Contacts of the helix formed by residues 78 - 110 (chain A) in PDB entry 2NCA
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 LYS 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLY* 1.3 72.0 - - - +
79A ALA* 1.3 63.1 + - - +
80A GLU 2.9 0.2 - - - -
81A LEU* 2.9 30.5 + - + +
82A GLU* 3.5 19.7 + - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 5.9 5.6 - - + -
74A ALA 5.8 0.4 - - - +
75A GLU 4.6 3.6 - - - +
76A GLY* 3.3 27.8 - - - +
77A GLY 2.9 0.6 - - - -
78A LYS* 1.3 78.7 - - - +
80A GLU* 1.3 61.5 + - - +
82A GLU* 3.1 21.0 + - + +
83A ARG* 3.0 31.2 + - + +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 5.3 14.2 - - + +
76A GLY 3.3 5.4 + - - +
77A GLY 2.9 15.5 + - - +
79A ALA* 1.3 78.8 - - - +
81A LEU* 1.3 66.8 + - + +
83A ARG* 3.6 4.4 + - - +
84A LEU* 2.9 31.8 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLY 5.1 1.3 - - - +
78A LYS* 2.9 21.3 + - + +
80A GLU* 1.3 87.3 - - + +
82A GLU* 1.3 57.8 + - - +
84A LEU* 3.7 22.3 - - + +
85A GLN* 2.7 39.7 + - + +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 3.5 18.2 + - - +
79A ALA* 3.1 25.6 + - - +
81A LEU* 1.3 79.2 - - - +
83A ARG* 1.3 73.4 + - - +
85A GLN* 3.8 4.2 - - - +
86A ALA* 3.0 31.2 + - - +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 5.6 2.2 - - - +
68A LEU* 4.4 33.3 - - + +
71A LEU* 4.2 40.0 - - + +
72A GLU* 5.0 12.1 - - + -
79A ALA* 3.0 19.3 + - + +
80A GLU* 4.1 4.7 - - - +
82A GLU* 1.3 87.4 + - - +
84A LEU* 1.3 60.5 + - - +
86A ALA* 4.1 9.5 - - - +
87A GLU* 2.9 34.1 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 2.9 19.1 + - - +
81A LEU* 3.7 28.0 - - + +
83A ARG* 1.3 77.3 - - - +
85A GLN* 1.3 67.1 + - + +
87A GLU* 4.0 10.2 - - - +
88A ALA* 2.9 40.0 + - + +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 2.7 26.2 + - + +
82A GLU* 3.8 6.3 - - - +
84A LEU* 1.3 80.5 - - + +
86A ALA* 1.3 59.9 + - - +
88A ALA* 4.1 1.7 - - - -
89A GLN* 2.9 69.1 + - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 5.3 2.9 - - + -
82A GLU 3.0 18.3 + - - +
83A ARG* 4.1 11.4 - - - +
85A GLN* 1.3 76.8 - - - +
87A GLU* 1.3 58.2 + - - +
89A GLN* 3.9 7.6 - - - +
90A GLN* 2.8 33.2 + - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 5.1 7.8 + - - +
68A LEU* 3.1 47.0 - - + +
72A GLU* 5.2 7.7 - - - +
83A ARG 2.9 20.9 + - - +
84A LEU* 4.0 7.9 - - - +
86A ALA* 1.3 72.9 - - - +
88A ALA* 1.3 61.1 - - - +
89A GLN 3.0 1.1 - - - -
90A GLN* 2.7 23.7 + - - +
91A LEU* 2.8 33.2 + - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 2.9 28.8 + - + +
85A GLN* 4.2 2.5 - - - +
87A GLU* 1.3 76.3 - - - +
89A GLN* 1.3 57.8 + - + +
91A LEU* 4.2 4.8 - - - +
92A ARG* 2.9 41.9 + - + +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLN* 2.9 60.3 + - + +
86A ALA* 3.9 6.3 + - - +
88A ALA* 1.3 76.7 - - + +
90A GLN* 1.3 60.6 + - - +
