Contacts of the helix formed by residues 166 - 177 (chain C) in PDB entry 3G33
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 LEU 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C TYR* 4.1 27.6 - - + +
40C LYS* 4.5 13.9 - - + -
65C LEU* 3.8 20.9 - - + -
96C LEU* 4.4 14.4 - - + -
98C PHE* 4.4 10.5 - - + -
163C ASP* 4.0 33.2 - - - +
164C PHE 3.0 7.9 + - - +
165C GLY* 1.3 78.3 - - - +
167C ALA* 1.3 63.5 + - - +
168C ARG 3.7 1.1 - - - -
169C ILE* 3.4 31.9 - - + -
170C TYR* 3.6 26.9 + - + +
174C MET* 5.3 0.2 - - - +
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Residues in contact with ALA 167 (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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61C GLU* 3.5 8.7 + - - +
144C ARG* 5.3 14.6 - - + +
164C PHE 4.9 0.4 + - - +
165C GLY 3.5 4.3 - - - -
166C LEU* 1.3 80.0 - - - +
168C ARG* 1.3 58.1 + - + +
169C ILE 3.2 1.1 + - - -
170C TYR* 4.2 1.0 - - - +
171C SER* 2.6 30.2 + - - -
174C MET* 5.2 1.2 - - - +
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Residues in contact with ARG 168 (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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57C SER* 3.4 40.6 + - - +
58C THR* 4.2 9.4 + - - -
60C ARG* 5.8 4.9 - - - +
61C GLU* 3.1 27.5 + - - +
167C ALA* 1.3 80.0 - - + +
169C ILE* 1.3 60.7 + - - +
170C TYR 3.4 0.4 - - - -
171C SER* 3.7 16.8 + - - +
172C TYR* 4.8 4.2 + - - +
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Residues in contact with ILE 169 (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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42C VAL* 4.0 30.3 - - + +
43C ARG 5.7 1.2 - - - +
44C VAL* 5.3 3.0 - - + +
58C THR* 4.1 26.7 - - + -
61C GLU* 3.7 23.8 - - + +
62C VAL* 4.3 23.1 - - + +
65C LEU* 4.9 1.6 - - + -
94C VAL* 6.4 0.4 - - + -
96C LEU* 4.8 6.5 - - + -
165C GLY 4.0 6.1 - - - +
166C LEU* 3.4 38.6 - - + +
167C ALA 3.2 0.4 - - - -
168C ARG* 1.3 78.1 - - - +
170C TYR* 1.3 73.8 + - + +
172C TYR* 4.8 6.4 + - - +
173C GLN* 4.9 5.4 + - - +
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Residues in contact with TYR 170 (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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21C ALA 3.6 5.8 - - - -
22C TYR* 2.2 69.6 + + + -
40C LYS* 3.0 34.4 - - + +
41C SER 3.9 0.5 + - - -
42C VAL* 2.3 43.4 - - + +
96C LEU* 4.9 3.3 - - + +
166C LEU* 3.6 19.0 + - + +
167C ALA 3.6 2.2 + - - -
168C ARG 3.4 0.2 - - - -
169C ILE* 1.3 88.5 - - + +
171C SER* 1.3 57.0 + - - +
172C TYR 3.3 2.2 - - - -
173C GLN* 3.9 11.7 - - + -
174C MET* 2.6 61.2 + - + +
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Residues in contact with SER 171 (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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167C ALA 2.6 26.1 + - - -
168C ARG* 3.7 14.6 + - - +
169C ILE 3.6 1.0 - - - -
170C TYR* 1.3 77.3 - - - +
172C TYR* 1.3 61.7 + - - +
174C MET* 4.2 4.9 - - - +
175C ALA* 3.1 26.9 + - - +
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Residues in contact with TYR 172 (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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43C ARG* 3.6 30.5 + - + -
44C VAL* 5.5 3.6 - - - -
45C PRO* 5.5 15.7 - - + -
91C GLU* 3.3 21.6 + - - +
168C ARG 4.8 4.3 + - - +
169C ILE 4.8 6.0 + - - +
170C TYR* 3.3 0.6 - - - +
171C SER* 1.3 80.7 - - - +
173C GLN* 1.3 68.6 + - + +
175C ALA* 3.4 5.6 + - - +
176C LEU* 3.2 58.0 + - + +
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Residues in contact with GLN 173 (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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22C TYR 4.6 13.5 - - - +
23C GLY* 5.6 1.4 - - - -
41C SER 4.1 3.7 + - - +
42C VAL* 3.5 21.3 - - + +
43C ARG* 3.4 60.0 + - + +
169C ILE 4.9 3.3 + - - +
170C TYR* 3.5 16.5 + - - +
171C SER 3.4 0.2 - - - -
172C TYR* 1.3 85.3 - - + +
174C MET* 1.3 59.7 + - - +
176C LEU* 2.7 30.2 + - - +
177C THR* 2.9 13.5 + - - -
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Residues in contact with MET 174 (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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21C ALA* 3.6 23.8 - - + +
22C TYR* 5.0 3.8 - - + -
166C LEU 5.3 0.2 - - - +
167C ALA 5.2 1.6 - - - +
170C TYR* 2.6 73.6 + - + +
171C SER* 3.9 5.2 - - - +
173C GLN* 1.3 76.9 - - - +
175C ALA* 1.3 62.6 + - - +
177C THR* 2.7 28.0 - - - +
178C PRO* 3.7 3.8 - - - +
179C VAL* 3.7 27.9 + - + -
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Residues in contact with ALA 175 (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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171C SER 3.1 19.3 + - - +
172C TYR* 3.6 6.7 - - - +
174C MET* 1.3 76.3 - - - +
176C LEU* 1.3 63.8 + - + +
177C THR 4.9 0.7 - - - -
178C PRO* 5.0 2.9 - - - +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 3.8 27.8 - - - +
172C TYR* 3.2 56.3 + - + +
173C GLN* 2.7 13.0 + - - +
175C ALA* 1.3 81.0 - - + +
177C THR* 1.3 60.5 + - - +
178C PRO* 3.4 9.7 - - - +
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Residues in contact with THR 177 (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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43C ARG* 4.4 10.4 + - - -
173C GLN 2.9 10.6 + - - -
174C MET* 2.7 16.1 - - - +
176C LEU* 1.3 80.9 - - - +
178C PRO* 1.3 77.8 - - + +
179C VAL* 2.9 19.5 + - + +
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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