Contacts of the helix formed by residues 79 - 100 (chain B) in PDB entry 5A0Q
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 GLY 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TYR* 5.3 2.2 - - - -
75B TYR* 3.5 27.7 - - - -
77B GLY 3.6 3.6 + - - -
78B MET* 1.3 69.6 - - - +
80B PRO* 1.3 73.3 - - - +
81B ASP 3.2 0.9 + - - -
82B TYR* 3.3 16.1 + - - +
83B ARG* 2.8 19.2 + - - +
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Residues in contact with PRO 80 (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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123A GLN* 2.7 25.1 - - + +
157A ALA* 3.1 38.8 - - + +
158A GLY* 3.6 12.0 - - - +
159A TYR* 3.7 24.5 - - + +
78B MET* 3.8 10.5 - - + -
79B GLY* 1.3 90.7 - - - +
81B ASP* 1.3 55.7 + - + +
83B ARG* 3.5 24.5 + - - +
127B ARG* 6.2 1.3 - - - +
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Residues in contact with ASP 81 (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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123A GLN* 3.3 17.7 + - - +
127A GLN* 3.2 23.2 - - - +
78B MET* 4.0 18.4 - - + +
79B GLY 3.3 0.4 - - - -
80B PRO* 1.3 76.6 - - - +
82B TYR* 1.3 63.9 + - - +
83B ARG 3.3 0.2 - - - -
84B VAL 3.6 1.4 + - - -
85B LEU* 3.2 21.0 + - - +
127B ARG* 3.9 9.5 + - - +
129B PHE* 3.2 25.1 - - - +
130B GLY 3.2 25.2 + - - -
131B VAL* 3.5 20.0 + - + +
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Residues in contact with TYR 82 (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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61B VAL* 5.4 4.5 - - + -
62B HIS 4.0 5.2 - - - -
63B LYS 3.0 22.7 + - - -
65B GLU* 3.2 44.9 + - + +
73B LEU* 3.4 27.4 - - + +
75B TYR* 3.2 54.1 - + + -
78B MET 4.2 0.2 - - - +
79B GLY 3.3 13.0 + - - +
81B ASP* 1.3 77.4 - - - +
83B ARG* 1.3 63.0 + - + +
85B LEU* 4.3 3.8 - - + -
86B VAL* 3.0 53.4 + - + +
131B VAL* 3.7 17.4 - - + +
133B LEU* 4.4 4.9 - - + -
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Residues in contact with ARG 83 (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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116A LYS* 6.0 0.4 - - + -
119A ALA* 4.9 0.4 - - - -
120A ASP* 3.7 15.5 - - - +
158A GLY 3.2 18.2 - - - -
159A TYR* 2.7 41.7 - - - +
160A TYR* 2.8 53.2 + - + +
61B VAL* 3.4 28.8 - - + +
65B GLU* 5.1 3.8 - - - +
75B TYR* 4.9 1.8 + - - -
79B GLY* 2.8 41.3 + - - +
80B PRO* 3.4 10.9 + - - +
81B ASP 3.3 0.6 - - - -
82B TYR* 1.3 81.6 - - + +
84B VAL* 1.3 54.3 + - + +
86B VAL* 4.2 3.3 - - - +
87B HIS* 2.7 43.4 + - + +
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Residues in contact with VAL 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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120A ASP* 4.0 36.6 - - + +
123A GLN* 3.0 38.3 + - - +
124A VAL* 6.6 0.2 - - + -
81B ASP 3.6 1.2 + - - -
82B TYR 3.2 0.2 - - - -
83B ARG* 1.3 77.1 - - + +
85B LEU* 1.3 67.9 + - - +
86B VAL 3.2 1.3 - - - -
87B HIS* 3.0 20.3 + - + +
88B ARG* 3.2 12.3 + - + +
120B TYR* 6.2 0.2 - - - +
129B PHE* 5.6 4.9 - - + -
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Residues in contact with LEU 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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73B LEU* 4.5 6.7 - - + -
81B ASP 3.2 17.9 + - - +
82B TYR* 3.3 6.5 + - + +
84B VAL* 1.3 78.2 - - - +
86B VAL* 1.3 63.8 + - + +
88B ARG* 3.3 7.7 + - + +
89B ALA* 3.0 18.6 + - + +
113B VAL* 4.1 19.5 - - + +
