Contacts of the helix formed by residues 86 - 96 (chain C) in PDB entry 3TQI
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 CYS 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C GLY 4.2 4.3 - - - +
84C GLY 3.9 0.2 + - - -
85C ILE* 1.3 66.3 - - - +
87C TYR* 1.3 67.4 + - - +
88C GLY 3.1 0.2 - - - -
89C MET* 3.2 6.4 + - - +
90C GLN* 3.1 15.6 + - - +
142C SER* 3.5 16.6 - - - +
145C ASP* 3.2 27.5 - - - +
178C LEU 2.8 18.8 + - - -
179C GLN* 3.8 7.8 - - - +
180C PHE* 3.6 22.0 - - - -
181C HIS* 3.3 43.7 - - + +
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Residues in contact with TYR 87 (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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15C PHE* 3.8 38.4 - + + -
58C GLY 3.7 18.8 + - - +
59C GLY* 3.9 10.8 - - - +
71C ALA 4.8 4.7 + - - -
85C ILE 3.1 1.2 + - - -
86C CYS* 1.3 77.4 - - - +
88C GLY* 1.3 65.9 + - - +
90C GLN* 3.1 37.2 + - - +
91C THR* 3.1 46.6 + - + +
145C ASP* 3.1 13.8 + - - +
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Residues in contact with GLY 88 (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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15C PHE* 5.1 1.8 - - - -
56C LEU* 3.7 24.0 - - - +
57C SER 3.1 15.5 + - - -
84C GLY* 3.6 6.7 - - - -
85C ILE 2.9 13.0 + - - -
87C TYR* 1.3 78.8 - - - +
89C MET* 1.3 59.5 + - - +
91C THR* 3.7 5.6 + - - -
92C MET* 3.1 24.8 + - - +
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Residues in contact with MET 89 (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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84C GLY* 3.4 17.7 - - - +
86C CYS 3.2 10.2 + - - +
88C GLY* 1.3 72.8 - - - +
90C GLN* 1.3 66.1 + - - +
92C MET* 3.4 5.4 + - - +
93C ALA* 2.9 21.7 + - - +
145C ASP 5.4 0.4 - - - +
147C VAL* 4.2 16.8 - - + -
165C LEU 3.5 23.3 - - - +
167C ALA 3.8 4.9 - - - +
168C MET* 3.2 56.1 - - + +
177C GLY* 3.8 5.4 - - - -
178C LEU 3.4 34.3 - - - +
179C GLN* 3.6 12.3 - - - -
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Residues in contact with GLN 90 (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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86C CYS 3.1 5.3 + - - -
87C TYR* 3.1 36.7 + - + +
89C MET* 1.3 75.6 - - - +
91C THR* 1.3 58.7 + - + +
93C ALA* 2.9 9.2 + - - +
94C TYR* 2.8 26.1 + - - +
100C VAL* 3.3 30.0 - - + +
101C ASN 3.5 22.2 - - - -
144C GLY 4.0 1.6 + - - -
145C ASP* 3.7 36.1 - - + +
146C ILE 3.2 23.3 + - - +
147C VAL* 4.7 2.5 - - + -
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Residues in contact with THR 91 (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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15C PHE* 4.5 5.5 - - - -
56C LEU* 4.8 1.9 - - - +
71C ALA* 4.1 15.5 - - + +
72C PRO* 4.3 7.8 - - - +
87C TYR* 3.1 50.8 + - + +
88C GLY* 3.7 7.6 + - - -
90C GLN* 1.3 76.5 - - + +
92C MET* 1.3 59.8 + - - +
94C TYR* 4.1 9.6 - - + -
95C GLN* 2.7 54.3 + - - +
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Residues in contact with MET 92 (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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56C LEU* 4.6 8.4 - - + +
76C PHE* 4.4 17.0 - - + -
82C VAL* 4.7 11.9 - - - +
84C GLY* 4.3 10.3 - - - -
88C GLY 3.1 18.9 + - - +
89C MET* 3.5 3.6 - - - +
91C THR* 1.3 76.9 + - - +
93C ALA* 1.3 63.0 + - - +
96C LEU* 3.3 36.4 + - + +
154C PHE* 3.2 36.6 - - + -
168C MET* 3.4 14.8 - - + -
175C PHE* 3.7 6.5 - - + -
176C PHE 3.3 43.3 - - - +
177C GLY* 4.6 0.7 - - - -
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Residues in contact with ALA 93 (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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89C MET 2.9 12.4 + - - +
90C GLN* 2.9 11.9 + - - +
92C MET* 1.3 77.3 - - - +
94C TYR* 1.3 64.2 + - - +
95C GLN 3.3 0.3 + - - -
96C LEU 3.1 3.1 - - - +
97C GLY 2.4 26.3 - - - +
98C GLY 4.6 2.5 - - - -
99C LYS 5.0 3.1 - - - +
100C VAL* 4.9 3.4 - - + -
147C VAL* 3.9 28.5 - - + -
149C GLU 5.3 0.4 - - - +
151C PRO* 3.9 18.4 - - + -
168C MET* 4.5 5.8 - - - -
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Residues in contact with TYR 94 (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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90C GLN 2.8 15.4 + - - +
91C THR* 3.8 14.8 - - + +
93C ALA* 1.3 73.3 - - - +
95C GLN* 1.3 61.6 + - + +
96C LEU 2.6 17.3 - - - +
98C GLY 4.2 13.3 - - - +
99C LYS* 6.3 1.8 - - - -
100C VAL* 4.0 27.4 - - + +
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Residues in contact with GLN 95 (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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71C ALA* 3.4 16.3 - - + +
72C PRO* 3.1 28.5 - - - +
73C ALA* 3.1 37.3 + - - +
76C PHE* 4.3 17.3 - - + -
91C THR* 2.7 40.1 + - - +
92C MET 4.6 0.4 - - - +
94C TYR* 1.3 76.6 - - + +
96C LEU* 1.3 66.7 + - - +
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Residues in contact with LEU 96 (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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76C PHE* 4.4 28.0 - - + -
92C MET* 3.3 25.3 + - + +
93C ALA 4.1 1.3 - - - +
94C TYR 2.6 20.6 - - - +
95C GLN* 1.3 81.3 - - + +
97C GLY* 1.3 64.8 + - - +
151C PRO* 4.2 8.1 - - + -
154C PHE* 3.5 30.3 - - + -
173C ARG* 3.9 26.2 - - - +
175C PHE* 3.8 20.4 - - + -
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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