Contacts of the helix formed by residues 202 - 212 (chain B) in PDB entry 3GB9
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 THR 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.2 20.9 - - - +
135A HIS* 3.0 43.1 + - + +
162A MET* 3.5 32.1 - - + +
163A SER* 4.2 1.8 - - - +
165A ALA* 5.2 0.9 - - + -
201B GLN* 1.3 76.6 - - - +
203B VAL* 1.3 59.9 + - - +
204B ALA 3.4 1.2 + - - -
205B GLU* 2.9 30.4 + - - +
206B CYS* 2.9 27.8 + - - +
246B ILE 4.8 1.3 - - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 3.6 7.5 + - - +
163A SER* 4.3 17.8 - - - +
202B THR* 1.3 74.0 - - - +
204B ALA* 1.3 62.1 + - - +
206B CYS* 3.3 2.9 + - - +
207B ARG* 3.0 30.9 + - - +
246B ILE* 3.9 23.3 - - + +
247B MET 3.6 26.0 - - - +
248B ASP* 3.6 24.0 - - - +
249B TYR* 3.7 34.1 - - + +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 2.9 22.6 + - + +
135A HIS 3.7 15.7 - - - +
136A ILE* 3.8 15.2 - - + +
191A THR* 4.0 14.1 - - + +
212A LEU 4.8 1.2 - - - +
213A GLY 6.5 0.2 - - - -
202B THR 3.2 0.2 - - - -
203B VAL* 1.3 78.0 - - - +
205B GLU* 1.3 57.7 + - - +
207B ARG* 3.3 9.8 + - - +
208B VAL* 3.0 28.2 + - - +
249B TYR* 4.1 3.1 + - - +
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Residues in contact with GLU 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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135A HIS* 3.5 14.2 + - - +
136A ILE* 4.0 10.1 - - + -
137A ASN* 3.0 33.1 + - - +
141A PHE* 3.9 22.7 - - + -
200B PHE 4.1 3.1 - - - +
201B GLN* 3.4 20.6 - - - +
202B THR* 2.9 38.8 + - - +
204B ALA* 1.3 72.8 - - - +
206B CYS* 1.3 64.9 + - - +
208B VAL* 3.8 9.6 - - - +
209B LEU* 3.1 29.8 + - - +
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Residues in contact with CYS 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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120B LEU* 3.7 17.3 - - - -
201B GLN* 4.1 4.6 - - + +
202B THR 2.9 17.4 + - - +
203B VAL 3.3 5.1 + - - +
205B GLU* 1.3 77.1 - - - +
207B ARG* 1.3 57.6 + - - +
209B LEU* 3.5 8.6 + - - +
210B GLN* 3.1 45.1 + - - +
245B VAL* 3.7 24.7 - - + -
246B ILE 3.7 10.1 - - - +
247B MET* 3.7 18.6 - - - -
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Residues in contact with ARG 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 VAL* 3.0 24.4 + - - +
204B ALA* 3.7 8.5 - - - +
205B GLU 3.2 0.2 - - - -
206B CYS* 1.3 75.2 - - - +
208B VAL* 1.3 59.8 + - - +
210B GLN* 3.5 18.4 + - - +
211B LYS* 3.0 48.6 + - - +
247B MET* 3.0 35.4 + - + +
248B ASP* 3.5 15.8 - - - +
249B TYR* 4.1 11.7 + - - -
299B SO4 2.9 35.7 + - - -
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Residues in contact with VAL 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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136A ILE* 3.9 17.5 - - + -
141A PHE* 4.0 17.0 - - + -
212A LEU* 3.7 41.3 - - + +
204B ALA 3.0 20.0 + - - +
205B GLU* 3.3 5.8 + - - +
207B ARG* 1.3 73.7 - - - +
209B LEU* 1.3 83.7 + - + +
211B LYS* 3.0 11.2 + - - +
212B LEU* 2.8 42.2 + - + +
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Residues in contact with LEU 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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141A PHE* 3.8 14.6 - - + -
120B LEU* 3.9 15.3 - - + -
138B LEU* 4.0 20.9 - - + -
193B VAL* 4.1 16.6 - - + -
195B VAL* 4.4 7.4 - - + -
201B GLN* 3.9 33.9 - - + +
205B GLU 3.1 16.4 + - - +
206B CYS* 3.6 6.7 - - - +
208B VAL* 1.3 98.7 - - + +
210B GLN* 1.3 61.3 + - - +
212B LEU* 3.4 13.2 + - + +
213B GLY 3.4 0.5 + - - -
214B ALA* 3.2 25.0 + - - +
217B VAL* 4.4 9.6 - - + -
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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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120B LEU* 3.3 36.8 - - + +
122B PRO* 5.7 2.7 - - + -
206B CYS* 3.1 25.7 + - - +
207B ARG* 3.7 23.1 - - - +
209B LEU* 1.3 76.8 - - - +
211B LYS* 1.3 57.7 + - - +
213B GLY* 2.9 21.3 + - - -
214B ALA 4.2 8.6 - - - +
245B VAL 5.4 0.2 - - - +
247B MET* 3.4 42.6 - - - +
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Residues in contact with LYS 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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211A LYS 3.6 23.5 + - - +
212A LEU* 3.9 20.6 + - + +
213A GLY* 4.3 7.1 - - - +
207B ARG* 3.0 34.4 + - - +
208B VAL* 3.0 13.9 + - - +
210B GLN* 1.3 76.3 - - - +
212B LEU* 1.3 62.2 + - + +
213B GLY 3.1 0.4 + - - -
211C LYS* 2.9 29.8 + - - +
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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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212A LEU* 4.5 22.0 - - + -
136B ILE* 3.6 13.0 - - + +
138B LEU* 4.5 21.1 - - + -
193B VAL* 5.6 1.3 - - + -
208B VAL* 2.8 34.0 + - + +
209B LEU* 3.5 18.8 - - + +
211B LYS* 1.3 80.0 - - + +
213B GLY* 1.3 59.5 - - - +
214B ALA* 3.6 0.7 - - + -
204C ALA* 4.8 1.6 - - - +
207C ARG* 5.9 0.9 - - - +
208C VAL* 3.3 45.3 + - + +
211C LYS* 3.6 10.8 + - + +
212C LEU* 4.7 9.9 - - + -
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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