116B VAL* 5.9 4.3 - - + -
117B MET* 4.1 32.3 - - + -
129B PHE* 4.0 31.6 - - + -
131B VAL* 4.4 9.4 - - + -
133B LEU* 3.2 33.4 - - + -
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Residues in contact with VAL 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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65B GLU* 3.3 17.9 - - - +
67B ILE* 3.8 11.7 - - + -
73B LEU* 3.7 8.1 - - + -
82B TYR* 3.0 59.2 + - + +
83B ARG 4.2 5.2 - - - +
85B LEU* 1.3 75.0 - - - +
87B HIS* 1.3 58.6 + - + +
89B ALA* 3.1 8.9 + - - +
90B ARG* 3.0 60.0 + - - +
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Residues in contact with HIS 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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116A LYS* 4.1 22.8 + - + +
120A ASP* 2.5 38.7 + - - +
83B ARG* 2.7 29.4 + - - +
84B VAL* 3.0 17.1 + - + +
86B VAL* 1.3 79.7 - - + +
88B ARG* 1.3 57.1 + - - +
90B ARG* 3.4 27.9 + - - +
91B LYS* 3.0 25.5 + - - +
65I LEU* 5.5 0.5 - - - +
69I SER* 5.5 2.7 - - - -
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Residues in contact with ARG 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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84B VAL* 3.2 9.3 + - + +
85B LEU* 3.9 7.2 - - + +
87B HIS* 1.3 80.3 - - - +
89B ALA* 1.4 59.9 + - - +
91B LYS* 3.2 39.3 + - - +
92B LEU* 3.1 35.9 + - + +
113B VAL* 6.1 0.4 - - + -
116B VAL* 3.5 40.2 - - + +
119B GLU* 3.0 37.6 + - - -
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Residues in contact with ALA 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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67B ILE* 3.8 20.5 - - + +
73B LEU* 4.6 8.7 - - + -
85B LEU* 3.0 13.8 + - + +
86B VAL* 3.1 13.0 + - - +
88B ARG* 1.4 76.4 - - - +
90B ARG* 1.3 56.1 + - - +
92B LEU* 3.5 1.4 + - - -
93B ALA* 3.1 23.4 + - - +
109B LEU* 3.4 13.2 - - + +
113B VAL* 3.8 29.3 - - + +
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Residues in contact with ARG 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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116A LYS* 6.2 1.0 - - - +
65B GLU* 3.9 26.1 + - - +
66B PRO* 3.4 24.9 + - - +
67B ILE* 3.8 18.6 - - - +
86B VAL* 3.0 33.5 + - + +
87B HIS* 3.5 22.8 + - - +
89B ALA* 1.3 72.6 - - - +
91B LYS* 1.3 60.9 + - - +
93B ALA* 3.8 1.3 - - - +
94B GLN* 3.0 33.3 + - - +
65I LEU* 3.7 15.5 - - + -
68I LEU* 3.3 43.5 + - + +
69I SER* 3.4 35.5 + - - +
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Residues in contact with LYS 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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87B HIS 3.0 14.0 + - - +
88B ARG* 3.2 52.4 + - + +
90B ARG* 1.3 75.7 - - - +
92B LEU* 1.3 62.1 + - - +
94B GLN* 4.1 2.6 - - - +
95B GLN* 3.0 47.5 + - + +
65I LEU* 4.8 10.7 - - + +
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Residues in contact with LEU 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 ARG* 3.1 33.1 + - + +
89B ALA 3.7 5.2 - - - +
90B ARG 3.4 0.2 - - - -
91B LYS* 1.3 82.6 - - - +
93B ALA* 1.3 56.5 + - - +
95B GLN* 4.0 13.9 - - - +
96B TYR* 3.1 28.4 + - - +
104B ILE* 4.7 2.2 - - + +
109B LEU* 3.7 9.4 - - + -
112B ARG* 3.8 40.4 - - + +
113B VAL* 3.5 34.5 - - + +
116B VAL* 4.2 10.1 - - + -
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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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67B ILE 3.9 17.7 - - - +
68B THR* 4.1 19.3 - - - +
