Contacts of the helix formed by residues 83 - 93 (chain B) in PDB entry 6T90
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLN* 2.5 30.3 + - - -
89A ALA* 3.8 4.0 - - - -
79B ARG* 4.1 16.2 - - - +
81B THR* 3.5 1.2 + - - -
82B VAL* 1.3 75.5 - - - +
84B ALA* 1.3 76.9 + - - +
85B MET* 3.7 19.6 + - + +
86B ASP* 3.0 36.0 + - - +
87B VAL* 3.3 13.0 + - - +
84D TYR* 4.3 1.6 - - - +
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Residues in contact with ALA 84 (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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86A GLN* 3.7 2.6 + - - -
88A SER* 3.5 30.7 - - - +
89A ALA* 4.1 12.3 - - - +
92A ALA* 4.8 1.2 - - + +
83B THR* 1.3 81.5 + - - +
85B MET* 1.3 58.2 + - + +
87B VAL* 3.2 5.6 + - - +
88B VAL* 2.9 31.2 + - - +
101B PHE* 4.1 23.3 - - + +
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Residues in contact with MET 85 (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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83B THR* 3.1 10.3 - - + +
84B ALA* 1.3 77.1 - - + +
86B ASP* 1.3 60.6 + - - +
88B VAL* 3.9 9.8 - - + +
89B TYR* 2.9 67.7 + - + +
101B PHE 4.1 17.7 - - - +
102B GLY* 4.1 11.2 - - - -
103B GLY* 4.0 23.8 - - - +
84D TYR* 3.7 19.5 - - + +
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Residues in contact with ASP 86 (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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70B ALA* 3.7 27.5 - - + +
73B TYR* 3.8 12.5 - - + +
74B THR* 3.3 13.8 + - - +
79B ARG* 3.0 22.5 + - - -
82B VAL* 4.3 0.9 - - + -
83B THR* 3.0 27.7 + - - +
85B MET* 1.3 77.1 - - - +
87B VAL* 1.3 58.8 + - - +
89B TYR* 4.1 3.9 - - - +
90B ALA* 3.0 28.1 + - - +
84D TYR* 2.6 34.3 + - - -
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Residues in contact with VAL 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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89A ALA* 3.9 22.2 - - + +
92A ALA* 3.7 22.7 - - + -
93A LEU* 3.8 32.3 - - + +
66B VAL* 4.5 1.3 - - + -
70B ALA* 4.2 16.6 - - + -
82B VAL* 4.3 4.7 - - + -
83B THR 3.3 10.3 + - - +
84B ALA 3.2 7.5 + - - +
86B ASP* 1.3 78.4 - - - +
88B VAL* 1.3 63.5 + - - +
90B ALA* 3.2 3.4 + - - +
91B LEU* 3.0 36.6 + - + +
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Residues in contact with VAL 88 (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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92A ALA* 5.0 2.0 - - + -
84B ALA 2.9 21.6 + - - +
85B MET* 3.9 14.4 - - + +
86B ASP 3.3 0.2 - - - -
87B VAL* 1.3 76.7 - - - +
89B TYR* 1.3 59.2 + - + +
91B LEU* 3.4 6.7 + - - +
92B LYS* 2.9 35.6 + - + +
97B THR* 6.4 1.1 - - + -
98B LEU* 4.5 27.7 + - + +
101B PHE* 4.1 26.9 - - + +
102B GLY 4.0 19.1 - - - +
103B GLY* 4.3 12.8 - - - -
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Residues in contact with TYR 89 (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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73B TYR* 3.8 26.2 + + + +
85B MET* 2.9 53.0 + - + +
86B ASP* 4.1 1.8 - - - +
88B VAL* 1.3 73.5 - - + +
90B ALA* 1.3 66.4 + - - +
92B LYS* 3.7 30.8 - - + +
93B ARG* 3.0 26.2 + - - +
103B GLY 5.1 2.1 + - - -
80D ARG* 5.0 22.2 - - + -
83D HIS* 6.0 1.6 - - - -
84D TYR* 3.6 55.6 - + + +
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Residues in contact with ALA 90 (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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66B VAL* 3.4 30.5 - - + +
69B ASP* 3.7 22.9 - - + +
70B ALA* 3.7 4.3 - - + +
73B TYR* 4.0 4.0 - - - -
86B ASP 3.0 19.1 + - - +
87B VAL 3.2 5.4 + - - +
89B TYR* 1.3 77.0 - - - +
91B LEU* 1.3 62.4 + - - +
93B ARG* 3.6 7.0 - - - +
94B GLN* 3.6 23.5 + - - +
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Residues in contact with LEU 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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92A ALA 4.5 0.2 - - - +
96A ALA* 3.7 28.5 - - + -
62B PHE* 4.3 7.4 - - + -
66B VAL* 3.7 32.5 - - + -
87B VAL* 3.0 30.7 + - + +
88B VAL* 3.8 3.6 - - - +
90B ALA* 1.3 73.9 - - - +
92B LYS* 1.3 65.7 + - - +
93B ARG 3.1 1.3 - - - -
94B GLN* 2.9 15.9 + - - +
96B ARG* 3.0 39.4 + - + +
98B LEU* 3.7 35.7 - - + -
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Residues in contact with LYS 92 (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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88B VAL* 2.9 25.0 + - + +
89B TYR* 3.2 28.5 + - + +
91B LEU* 1.3 75.5 - - - +
93B ARG* 1.3 63.1 + - - +
95B GLY* 3.0 15.6 + - - -
96B ARG 3.8 10.7 + - - -
97B THR* 4.4 25.9 + - - +
103B GLY* 2.8 29.5 + - - -
80D ARG* 4.7 16.0 - - - +
69H ASP* 5.8 4.1 + - - -
72H GLU* 4.1 18.2 + - - +
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Residues in contact with ARG 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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69B ASP* 3.2 28.3 + - - +
73B TYR* 3.7 22.8 + - - +
89B TYR 3.0 12.9 + - - +
90B ALA 3.6 6.7 - - - +
92B LYS* 1.3 82.7 - - - +
94B GLN* 1.3 61.0 + - - +
95B GLY 3.2 1.4 + - - -
77D GLU* 4.5 11.7 + - - +
101D LEU* 2.6 47.9 + - - +
102D LEU* 3.6 20.8 - - - +
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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