Contacts of the helix formed by residues 93 - 117 (chain B) in PDB entry 1Q0K
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 ASP 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLN* 3.4 2.3 + - - -
91B SER* 2.9 12.9 + - - +
92B THR* 1.3 78.8 + - - +
94B PRO* 1.3 62.7 - - - +
95B ALA* 2.8 39.3 + - - +
96B THR* 2.6 34.9 + - + -
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Residues in contact with PRO 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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22B LYS* 3.7 21.3 - - + +
25B GLN* 3.3 36.6 - - + +
26B GLU* 3.9 25.1 - - + +
29B ALA* 5.6 6.1 - - + -
92B THR 3.2 7.4 - - - +
93B ASP* 1.3 88.5 - - - +
95B ALA* 1.3 60.1 + - - +
96B THR 3.3 0.2 - - - -
97B GLY* 3.2 3.5 + - - -
98B GLN 3.1 16.5 + - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP* 2.8 22.8 + - - +
94B PRO* 1.3 77.2 - - - +
96B THR* 1.3 65.9 + - + +
98B GLN* 3.1 9.0 + - - +
99B LYS* 3.0 23.2 + - - +
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Residues in contact with THR 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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25B GLN* 2.8 20.4 + - - -
84B ALA* 4.3 3.8 - - - +
87B ALA* 4.6 9.9 - - + +
88B ALA* 3.7 20.1 - - - +
91B SER* 3.3 28.2 + - - +
93B ASP* 2.6 26.2 + - + +
95B ALA* 1.3 77.5 - - + +
97B GLY* 1.3 59.6 + - - +
99B LYS* 3.5 10.1 + - - +
100B ALA* 3.4 18.7 + - - +
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Residues in contact with GLY 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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18B ALA 4.8 1.7 - - - +
21B VAL* 4.7 4.9 - - - -
22B LYS* 4.2 13.6 - - - +
25B GLN* 3.3 20.8 + - - -
88B ALA* 4.5 7.6 - - - -
94B PRO 3.2 4.5 + - - -
95B ALA 3.1 0.6 - - - -
96B THR* 1.3 84.9 + - - +
98B GLN* 1.3 60.6 + - - +
100B ALA* 3.4 6.1 + - - +
101B LEU* 3.2 24.6 + - - +
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 2.5 39.3 + - - +
94B PRO 3.1 12.9 + - - +
95B ALA* 3.1 12.1 + - - +
97B GLY* 1.3 75.0 - - - +
99B LYS* 1.3 59.3 + - - +
101B LEU* 3.1 17.4 + - - +
102B ASP* 2.7 64.6 + - - +
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Residues in contact with LYS 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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84B ALA* 4.5 11.2 - - + +
95B ALA 3.0 11.7 + - - +
96B THR* 3.7 13.0 - - - +
97B GLY 3.3 0.2 - - - -
98B GLN* 1.3 77.1 - - - +
100B ALA* 1.3 61.5 + - - +
102B ASP* 3.3 12.2 + - + +
103B TYR* 3.1 59.6 + - + -
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Residues in contact with ALA 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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18B ALA* 5.0 3.8 - - + -
21B VAL* 6.5 0.2 - - + -
81B ALA* 4.8 1.7 - - - +
84B ALA* 4.1 17.7 - - + +
85B LEU* 3.7 36.6 - - + +
88B ALA* 5.3 1.1 - - + -
96B THR 3.4 8.3 + - - +
97B GLY* 3.4 11.5 + - - +
98B GLN 3.2 0.2 - - - -
99B LYS* 1.3 78.6 - - - +
101B LEU* 1.3 58.3 + - - +
103B TYR* 3.1 6.4 + - - +
104B ILE* 2.9 34.8 + - + +
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Residues in contact with LEU 101 (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 ARG* 4.1 11.4 - - + +
18B ALA* 3.5 35.2 - - + +
19B GLU* 3.8 21.1 - - + +
22B LYS* 3.9 31.2 - - + -
97B GLY 3.4 14.8 - - - +
98B GLN* 3.1 21.4 + - - +
100B ALA* 1.3 78.6 - - - +
102B ASP* 1.3 58.7 + - - +
104B ILE* 3.4 6.5 + - + +
105B ALA* 2.9 28.8 + - - +
