Contacts of the helix formed by residues 86 - 96 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLY 4.6 4.3 - - - +
85B ILE* 1.3 71.4 - - + +
87B TYR* 1.3 65.0 + - - +
89B MET* 2.9 16.3 + - - +
90B GLN 3.2 7.6 + - - -
142B SER* 3.6 16.2 - - - -
145B ASP* 3.4 26.0 - - - +
178B LEU 2.8 18.4 + - - -
179B GLN* 3.8 6.2 - - - +
180B PHE* 3.5 30.5 - - - -
181B HIS* 3.4 35.0 - - + +
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Residues in contact with TYR 87 (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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15B PHE* 4.0 33.2 - + + -
58B GLY 4.0 3.1 + - - +
59B GLY* 3.9 27.6 - - - +
71B ALA* 5.0 4.3 + - - +
85B ILE 3.0 1.0 + - - -
86B CYS* 1.3 78.3 - - - +
88B GLY* 1.3 56.5 + - - +
90B GLN* 2.9 26.9 + - - +
91B THR* 2.9 64.5 + - + +
145B ASP* 3.1 19.3 + - - +
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 5.3 1.1 - - - -
56B LEU* 3.8 23.0 - - - +
57B SER 3.3 11.0 + - - -
84B GLY* 3.6 7.4 - - - -
85B ILE 2.7 21.2 + - - -
87B TYR* 1.3 74.2 - - - +
89B MET* 1.3 58.4 + - - -
91B THR* 3.3 7.3 + - - -
92B MET* 3.1 26.2 + - - +
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY* 3.6 10.9 - - - +
86B CYS 2.9 10.6 + - - +
88B GLY* 1.3 77.3 - - - +
90B GLN* 1.3 61.1 + - - +
92B MET* 3.5 5.6 - - - +
93B ALA* 3.0 22.2 + - - +
145B ASP 5.6 2.0 - - - +
147B VAL* 3.5 24.9 - - + -
165B LEU 3.4 26.0 - - - +
166B ALA* 4.1 0.9 - - - +
167B ALA* 3.9 8.3 - - - +
168B MET* 3.5 36.4 - - + +
177B GLY* 3.5 6.5 - - - -
178B LEU 3.3 45.5 - - - +
179B GLN* 3.5 10.5 - - + -
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B CYS 3.2 2.2 + - - -
87B TYR* 2.9 34.6 + - + +
89B MET* 1.3 78.9 - - - +
91B THR* 1.3 52.9 + - + +
93B ALA* 3.0 4.5 + - - +
94B TYR* 2.8 35.8 + - - +
100B VAL* 3.4 33.8 - - + +
101B ASN 3.7 13.2 - - - +
144B GLY 4.2 2.0 + - - -
145B ASP* 3.7 28.0 + - + +
146B ILE 3.0 29.9 + - - +
147B VAL* 4.0 7.2 - - + +
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Residues in contact with THR 91 (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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15B PHE* 4.7 5.0 - - + -
56B LEU* 4.7 5.0 - - - +
71B ALA* 4.2 16.4 - - + +
72B PRO* 4.6 4.9 - - + -
76B PHE* 5.4 0.2 - - - -
87B TYR* 2.9 58.0 + - + +
88B GLY* 3.3 10.4 + - - -
90B GLN* 1.3 73.8 - - - +
92B MET* 1.3 57.6 + - - +
94B TYR* 3.7 11.8 - - + +
95B GLN* 2.8 51.6 + - - +
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Residues in contact with MET 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.6 3.3 - - + +
76B PHE* 4.2 30.7 - - + -
82B VAL* 4.4 7.6 - - - +
84B GLY* 4.3 9.4 - - - -
88B GLY 3.1 19.0 + - - +
89B MET 3.5 3.1 - - - +
91B THR* 1.3 77.9 - - - +
93B ALA* 1.3 61.3 + - - +
95B GLN* 4.1 0.7 - - - +
96B LEU* 3.2 38.0 + - + +
154B PHE* 3.2 37.0 - - + -
168B MET* 3.6 12.6 - - + -
175B PHE* 3.7 7.2 - - + -
176B PHE 3.4 43.3 - - - +
177B GLY* 4.8 0.4 - - - -
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Residues in contact with ALA 93 (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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89B MET 3.0 12.9 + - - +
90B GLN 3.0 9.5 + - - +
92B MET* 1.3 76.7 - - - +
94B TYR* 1.3 56.9 + - - +
95B GLN 3.2 0.2 + - - -
96B LEU* 2.9 12.1 + - - +
97B GLY 2.5 26.7 - - - +
98B GLY 4.6 2.0 - - - -
99B LYS 5.1 3.4 - - - +
100B VAL* 4.7 3.1 - - + -
147B VAL* 3.9 22.2 - - + -
149B GLU 5.4 2.2 - - - +
151B PRO* 4.0 18.2 - - + -
168B MET* 4.3 12.3 - - + -
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Residues in contact with TYR 94 (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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71B ALA* 5.9 6.1 - - + -
90B GLN 2.8 18.5 + - - +
91B THR* 3.8 12.6 - - + +
93B ALA* 1.3 73.3 - - - +
95B GLN* 1.3 66.9 + - + +
96B LEU 2.9 10.7 - - - +
98B GLY 4.2 15.3 - - - +
99B LYS* 6.1 0.4 - - - -
100B VAL* 5.1 19.9 - - + +
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Residues in contact with GLN 95 (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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71B ALA* 3.1 28.8 + - + +
72B PRO* 3.2 19.1 - - - +
73B ALA* 3.1 37.9 - - - +
76B PHE* 4.3 17.4 - - + -
91B THR* 2.8 31.3 + - - +
92B MET 4.3 0.2 - - - +
94B TYR* 1.3 79.4 - - + +
96B LEU* 1.3 68.0 + - - +
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Residues in contact with LEU 96 (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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76B PHE* 4.5 26.0 - - + -
92B MET* 3.2 24.3 + - + +
93B ALA 3.2 3.6 + - - +
94B TYR 2.9 18.0 - - - +
95B GLN* 1.3 80.1 - - - +
97B GLY* 1.3 67.3 + - - +
98B GLY 4.7 0.2 - - - +
151B PRO* 4.2 9.2 - - + -
154B PHE* 3.7 31.4 - - + -
173B ARG* 3.7 26.5 - - - +
175B PHE* 3.9 15.9 - - + -
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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