Contacts of the helix formed by residues 202 - 212 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ASP* 3.2 22.0 - - - +
135B HIS* 3.0 42.4 + - + +
162B MET* 3.5 30.7 - - + +
163B SER* 5.0 0.2 - - - -
165B ALA* 5.2 1.3 - - + -
200C PHE 3.8 0.2 + - - -
201C GLN* 1.3 75.4 - - - +
203C VAL* 1.3 59.3 + - - +
204C ALA 3.4 0.3 + - - -
205C GLU* 2.9 32.7 + - - +
206C CYS* 2.8 27.2 + - - +
246C ILE 4.8 1.3 - - - -
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ASP* 3.5 9.2 + - - +
163B SER* 4.2 17.4 - - - +
202C THR* 1.3 72.9 - - - +
204C ALA* 1.3 58.4 + - - +
206C CYS* 3.1 4.3 + - - +
207C ARG* 2.9 34.7 + - - +
246C ILE* 3.8 24.7 - - + +
247C MET 3.6 25.4 - - - +
248C ASP* 3.7 22.7 - - - +
249C TYR* 3.7 33.4 - - + +
251C SER* 5.5 0.9 - - - +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ASP* 2.9 21.6 + - - +
135B HIS 3.5 17.3 - - - +
136B ILE* 3.8 13.6 - - + +
191B THR* 3.8 15.7 - - + +
212B LEU 4.8 1.3 - - - +
213B GLY 5.9 0.4 - - - +
202C THR 3.2 0.2 - - - -
203C VAL* 1.3 76.1 - - - +
205C GLU* 1.3 62.2 + - - +
207C ARG* 3.2 10.2 + - - +
208C VAL* 3.1 27.0 + - - +
249C TYR* 4.4 3.4 - - - +
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Residues in contact with GLU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B HIS* 3.6 13.9 + - - +
136B ILE* 3.9 9.9 - - + -
137B ASN* 2.8 35.9 + - - +
141B PHE* 4.1 19.7 - - + -
162B MET* 6.0 0.2 - - - +
200C PHE 4.3 2.9 - - - +
201C GLN* 3.4 24.3 - - - +
202C THR* 2.9 42.4 + - - +
204C ALA* 1.3 73.4 - - - +
206C CYS* 1.3 65.0 + - - +
208C VAL* 3.1 11.2 + - - +
209C LEU* 3.1 26.7 + - - +
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Residues in contact with CYS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 3.8 11.2 - - - -
201C GLN* 4.2 5.2 - - + +
202C THR 2.8 14.1 + - - +
203C VAL 3.1 8.3 + - - +
205C GLU* 1.3 75.7 - - - +
207C ARG* 1.3 57.7 + - - +
209C LEU* 3.3 8.7 + - - +
210C GLN* 2.9 49.2 + - - +
245C VAL* 3.5 34.3 - - + -
246C ILE 3.7 5.8 - - - +
247C MET* 3.8 17.3 - - - -
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU 5.9 0.7 - - - +
298B SO4 3.1 37.4 + - - -
203C VAL* 2.9 25.0 + - - +
204C ALA* 3.7 7.4 - - - +
205C GLU 3.2 0.6 - - - -
206C CYS* 1.3 77.4 - - - +
208C VAL* 1.3 56.6 + - + +
210C GLN* 3.5 20.3 + - - +
211C LYS* 3.0 45.1 + - - +
247C MET* 2.9 32.0 + - + +
248C ASP* 3.6 15.4 - - - +
249C TYR* 3.9 10.9 - - - -
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ILE* 4.0 15.9 - - + -
141B PHE* 4.1 18.8 - - + -
212B LEU* 3.3 48.0 - - + +
204C ALA 3.1 15.9 + - - +
205C GLU* 3.1 8.8 + - - +
207C ARG* 1.3 73.1 - - - +
209C LEU* 1.3 76.5 + - + +
211C LYS* 3.1 8.2 + - - +
212C LEU* 2.8 44.1 + - + +
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 4.1 7.0 - - + -
120C LEU* 3.7 15.7 - - + -
138C LEU* 3.9 28.3 - - + -
193C VAL* 4.0 16.8 - - + -
195C VAL* 4.4 3.4 - - + -
201C GLN* 4.1 31.4 - - + +
205C GLU 3.1 11.0 + - - +
206C CYS* 3.5 9.9 - - - +
208C VAL* 1.3 95.4 - - + +
210C GLN* 1.3 61.1 + - - +
212C LEU* 3.5 11.8 + - + +
213C GLY 3.4 3.3 + - - -
214C ALA* 3.2 23.6 + - - +
217C VAL* 4.1 19.5 - - + -
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 3.0 38.4 - - + +
122C PRO* 4.8 3.6 - - + +
206C CYS* 2.9 25.8 + - - +
207C ARG* 3.6 34.4 - - - +
208C VAL 3.3 0.2 - - - -
209C LEU* 1.3 75.6 - - - +
211C LYS* 1.3 57.6 + - + +
213C GLY* 2.9 19.9 + - - -
214C ALA 4.3 6.6 + - - +
245C VAL 5.5 0.2 - - - +
247C MET* 3.4 37.4 - - - +
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Residues in contact with LYS 211 (chain C).
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* 3.1 28.8 + - - +
211B LYS 2.9 29.9 + - - +
212B LEU* 3.6 19.9 + - + -
213B GLY* 3.8 6.7 - - - +
207C ARG* 3.0 33.5 + - - +
208C VAL* 3.1 7.8 + - - +
210C GLN* 1.3 77.2 - - + +
212C LEU* 1.3 61.3 + - + +
213C GLY 3.1 0.4 - - - -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ALA 4.8 1.0 - - - +
207A ARG* 5.9 0.7 - - - +
208A VAL* 3.5 38.8 + - + +
211A LYS* 3.7 12.9 + - + +
212A LEU* 4.3 23.6 - - + -
141B PHE* 6.1 0.7 - - + -
212B LEU* 4.7 12.8 - - + -
136C ILE* 3.6 12.1 - - + +
138C LEU* 4.7 18.8 - - + -
193C VAL* 6.1 1.6 - - + -
208C VAL* 2.8 34.5 + - + +
209C LEU* 3.5 17.3 - - + +
211C LYS* 1.3 82.5 - - + +
213C GLY* 1.3 57.0 + - - +
214C ALA* 3.5 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