 12.5 + - - +
205B ALA 3.1 0.8 - - - -
206B ALA* 1.3 75.4 - - + +
208B ALA* 1.3 68.8 + - - +
210B GLN* 3.2 16.1 + - - +
211B VAL* 3.2 17.2 + - - +
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Residues in contact with ALA 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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191B ALA* 4.4 3.6 - - + -
195B THR* 3.4 32.7 - - + +
197B ILE* 4.2 10.9 - - + +
199B VAL* 3.8 22.4 - - + -
204B ASP 2.9 13.0 + - - +
205B ALA 3.5 6.5 - - - +
207B LYS* 1.3 78.8 - - - +
209B ALA* 1.3 64.1 + - - +
211B VAL 3.3 6.8 + - - -
212B LEU* 3.3 9.7 + - - +
222B ILE* 3.9 10.5 - - + -
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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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205B ALA 2.7 16.6 + - - +
206B ALA* 3.7 7.2 - - - +
208B ALA* 1.3 78.1 - - - +
210B GLN* 1.3 51.6 + - - +
212B LEU* 2.8 5.9 + - - +
213B HIS* 2.7 55.2 + - + -
220B VAL* 4.1 23.6 - - + -
222B ILE* 4.0 4.6 - - + +
230B TRP* 4.7 3.4 - - + -
232B SER* 4.1 11.0 - - - +
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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 ALA 3.0 17.6 + - - +
207B LYS* 3.2 9.3 + - - +
209B ALA* 1.3 75.8 - - - +
211B VAL* 1.3 58.8 + - - +
213B HIS* 3.1 12.1 + - + +
214B GLU* 2.8 49.3 + - + +
235B GLY* 6.0 4.5 - - - -
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Residues in contact with VAL 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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194B LEU 4.9 0.2 - - - +
195B THR* 3.9 28.5 - - + +
197B ILE* 4.1 19.1 - - + -
207B LYS 3.2 13.9 + - - +
208B ALA 3.6 6.7 - - - +
209B ALA 3.3 0.2 - - - -
210B GLN* 1.3 78.1 - - - +
212B LEU* 1.3 63.4 + - + +
214B GLU* 3.4 7.3 + - - +
215B LYS* 3.0 43.7 + - + +
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Residues in contact with LEU 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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178B LEU* 4.6 17.5 - - + -
184B ILE* 3.9 15.5 - - + -
186B PRO* 4.1 16.2 - - + -
191B ALA* 5.5 2.0 - - + -
194B LEU* 4.4 23.3 - - + +
195B THR* 3.9 18.2 - - + -
208B ALA 3.3 12.3 + - - +
209B ALA* 2.8 8.6 + - - +
211B VAL* 1.3 81.5 - - + +
213B HIS* 1.3 63.8 + - - +
215B LYS* 3.1 15.6 + - + +
217B ILE* 3.3 29.2 + - + +
220B VAL* 3.9 31.0 - - + -
222B ILE* 5.3 2.7 - - + -
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Residues in contact with HIS 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* 2.7 32.2 + - + +
210B GLN* 3.5 11.5 + - + +
212B LEU* 1.3 74.1 - - - +
214B GLU* 1.3 61.0 + - + +
216B GLY* 2.9 18.9 + - - -
217B ILE 2.7 32.1 + - - +
218B ARG* 3.1 14.0 + - - -
220B VAL* 3.6 8.7 - - + +
232B SER* 3.0 53.5 + - - -
234B ASN* 3.4 11.5 + - - +
235B GLY* 3.4 21.7 + - - +
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Residues in contact with GLU 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 GLN* 2.8 40.6 + - + +
211B VAL* 3.8 6.5 - - - +
213B HIS* 1.3 75.7 - - + +
215B LYS* 1.3 61.3 + - - +
216B GLY* 3.1 1.4 + - - -
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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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175B ASP* 3.1 36.6 + - + +
178B LEU* 3.8 34.8 - - + +
179B ALA* 3.6 23.7 + - - +
194B LEU 4.2 11.5 + - - -
211B VAL* 3.0 36.2 + - + +
212B LEU* 3.1 12.8 + - - +
214B GLU* 1.3 78.7 - - - +
216B GLY* 1.3 55.4 + - - +
217B ILE* 3.7 0.9 - - + -
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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