Contacts of the helix formed by residues 82 - 111 (chain N) in PDB entry 2X17
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 SER 82 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 3.3 10.7 + - - -
80N TRP* 3.3 1.6 - - - +
81N GLU* 1.3 78.6 - - - +
83N PRO* 1.4 70.7 - - - +
84N LEU* 3.5 12.6 + - - +
85N LYS* 3.1 28.4 + - - +
86N ALA* 3.0 26.7 + - - +
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Residues in contact with PRO 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 3.9 7.2 - - + +
31N PHE* 3.7 25.1 - - + -
34N LEU* 4.1 20.4 - - + -
36N LEU* 4.2 10.3 - - + -
39N PHE* 5.1 0.7 - - + -
82N SER* 1.4 86.3 - - - +
84N LEU* 1.3 58.9 + - - +
86N ALA* 3.6 2.1 + - + +
87N PHE* 3.3 20.8 + - - -
141N LEU* 3.4 19.8 - - + +
151N LEU* 4.3 27.8 - - + -
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Residues in contact with LEU 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82N SER* 3.1 12.0 + - - +
83N PRO* 1.3 79.0 - - - +
85N LYS* 1.3 63.1 + - + +
87N PHE* 3.3 4.2 + - - +
88N GLU* 3.0 48.4 + - - +
138N LEU* 3.9 9.0 - - + +
141N LEU* 3.8 26.5 - - + +
142N LYS* 3.7 44.6 - - + +
145N LYS* 5.4 12.1 - - + -
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Residues in contact with LYS 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N TRP* 3.9 6.0 - - + -
81N GLU* 4.0 34.8 - - + +
82N SER* 3.1 29.7 + - - +
84N LEU* 1.3 77.7 - - + +
86N ALA* 1.3 59.9 + - - +
88N GLU* 3.4 29.3 + - + +
89N ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N MET* 3.4 15.5 - - + +
30N TYR* 4.0 9.6 - - + -
31N PHE* 3.9 21.5 - - + -
80N TRP* 3.8 29.3 - - + +
82N SER 3.0 15.0 + - - +
83N PRO 3.7 6.5 - - - +
84N LEU 3.3 0.2 - - - -
85N LYS* 1.3 77.4 - - - +
87N PHE* 1.3 57.9 + - - +
89N ALA* 3.6 0.7 + - - +
90N ALA* 3.1 23.7 + - - +
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Residues in contact with PHE 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N PHE* 3.7 13.0 - + - -
39N PHE* 3.7 29.2 - + - -
42N TRP* 4.5 12.6 - + + -
43N MET* 3.7 27.4 - - + -
83N PRO 3.3 15.2 + - - +
84N LEU 3.3 8.3 + - - +
85N LYS 3.3 0.2 - - - -
86N ALA* 1.3 76.3 - - - +
88N GLU* 1.3 59.9 + - - +
89N ALA 3.3 0.4 - - - -
90N ALA* 3.5 4.4 - - + +
91N TYR* 2.9 24.3 + - - +
134N VAL* 3.8 33.2 - - + +
137N ILE* 3.7 39.0 - - + -
138N LEU* 3.4 19.4 - - + +
141N LEU* 3.6 16.2 - - + -
158N LEU* 4.9 1.8 - - + -
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Residues in contact with GLU 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N LEU* 3.0 40.4 + - - +
85N LYS* 3.4 41.9 + - + +
87N PHE* 1.3 77.6 - - - +
89N ALA* 1.3 56.8 + - - +
91N TYR* 3.6 2.3 + - - +
92N GLU* 3.1 28.3 + - - +
138N LEU* 3.8 22.9 - - + -
142N LYS* 4.4 11.1 - - - -
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Residues in contact with ALA 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N LEU* 5.2 0.9 - - - +
27N MET* 4.3 6.1 - - + +
80N TRP* 3.5 30.1 - - + +
85N LYS 3.0 12.6 + - - +
86N ALA 3.8 2.9 - - - +