89B ALA 3.1 16.3 + - - +
90B ARG 3.8 4.3 - - - +
91B LYS 3.3 0.4 - - - -
92B LEU* 1.3 76.2 - - - +
94B GLN* 1.4 60.0 + - + +
96B TYR* 3.3 6.2 + - - +
97B TYR* 3.1 24.9 + - - +
103B PRO* 6.0 0.3 - - - +
104B ILE* 4.3 15.0 + - + +
109B LEU* 4.2 10.5 - - + +
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Residues in contact with GLN 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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90B ARG 3.0 18.8 + - - +
91B LYS* 4.3 2.5 - - - +
93B ALA* 1.4 75.1 + - + +
95B GLN* 1.4 59.9 + - - +
97B TYR* 3.2 24.0 + - - +
98B LEU* 3.1 30.7 + - - +
61I SER* 2.8 39.6 - - - +
64I GLU* 3.2 20.9 + - - +
65I LEU* 3.1 33.5 + - + -
68I LEU* 4.8 8.5 - - + -
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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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91B LYS* 3.0 36.9 + - + +
92B LEU* 4.0 13.2 - - - +
94B GLN* 1.4 72.4 - - - +
96B TYR* 1.3 66.2 + - - +
98B LEU* 3.4 18.2 - - + +
99B VAL* 3.2 33.6 + - + +
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Residues in contact with TYR 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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92B LEU 3.1 20.7 + - - +
93B ALA 3.4 5.6 - - - +
95B GLN* 1.3 77.3 - - - +
97B TYR* 1.3 56.3 + - - +
99B VAL* 4.8 0.2 - - - -
100B TYR* 2.9 63.4 + + + +
102B GLU* 3.2 29.9 + - - -
104B ILE* 3.3 38.4 - - + -
105B PRO* 3.2 9.9 - - - +
108B GLN* 4.6 0.6 - - + +
112B ARG* 3.3 38.8 - - - -
73J TYR* 2.4 34.0 + + - -
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Residues in contact with TYR 97 (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 LYS* 3.9 30.1 + - - -
93B ALA 3.1 13.1 + - - +
94B GLN* 3.2 27.0 + - - +
96B TYR* 1.3 75.4 - - - +
98B LEU* 1.4 61.8 + - - +
101B GLN* 2.9 70.6 + - - +
102B GLU* 3.6 26.7 - - - +
103B PRO* 4.0 6.7 - - + -
36I PHE* 5.8 6.2 - + - -
60I SER* 5.0 11.0 - - - -
61I SER* 5.6 6.3 - - - -
64I GLU* 5.1 9.2 - - - -
84J TYR* 5.6 1.7 + - - -
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Residues in contact with LEU 98 (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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94B GLN 3.1 17.9 + - - +
95B GLN* 3.4 19.7 - - + +
97B TYR* 1.4 79.1 - - - +
99B VAL* 1.4 77.6 + - + +
101B GLN* 3.5 18.9 + - - +
57I GLN* 3.9 20.7 - - + +
58I LEU* 5.2 11.4 - - + -
61I SER* 3.4 29.6 - - - +
88J SER* 5.4 0.7 - - - -
92J ASN* 3.9 18.7 - - - +
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Residues in contact with VAL 99 (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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95B GLN* 3.2 26.4 + - + +
98B LEU* 1.4 91.1 - - + +
100B TYR* 1.4 88.6 + - + +
101B GLN 3.7 0.2 - - - -
69J ARG* 4.9 10.5 - - - +
88J SER* 3.5 28.5 - - - +
89J MET* 4.2 5.9 + - + -
92J ASN* 4.2 25.1 - - + +
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Residues in contact with TYR 100 (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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96B TYR* 2.9 57.4 + + + +
99B VAL* 1.4 93.8 - - + +
101B GLN* 1.3 68.6 + - - +
102B GLU* 3.2 17.5 - - - +
112B ARG* 4.3 10.5 + - - -
69J ARG 5.4 2.8 + - - -
73J TYR* 4.0 25.5 - + + +
85J THR* 3.2 45.7 + - + +
88J SER* 3.8 2.6 - - - -
89J MET* 3.7 23.1 - - + -
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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