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Residues in contact with ASP 102 (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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98B GLN* 2.7 52.7 + - - +
99B LYS* 3.5 12.8 - - + +
100B ALA 3.1 0.2 - - - -
101B LEU* 1.3 77.1 - - - +
103B TYR* 1.3 60.6 + - + +
105B ALA* 3.3 8.5 + - - +
106B GLN* 3.3 26.7 + - - +
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Residues in contact with TYR 103 (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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77B LEU* 3.5 27.4 - - + +
80B GLU* 3.3 48.4 + - + +
81B ALA* 3.7 17.7 - - + -
84B ALA* 4.0 13.7 - - + -
99B LYS* 3.1 51.8 + - + -
100B ALA 3.1 7.5 + - - +
102B ASP* 1.3 77.0 - - + +
104B ILE* 1.3 66.4 + - - +
106B GLN* 3.0 23.7 + - - +
107B ILE* 3.0 18.7 + - - +
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Residues in contact with ILE 104 (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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11B PRO* 4.3 11.0 - - + +
14B ALA* 3.8 21.5 - - + +
15B ARG* 4.1 29.6 - - + +
18B ALA* 3.5 31.0 - - + -
51B ALA* 5.2 0.2 - - + -
55B LEU* 4.0 26.9 - - + -
81B ALA* 5.1 2.0 - - + +
85B LEU* 5.0 7.9 - - + -
100B ALA* 2.9 20.8 + - + +
101B LEU* 3.7 7.0 - - + +
103B TYR* 1.3 76.1 - - - +
105B ALA* 1.3 57.7 + - - +
107B ILE* 3.2 8.9 + - + +
108B ASP* 2.8 30.1 + - + +
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Residues in contact with ALA 105 (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 ARG* 6.5 1.1 - - - +
101B LEU 2.9 14.5 + - - +
102B ASP* 3.4 13.5 - - - +
103B TYR 3.1 0.2 - - - -
104B ILE* 1.3 78.0 - - - +
106B GLN* 1.3 56.4 + - + +
108B ASP* 3.4 8.7 - - - +
109B LYS* 3.0 27.9 + - - +
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Residues in contact with GLN 106 (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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77B LEU* 3.7 22.2 - - + +
102B ASP* 3.3 12.1 + - - +
103B TYR* 3.0 32.8 + - - +
105B ALA* 1.3 77.6 - - + +
107B ILE* 1.3 64.4 + - - +
109B LYS* 3.3 9.6 + - + +
110B ILE* 3.1 26.2 + - - +
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Residues in contact with ILE 107 (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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11B PRO* 5.2 3.4 - - + -
55B LEU* 4.1 18.8 - - + -
58B LEU* 4.7 16.2 - - + -
63B PHE* 4.2 25.2 - - + -
74B LEU* 5.1 1.6 - - + -
77B LEU* 3.6 22.4 - - + -
78B VAL* 4.0 23.6 - - + -
81B ALA* 3.7 30.3 - - + -
103B TYR 3.0 11.9 + - - +
104B ILE* 3.6 8.5 - - + +
106B GLN* 1.3 73.8 - - - +
108B ASP* 1.3 56.0 + - - +
110B ILE* 3.2 5.1 + - - +
111B PHE* 2.7 33.3 + - - +
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Residues in contact with ASP 108 (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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10B ASP* 5.0 0.7 - - - +
11B PRO* 3.6 23.6 - - + +
12B ALA 5.0 0.2 + - - -
15B ARG* 3.9 19.8 + - - +
104B ILE* 2.8 17.9 + - + +
105B ALA* 3.4 10.5 - - - +
107B ILE* 1.3 76.7 - - - +
109B LYS* 1.3 63.0 + - - +
111B PHE* 3.0 17.1 + - - +
112B TRP* 3.1 46.6 + - - -
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Residues in contact with LYS 109 (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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105B ALA 3.0 14.6 + - - +
106B GLN* 3.5 12.8 - - + +
107B ILE 3.2 0.2 - - - -
108B ASP* 1.3 79.4 - - - +
