Contacts of the helix formed by residues 203 - 209 (chain B) in PDB entry 3GXT
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NOJ 3.5 31.6 - - - -
168B LYS* 3.7 15.9 - - + +
169B PHE 3.4 6.2 + - - +
170B ASP* 3.0 32.9 - - - +
184B TYR* 2.9 19.0 + - - +
201B SER* 5.9 0.2 - - - +
202B CYS* 1.3 75.9 - - - +
204B TRP* 1.3 67.8 + - - +
205B PRO* 3.1 6.3 - - - -
206B LEU* 3.2 30.1 + - + +
207B TYR* 3.5 20.7 + - + -
227B ARG* 3.7 28.3 - - + +
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Residues in contact with TRP 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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180B LEU* 4.1 10.7 - - + +
181B ALA* 3.8 37.3 - - + +
184B TYR* 3.2 44.2 - + + -
185B LYS* 3.7 35.2 - - + -
202B CYS* 4.4 4.7 - - + -
203B GLU* 1.3 75.7 - - - +
205B PRO* 1.3 70.0 - - + +
207B TYR* 3.4 2.8 + - - +
208B MET* 3.1 44.1 + - + +
218B GLU* 4.0 20.4 - - + -
219B ILE* 3.9 40.6 - - + -
222B TYR* 4.4 14.4 - + + -
223B CYS* 4.3 7.9 - - - -
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Residues in contact with PRO 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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203B GLU 3.3 6.3 - - - -
204B TRP* 1.3 94.0 - - + +
206B LEU* 1.3 53.9 + - - +
208B MET* 2.9 2.3 + - + -
209B TRP* 2.7 38.7 + - + -
214B PRO* 3.8 30.5 - - + +
216B TYR* 3.8 12.3 - - + +
219B ILE* 4.0 11.7 - - + -
226B TRP* 3.7 28.3 - - + -
227B ARG 3.3 17.3 - - - +
228B ASN* 3.7 9.2 - - - +
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Residues in contact with LEU 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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1B NOJ 5.5 0.7 - - - -
203B GLU* 3.2 28.4 + - - +
205B PRO* 1.3 79.8 - - - +
207B TYR* 1.3 72.3 + - + +
209B TRP* 3.5 14.0 - - + +
210B PRO* 3.5 8.6 - - + +
227B ARG* 3.3 29.6 + - + +
228B ASN 3.5 14.5 + - - +
229B PHE* 3.1 37.2 - - + +
230B ALA* 4.2 7.4 - - - +
231B ASP* 5.2 3.8 - - - +
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Residues in contact with TYR 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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1B NOJ 4.3 5.0 + - - -
142B CYS* 3.4 20.4 - - - -
170B ASP* 2.7 29.8 + - - -
171B GLY* 3.1 38.4 - - - +
172B CYS* 3.7 8.0 - - - -
177B LEU* 5.5 0.2 - - - +
180B LEU* 3.8 22.4 - - + +
184B TYR* 4.6 0.2 - - - -
203B GLU* 3.5 28.4 + - + -
204B TRP 3.4 2.8 + - - +
205B PRO 3.1 0.6 - - - -
206B LEU* 1.3 88.8 - - + +
208B MET* 1.3 61.8 + - - +
210B PRO* 3.1 16.0 - - - +
211B PHE* 3.8 13.2 - - - -
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Residues in contact with MET 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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177B LEU* 3.7 23.1 - - + -
180B LEU* 3.9 8.9 - - + +
181B ALA* 6.0 3.6 - - + -
204B TRP* 3.1 42.6 + - + +
205B PRO* 2.9 4.4 + - + +
207B TYR* 1.3 74.3 - - - +
209B TRP* 1.3 66.0 + - - +
210B PRO* 3.2 1.0 - - - +
211B PHE* 3.0 19.1 + - - +
212B GLN* 3.2 43.6 + - - +
213B LYS 3.9 7.9 - - - +
214B PRO* 3.4 26.7 - - + -
215B ASN* 4.2 10.3 - - + +
218B GLU* 5.7 2.9 - - - +
219B ILE* 5.0 1.8 - - - -
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Residues in contact with TRP 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 PRO 2.7 27.6 + - - +
206B LEU* 3.5 6.7 - - + +
208B MET* 1.3 71.5 - - - +
210B PRO* 1.3 64.8 - - + +
211B PHE 2.9 6.5 + - - -
212B GLN* 3.5 11.1 + - - -
213B LYS* 3.6 34.5 - - + -
214B PRO* 3.6 18.4 - - + +
216B TYR* 2.8 32.2 + + - -
228B ASN 3.4 25.3 + - - -
245B TRP* 3.9 14.2 - + - -
249B ASN* 4.3 20.0 - - - -
252B ARG* 4.3 16.4 - - - -
253B ILE* 5.9 0.7 - - + -
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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