92A ARG* 4.3 4.3 - - - -
93A LYS* 2.9 45.9 + - + +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 4.6 12.4 + - - +
61A VAL* 5.2 3.8 - - + -
64A CYS* 3.3 39.9 - - + +
68A LEU* 5.7 2.7 - - + -
86A ALA* 2.8 23.4 + - - +
87A GLU* 2.7 14.4 + - - +
89A GLN* 1.3 72.6 - - - +
91A LEU* 1.3 67.1 + - + +
93A LYS* 4.7 1.1 - - - -
94A GLU* 2.6 65.5 + - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.5 38.4 - - + -
65A GLN* 6.1 4.5 - - + +
68A LEU* 5.7 1.1 - - + -
87A GLU* 2.8 53.0 + - + +
88A ALA* 4.3 3.8 - - - +
90A GLN* 1.3 83.8 - - + +
92A ARG* 1.3 63.8 + - + +
94A GLU* 2.9 3.8 + - + +
95A GLU* 2.8 53.1 + - - +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 2.9 33.3 + - + +
89A GLN* 4.1 4.5 - - - +
91A LEU* 1.3 75.9 - - + +
93A LYS* 1.3 59.0 + - + +
95A GLU* 4.3 5.0 - - - +
96A ARG* 2.9 32.4 + - - +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 2.9 34.7 + - + +
90A GLN* 3.8 3.6 - - - +
92A ARG* 1.3 76.1 - - + +
94A GLU* 1.3 64.3 + - - +
96A ARG* 4.3 5.5 - - + +
97A SER* 2.8 45.0 + - - +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A CYS* 3.4 33.0 - - + -
60A LYS* 4.9 8.0 + - - +
61A VAL* 4.0 12.5 - - + +
90A GLN* 2.6 59.7 + - - +
91A LEU* 3.4 7.6 - - - +
93A LYS* 1.3 82.9 - - - +
95A GLU* 1.3 60.7 + - - +
98A TRP* 3.0 51.7 + - + +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 2.8 45.5 + - - +
92A ARG* 4.3 4.2 - - - +
94A GLU* 1.3 75.0 - - - +
96A ARG* 1.3 59.1 + - - +
98A TRP* 3.9 3.6 - - - +
99A GLU* 2.8 36.3 + - - +
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG 2.9 23.3 + - - +
93A LYS* 4.0 7.4 - - + +
95A GLU* 1.3 77.7 - - - +
97A SER* 1.3 57.0 + - - +
99A GLU* 3.7 32.9 + - - +
100A GLN* 3.0 65.3 + - - +
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 2.8 33.7 + - - +
96A ARG* 1.3 72.4 - - - +
98A TRP* 1.3 74.6 + - - +
100A GLN* 3.9 2.9 - - - +
101A LYS* 2.7 39.7 + - - +
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Residues in contact with TRP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 5.3 5.6 + - + -
53A GLY* 3.1 48.2 + - - -
54A CYS* 4.0 2.3 - - - +
56A GLU* 5.2 7.0 - - + -
57A CYS* 3.7 23.6 - - + +
94A GLU* 3.0 48.0 + - + +
95A GLU* 3.9 4.3 - - - +
97A SER* 1.3 89.1 - - - +
99A GLU* 1.3 54.5 + - - +
101A LYS* 4.0 23.0 - - + +
102A LEU* 2.7 38.4 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 2.8 23.2 + - - +
96A ARG* 3.7 24.5 + - - +
98A TRP* 1.3 74.1 - - - +
100A GLN* 1.3 62.9 + - - +
102A LEU* 3.3 9.7 - - + +
103A GLU* 3.0 24.7 + - + +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.0 45.7 + - - +
97A SER* 3.9 3.1 - - - +
99A GLU* 1.3 75.0 - - - +
101A LYS* 1.3 68.1 + - - +
102A LEU 3.0 1.2 + - - -
103A GLU* 3.1 7.0 + - - +
104A GLU* 3.0 44.2 + - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 4.5 23.5 + - - +
50A LEU* 5.2 4.6 - - - +