110B ILE* 1.3 62.9 + - + +
112B TRP* 3.6 4.4 + - - +
113B GLU* 3.3 43.2 + - + +
116B LYS* 5.5 0.2 + - - -
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Residues in contact with ILE 110 (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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63B PHE* 4.4 5.8 - - + -
71B TYR* 4.0 47.1 - - + -
73B GLU* 4.2 15.9 - - + +
74B LEU* 4.1 21.1 - - + -
77B LEU* 4.0 26.0 - - + -
106B GLN* 3.1 9.0 + - + +
107B ILE* 3.7 7.4 - - - +
109B LYS* 1.3 77.1 - - + +
111B PHE* 1.3 63.2 + - - +
113B GLU* 3.3 10.8 + - - +
114B THR* 3.0 33.2 + - + +
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Residues in contact with PHE 111 (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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9B TYR* 3.6 33.2 - - + -
11B PRO* 3.3 36.8 - - + -
58B LEU* 4.4 5.4 - - + -
62B TYR* 3.4 42.6 - + - -
63B PHE* 4.4 11.7 - + + -
107B ILE 2.7 14.1 + - - +
108B ASP 3.0 10.1 + - - +
110B ILE* 1.3 77.0 - - - +
112B TRP* 1.3 92.1 + + - +
114B THR* 2.4 26.5 + - - -
115B LYS* 3.1 32.7 + - + +
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Residues in contact with TRP 112 (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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9B TYR 5.3 2.7 - - - -
10B ASP* 4.1 23.1 + - - -
11B PRO* 4.7 0.4 - - - +
108B ASP* 3.1 51.0 + - - +
109B LYS* 4.3 4.3 - - - +
111B PHE* 1.3 96.3 - + - +
113B GLU* 1.3 56.4 + - - +
115B LYS* 3.0 30.8 + - + +
116B LYS* 2.8 46.8 + - + +
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Residues in contact with GLU 113 (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 TYR* 2.8 30.9 + - - +
109B LYS* 3.3 35.2 + - + +
110B ILE* 3.3 13.8 + - - +
111B PHE 3.1 0.6 - - - -
112B TRP* 1.3 77.6 - - - +
114B THR* 1.3 57.7 + - - +
116B LYS* 3.6 21.9 + - - +
117B ALA* 3.1 28.1 + - - +
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Residues in contact with THR 114 (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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62B TYR* 2.7 31.3 + - - -
63B PHE* 4.3 7.6 - - + -
67B HIS* 3.8 32.3 + - + -
71B TYR* 3.9 23.1 - - + -
110B ILE* 3.0 20.4 - - + +
111B PHE* 2.4 21.8 + - - -
113B GLU* 1.3 76.7 - - - +
115B LYS* 1.3 61.2 + - - +
117B ALA* 3.8 17.4 - - - +
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Residues in contact with LYS 115 (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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7B GLY 4.9 10.9 + - - -
9B TYR* 5.4 5.6 + - - +
62B TYR* 3.1 30.7 - - + +
111B PHE* 3.2 35.5 - - + +
112B TRP* 3.0 40.8 + - + +
114B THR* 1.3 76.0 - - - +
116B LYS* 1.3 65.6 + - + +
117B ALA* 3.2 9.0 + - - +
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Residues in contact with LYS 116 (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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109B LYS 5.5 0.2 + - - -
112B TRP* 2.8 33.1 + - + +
113B GLU* 3.6 26.1 - - - +
115B LYS* 1.3 75.7 - - + +
117B ALA* 1.3 67.9 + - - +
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Residues in contact with ALA 117 (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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113B GLU 3.1 19.3 + - - +
114B THR* 3.8 16.5 - - - +
115B LYS 3.2 8.0 - - - +
116B LYS* 1.3 82.7 - - - +
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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