Contacts of the helix formed by residues 82 - 93 (chain H) in PDB entry 1TZY
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 82 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ARG* 4.7 10.7 + - - +
83F TYR* 3.8 4.2 + - - -
85G GLN* 3.6 28.9 - - + +
88G ALA* 3.6 4.7 - - - -
78H ARG* 4.1 17.4 + - - +
80H THR* 3.6 15.7 - - + +
81H VAL* 1.3 75.8 - - - +
83H ALA* 1.3 65.8 + - - +
84H MET* 3.5 6.7 + - - +
85H ASP* 3.0 38.7 + - - +
86H VAL* 3.2 14.4 + - - +
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Residues in contact with ALA 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G GLN* 3.3 7.8 + - - +
87G SER* 3.6 34.8 - - - +
88G ALA* 3.7 11.4 - - - +
91G ALA* 4.7 1.5 - - + +
82H THR* 1.3 73.3 - - - +
84H MET* 1.3 58.1 + - - +
86H VAL* 3.0 7.3 + - - +
87H VAL* 2.9 31.8 + - - +
100H PHE* 4.2 25.4 - - + +
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Residues in contact with MET 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 5.4 11.9 - - + +
34B LYS* 4.2 25.1 - - + +
1614B CL 4.4 2.9 - - + -
83F TYR* 3.5 30.7 - - + +
82H THR* 3.3 6.1 + - - +
83H ALA* 1.3 78.6 - - - +
85H ASP* 1.3 56.0 + - - +
87H VAL* 3.7 18.6 - - + -
88H TYR* 2.9 55.9 + - + -
100H PHE 3.6 9.8 + - - +
101H GLY* 3.6 32.8 - - - +
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Residues in contact with ASP 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F TYR* 2.5 29.4 + - - -
69H ALA* 3.8 13.8 - - - +
72H TYR* 3.9 8.5 - - + +
73H THR* 2.6 32.7 + - - +
78H ARG* 2.7 24.3 + - - -
81H VAL* 3.7 6.0 - - + -
82H THR* 3.0 33.4 + - - +
84H MET* 1.3 74.4 - - - +
86H VAL* 1.3 56.8 + - - +
88H TYR* 3.8 3.4 - - - +
89H ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ALA* 3.8 22.4 - - + +
91G ALA* 3.8 23.3 - - + -
92G LEU* 3.7 34.8 - - + +
65H VAL* 4.6 1.3 - - + -
69H ALA* 4.2 15.3 - - + -
81H VAL* 4.3 5.4 - - + -
82H THR 3.2 10.7 + - - +
83H ALA 3.0 8.6 + - - +
85H ASP* 1.3 75.6 - - - +
87H VAL* 1.3 58.3 + - - +
89H ALA* 3.2 2.7 + - - +
90H LEU* 2.9 44.6 + - + +
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Residues in contact with VAL 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 5.3 9.6 - - - +
91G ALA* 5.2 0.9 - - + -
83H ALA 2.9 23.9 + - - +
84H MET* 3.3 26.0 + - + +
86H VAL* 1.3 72.6 - - - +
88H TYR* 1.3 64.2 + - + +
90H LEU* 3.3 9.2 + - - +
91H LYS* 3.1 23.6 + - + +
95H ARG 4.7 0.9 - - - +
96H THR* 6.3 0.7 - - + -
97H LEU* 4.1 37.0 + - + +
100H PHE* 3.9 25.6 - - + -
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Residues in contact with TYR 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 5.2 9.0 - - - -
76F GLU* 5.3 0.7 - - - -
79F ARG* 4.5 24.8 + - + -
82F HIS* 5.0 5.9 + - - -
83F TYR* 3.7 45.9 + + + +
72H TYR* 3.7 42.0 + + + -
84H MET* 2.9 52.2 + - + +
85H ASP* 3.8 3.6 - - - +
87H VAL* 1.3 76.3 - - + +
89H ALA* 1.3 66.1 + - - +
91H LYS* 3.2 9.0 + - + +
92H ARG* 3.0 22.2 + - - +
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H VAL* 3.6 16.9 - - + +
68H ASP* 3.7 11.9 - - + +
69H ALA* 3.4 33.4 - - + +
72H TYR* 3.9 8.4 - - - -
85H ASP 3.0 14.6 + - - +
86H VAL 3.2 4.7 + - - +
88H TYR* 1.3 74.6 - - - +
90H LEU* 1.3 63.9 + - - +
92H ARG* 3.1 14.6 + - - +
93H GLN* 3.3 14.4 + - - +
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Residues in contact with LEU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G ALA* 3.5 34.1 - - + -
61H PHE* 4.2 8.5 - - + -
65H VAL* 3.8 30.3 - - + -
86H VAL* 2.9 29.6 + - + +
87H VAL* 3.6 5.2 - - - +
89H ALA* 1.3 73.8 - - - +
91H LYS* 1.3 66.4 + - - +
93H GLN* 2.9 17.7 + - + +
95H ARG* 3.0 42.4 + - + +
97H LEU* 3.8 29.2 - - + -
1605H CL 4.2 1.1 - - + -
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Residues in contact with LYS 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 5.1 6.1 - - - +
68B ASP* 4.2 12.4 + - - +
71B GLU* 4.5 12.1 + - - -
79F ARG* 6.1 4.9 - - - -
87H VAL* 3.1 16.0 + - + +
88H TYR* 3.2 12.3 + - - +
90H LEU* 1.3 74.9 - - - +
92H ARG* 1.3 59.1 + - - +
94H GLY* 2.8 23.6 + - - -
95H ARG 3.1 8.4 + - - +
96H THR* 3.6 36.8 + - - +
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Residues in contact with ARG 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F GLU* 3.9 19.4 + - - -
79F ARG* 5.0 6.7 - - - +
100F LEU* 3.9 37.4 + - + +
101F LEU* 3.5 31.4 + - - +
68H ASP* 3.8 20.6 - - - +
72H TYR* 4.4 9.0 - - + +
88H TYR 3.0 12.3 + - - +
89H ALA* 3.4 13.0 - - - +
90H LEU 3.0 0.4 - - - -
91H LYS* 1.3 79.9 + - - +
93H GLN* 1.4 54.9 + - - +
94H GLY 3.6 0.3 + - - -
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Residues in contact with GLN 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H PHE* 4.9 10.7 - - + -
64H ASN* 3.7 34.5 + - - +
65H VAL* 4.1 21.1 - - + -
68H ASP* 4.3 14.1 + - - -
89H ALA 3.3 13.7 + - - +
90H LEU* 2.9 10.7 + - - +
92H ARG* 1.4 73.3 - - - +
94H GLY* 1.3 60.3 + - - +
95H ARG* 3.5 17.5 + - - +
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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