88N GLU* 1.3 76.5 - - - +
90N ALA* 1.3 57.6 + - - +
91N TYR 3.5 0.2 - - - -
92N GLU* 3.7 12.6 + - - +
93N HIS* 3.1 26.9 + - - +
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Residues in contact with ALA 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N TYR* 3.9 15.4 + - + +
27N MET* 3.9 21.3 - - + +
43N MET* 4.8 5.6 - - + -
86N ALA 3.1 17.8 + - - +
87N PHE* 3.5 11.0 - - + +
88N GLU 3.3 0.4 - - - -
89N ALA* 1.3 76.6 - - - +
91N TYR* 1.3 59.0 + - - +
93N HIS* 3.3 6.0 + - - +
94N GLU* 2.9 31.9 + - - +
134N VAL* 4.1 13.5 - - + -
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Residues in contact with TYR 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N PHE 2.9 17.0 + - - +
88N GLU 4.1 2.9 - - - +
90N ALA* 1.3 73.6 - - - +
92N GLU* 1.3 64.3 + - - +
94N GLU* 3.7 4.2 - - + +
95N LYS* 3.2 50.2 + - + +
131N GLU* 3.6 50.8 + - + -
134N VAL* 3.8 10.5 - - + +
135N LYS* 3.6 39.6 - - + +
138N LEU* 3.6 17.9 - - + -
1Q MET* 3.7 25.0 + - + +
65Q ASN* 4.9 5.2 - - - +
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Residues in contact with GLU 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N GLU 3.1 18.9 + - - +
89N ALA* 3.7 12.3 - - - +
91N TYR* 1.3 76.7 - - - +
93N HIS* 1.3 57.1 + - - +
95N LYS* 3.5 18.7 + - - +
96N PHE* 3.2 23.4 + - - +
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Residues in contact with HIS 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N TYR* 3.7 31.0 - + - -
20N SER* 2.9 33.4 + - - -
23N LEU* 3.5 24.1 - - + +
24N TYR* 4.2 15.0 - + - -
89N ALA 3.1 18.7 + - - +
90N ALA* 3.6 5.2 - - - +
91N TYR 3.3 0.2 - - - -
92N GLU* 1.3 76.5 - - - +
94N GLU* 1.3 60.3 + - - +
96N PHE* 3.2 29.7 + + - +
97N ILE* 3.0 35.9 + - + +
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Residues in contact with GLU 94 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N SER* 5.5 0.2 + - - -
24N TYR* 2.6 32.9 + - - +
50N GLU* 3.9 3.3 - - - +
90N ALA 2.9 15.4 + - - +
91N TYR* 3.7 9.0 - - + +
92N GLU 3.3 0.2 - - - -
93N HIS* 1.3 79.0 - - - +
95N LYS* 1.3 59.6 + - - +
97N ILE* 3.7 6.6 + - - +
98N SER* 3.0 29.5 + - - -
127N GLN* 2.9 30.7 + - - +
130N GLU* 3.1 38.3 - - - +
131N GLU* 3.7 16.1 + - + +
134N VAL* 4.0 19.1 - - + -
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Residues in contact with LYS 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91N TYR* 3.2 46.2 + - + +
92N GLU* 3.7 17.4 - - - +
93N HIS 3.3 0.2 - - - -
94N GLU* 1.3 74.1 - - - +
96N PHE* 1.3 60.2 + - - +
98N SER* 3.5 2.6 + - - -
99N LYS* 3.0 29.2 + - - +
102N TYR* 5.8 0.2 - - - -
131N GLU* 3.9 24.5 - - - +
1Q MET* 4.9 14.8 - - + +
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Residues in contact with PHE 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N ARG* 4.2 34.1 - - + -
19N TYR* 6.0 2.5 - + - -
92N GLU 3.2 13.9 + - - +
93N HIS* 3.2 32.7 + + - +
95N LYS* 1.3 74.9 - - - +
97N ILE* 1.3 72.5 + - + +
99N LYS* 3.4 10.6 + - + +
100N SER* 3.2 23.6 + - - -