53A GLY* 5.8 0.8 - - - -
97A SER* 2.7 23.4 + - - +
98A TRP* 4.1 26.0 + - + +
100A GLN* 1.3 74.6 - - - +
102A LEU* 1.3 61.0 + - - +
104A GLU* 3.8 6.8 - - - +
105A MET* 2.7 66.3 + - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.7 9.9 - - + -
98A TRP 2.7 20.1 + - - +
99A GLU* 3.3 10.8 - - + +
100A GLN 3.0 0.2 - - - -
101A LYS* 1.3 84.9 - - - +
103A GLU* 1.3 70.7 + - - +
105A MET* 3.0 19.1 + - + +
106A ARG* 2.9 54.4 + - - +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 3.0 14.7 + - + +
100A GLN* 3.1 8.7 + - - +
102A LEU* 1.3 78.4 - - - +
104A GLU* 1.3 58.2 + - + +
106A ARG* 4.1 4.0 - - - +
107A LYS* 2.9 44.6 + - + +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLN* 3.0 39.4 + - - +
101A LYS* 3.9 6.1 - - - +
103A GLU* 1.3 76.0 - - + +
105A MET* 1.3 61.1 + - - +
107A LYS* 3.7 8.6 - - + +
108A LYS* 2.8 34.5 + - - +
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Residues in contact with MET 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 6.3 0.4 - - + -
46A GLU* 4.1 21.8 - - + +
49A GLU* 3.5 35.9 - - + +
50A LEU* 3.9 17.7 - - + -
101A LYS* 2.7 50.4 + - + +
102A LEU* 3.4 24.5 - - + +
104A GLU* 1.3 73.4 - - - +
106A ARG* 1.3 59.0 + - + +
108A LYS* 4.2 2.1 - - - +
109A GLU* 2.9 47.7 + - + +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 5.8 1.3 - - - +
46A GLU* 4.5 28.5 + - + +
50A LEU* 5.3 9.1 - - - +
102A LEU* 2.9 37.9 + - + +
103A GLU* 4.2 4.5 - - - +
105A MET* 1.3 79.4 - - + +
107A LYS* 1.3 61.0 + - - +
108A LYS 3.2 0.4 - - - -
109A GLU* 4.4 4.0 - - + -
110A LYS* 2.9 64.3 + - + +
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TRP* 5.1 17.9 - - + -
8A ASP* 4.0 18.1 + - - -
14A ASP* 5.7 5.5 + - - -
103A GLU* 2.9 33.9 + - + +
104A GLU* 3.7 9.4 - - + +
106A ARG* 1.3 77.5 - - - +
108A LYS* 1.3 61.4 + - - +
110A LYS* 4.2 7.0 - - - +
111A SER* 3.8 18.2 + - - -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU 2.8 17.3 + - - +
105A MET* 4.2 2.5 - - - +
107A LYS* 1.3 77.1 - - - +
109A GLU* 1.3 56.4 + - + +
110A LYS 3.1 1.8 - - - -
111A SER* 2.9 7.4 + - - -
112A MET* 2.7 36.5 + - - -
113A PRO* 6.1 1.8 - - + -
122A ASP* 6.1 1.1 - - - -
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 2.6 61.2 - - + +
45A LYS* 3.0 32.9 - - - +
46A GLU* 3.6 8.3 + - + +
105A MET* 2.9 36.2 + - + +
106A ARG* 4.2 4.0 - - - +
108A LYS* 1.3 78.4 - - + +
110A LYS* 1.3 55.9 + - - +
112A MET* 3.0 32.0 - - - +
124A PHE* 3.9 12.0 - - - -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 5.3 2.3 - - - -
42A GLN* 3.2 27.2 - - - +
106A ARG* 2.9 58.6 + - + +
107A LYS* 4.2 7.4 - - - +
109A GLU* 1.3 77.1 - - - +
111A SER* 1.3 60.3 + - - +
112A MET 3.4 0.6 + - - -
115A ASN* 4.2 15.2 + - - +
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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