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Residues in contact with ILE 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N GLN* 4.0 6.3 - - - +
16N ARG* 4.2 24.5 - - + +
17N GLU* 3.9 19.1 - - - +
20N SER* 3.4 26.2 - - - +
50N GLU* 5.6 1.3 - - - +
93N HIS* 3.0 32.4 + - + +
94N GLU* 4.0 10.5 - - - +
96N PHE* 1.3 83.8 - - + +
98N SER* 1.3 63.9 + - - +
100N SER* 2.7 19.4 + - - +
101N ILE* 3.1 13.5 + - + +
127N GLN* 3.6 29.6 - - + +
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Residues in contact with SER 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N GLU 3.0 12.6 + - - -
95N LYS* 3.7 5.6 - - - -
96N PHE 3.4 0.2 - - - -
97N ILE* 1.3 77.6 - - - +
99N LYS* 1.3 56.5 + - - +
101N ILE* 3.2 9.3 + - - +
102N TYR* 3.0 52.3 + - - -
127N GLN* 3.3 26.6 + - - +
131N GLU* 2.7 28.3 + - - -
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Residues in contact with LYS 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95N LYS 3.0 18.9 + - - +
96N PHE* 3.6 11.9 - - + +
97N ILE 3.3 0.2 - - - -
98N SER* 1.3 74.8 - - - +
100N SER* 1.3 57.9 + - - +
102N TYR* 3.2 16.5 + - + +
103N GLU* 2.9 49.0 + - + +
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Residues in contact with SER 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N GLN* 2.9 25.3 + - - -
16N ARG* 3.9 25.2 + - - -
96N PHE* 3.2 13.9 + - - -
97N ILE* 2.7 24.1 + - - -
99N LYS* 1.3 75.6 - - - +
101N ILE* 1.3 59.5 + - - +
103N GLU* 3.9 13.7 - - - +
104N LEU* 3.1 30.7 + - - +
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Residues in contact with ILE 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N GLN* 3.8 31.6 - - + +
17N GLU* 4.5 3.8 - - - +
57N PHE* 4.1 10.3 - - + -
97N ILE* 3.1 25.5 + - + +
98N SER* 3.2 11.2 + - - +
100N SER* 1.3 75.2 - - - +
102N TYR* 1.3 62.0 + - + +
104N LEU* 3.3 4.8 + - + +
105N ALA* 2.9 27.4 + - - +
120N LEU* 4.4 11.9 - - + +
123N PHE* 4.1 23.3 - - + +
124N ILE* 3.8 37.2 - - + +
127N GLN* 4.6 7.0 - - + -
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Residues in contact with TYR 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N SER* 3.0 40.7 + - - -
99N LYS* 3.4 17.3 - - + +
101N ILE* 1.3 81.4 - - + +
103N GLU* 1.3 52.9 + - + +
105N ALA* 3.2 6.4 + - - +
106N ALA* 2.8 35.4 + - - +
124N ILE* 4.5 11.0 - - + -
127N GLN* 6.1 0.2 - - - +
131N GLU* 4.8 0.3 + - - -
64Q ARG* 3.5 16.4 + - - -
112Q LYS 5.7 2.0 - - - -
113Q ASP* 5.5 0.8 + - - -
114Q TYR* 3.6 45.7 - + + -
115Q SER* 2.6 29.4 + - - -
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Residues in contact with GLU 103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N ARG* 5.7 2.3 + - - -
99N LYS* 2.9 41.5 + - + +
100N SER* 3.9 12.0 - - - +
101N ILE 3.3 0.2 - - - -
102N TYR* 1.3 74.8 - - + +
104N LEU* 1.3 57.6 + - - +
106N ALA* 3.7 7.7 + - - +
107N LEU* 3.1 27.0 + - - +
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Residues in contact with LEU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N MET* 4.2 11.8 - - - +
9N ALA* 3.8 36.3 - - + +
10N LEU* 4.1 16.4 - - + -
13N GLN* 3.6 38.1 - - + +
16N ARG* 5.3 2.0 - - - +
57N PHE* 4.3 4.0 - - + -
100N SER 3.1 18.8 + - - +
101N ILE* 3.5 7.2 - - + +
102N TYR 3.2 0.2 - - - -
103N GLU* 1.3 76.1 - - - +
105N ALA* 1.3 58.7 + - - +
107N LEU* 3.3 6.6 + - + +
108N ALA* 3.0 28.4 + - - +
120N LEU* 3.6 27.2 - - + +
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Residues in contact with ALA 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N ILE 2.9 16.8 + - - +
102N TYR* 3.2 8.3 + - - +
104N LEU* 1.3 76.5 - - - +
106N ALA* 1.3 58.0 + - - +
108N ALA* 3.4 0.6 + - - -
109N GLU* 3.1 34.9 + - - +
117N ARG* 3.6 20.7 - - - +
120N LEU* 3.8 11.6 - - + +
124N ILE* 4.4 9.9 - - + -
114Q TYR* 4.0 21.1 - - + -
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Residues in contact with ALA 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N TYR 2.8 19.5 + - - +
103N GLU* 3.9 8.5 - - - +
104N LEU 3.3 0.2 - - - -
105N ALA* 1.3 71.2 - - - +
107N LEU* 1.3 59.5 + - - +
109N GLU* 3.5 4.8 + - - +
110N GLU* 3.0 30.2 + - - +
112Q LYS* 6.5 1.8 - - + -
114Q TYR* 3.4 20.1 + - + +
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Residues in contact with LEU 107 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N ARG* 3.8 37.2 - - + +
6N MET* 3.8 21.2 - - + +
9N ALA* 3.8 30.1 - - + -
103N GLU 3.1 19.5 + - - +
104N LEU* 3.6 7.4 - - + +
105N ALA 3.3 0.2 - - - -
106N ALA* 1.3 75.8 - - - +
108N ALA* 1.3 59.2 + - - +
110N GLU* 3.5 16.7 + - + +
111N GLU* 3.0 39.5 + - + +
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Residues in contact with ALA 108 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N MET* 3.6 17.0 - - + +
104N LEU 3.0 17.2 + - - +
105N ALA* 3.7 6.7 - - - +
106N ALA 3.3 0.2 - - - -
107N LEU* 1.3 76.7 - - - +
109N GLU* 1.3 57.1 + - - +
111N GLU 3.6 0.2 - - - -
112N LYS* 3.0 5.5 + - - -
113N ASP* 2.8 36.8 + - - +
116N THR* 4.3 6.3 - - + -
117N ARG* 3.8 33.4 - - + +
120N LEU* 4.5 0.4 - - + -
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Residues in contact with GLU 109 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105N ALA 3.1 16.2 + - - +
106N ALA* 3.8 4.1 - - - +
108N ALA* 1.3 73.7 - - - +
110N GLU* 1.3 64.7 + - - +
112N LYS* 3.4 19.6 + - - +
117N ARG* 3.1 35.2 + - + +
114Q TYR* 3.0 33.6 + - - -
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Residues in contact with GLU 110 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106N ALA 3.0 18.1 + - - +
107N LEU* 3.7 18.7 - - + +
108N ALA 3.3 0.2 - - - -
109N GLU* 1.3 78.2 - - - +
111N GLU* 1.3 60.8 + - + +
112N LYS* 3.2 11.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N SER* 2.6 35.8 + - - -
5N ARG* 3.9 23.9 - - - +
6N MET* 3.5 19.9 - - - +
107N LEU* 3.0 26.3 + - + +
108N ALA 4.4 1.6 - - - +
110N GLU* 1.3 78.4 - - + +
112N LYS* 1.3 69.8 + - - +
113N ASP* 2.9 12.2 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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