Contacts of the helix formed by residues 100 - 123 (chain B) in PDB entry 4EOZ
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 ASN 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASN 4.1 1.2 - - - -
99B ASN* 1.3 82.3 + - - +
101B PHE* 1.3 56.7 + - - +
102B LEU 3.6 2.2 - - - -
103B GLN* 3.5 34.1 + - + +
104B THR* 2.6 38.7 + - - +
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Residues in contact with PHE 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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93B VAL* 3.9 19.3 - - + -
96B SER* 3.3 28.0 - - - +
97B LEU* 3.6 24.2 - - + -
98B ASN 4.4 2.9 - - - +
99B ASN 3.3 0.6 - - - +
100B ASN* 1.3 73.4 - - - +
102B LEU* 1.3 86.6 + - + +
104B THR* 3.1 2.6 + - - -
105B LEU* 2.8 41.1 + - + +
157B ILE* 3.9 18.8 - - + -
160B HIS* 3.5 27.6 - + + +
161B LEU* 3.5 38.6 - - + -
164B THR* 4.1 4.9 - - + +
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Residues in contact with LEU 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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100B ASN 3.6 0.4 - - - -
101B PHE* 1.3 104.9 - - + +
103B GLN* 1.3 53.8 + - - +
105B LEU* 3.8 5.2 - - + +
106B ASN* 2.8 37.0 + - - +
161B LEU* 4.4 12.1 - - + -
164B THR* 3.4 21.3 - - + -
165B LEU* 4.2 16.8 - - + -
168B MSE 3.8 29.8 - - + -
182B ALA* 4.1 31.9 - - + +
186B ALA* 5.2 2.9 - - + -
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Residues in contact with GLN 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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100B ASN* 3.5 38.4 + - + +
101B PHE 3.4 0.2 - - - -
102B LEU* 1.3 78.6 - - - +
104B THR* 1.3 63.1 + - - +
106B ASN* 3.8 5.6 - - - +
107B GLN* 2.9 35.5 + - + +
182B ALA* 6.1 0.2 - - - +
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Residues in contact with THR 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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92B ASP* 4.0 18.4 - - + +
93B VAL* 4.2 9.4 - - + -
96B SER* 3.5 30.3 - - - +
99B ASN 4.3 1.0 + - - -
100B ASN* 2.6 26.5 + - - +
101B PHE 3.5 0.4 - - - -
103B GLN* 1.3 81.4 + - - +
105B LEU* 1.3 65.3 + - - +
107B GLN* 3.2 5.9 + - + +
108B ALA* 3.0 22.4 + - + +
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Residues in contact with LEU 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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93B VAL* 4.2 22.3 - - + +
101B PHE* 2.8 34.9 + - + +
102B LEU* 3.8 5.6 - - + +
104B THR* 1.3 72.6 - - - +
106B ASN* 1.3 65.6 + - - +
108B ALA* 3.0 4.3 + - - +
109B TRP* 2.9 22.7 + - - +
147B PHE* 4.4 5.2 - - + -
151B VAL* 4.1 26.0 - - + -
152B VAL* 4.3 12.8 - - + -
157B ILE* 4.6 5.2 - - + -
161B LEU* 4.0 31.4 - - + -
186B ALA* 6.1 0.7 - - + -
189B MSE 4.2 20.6 - - + -
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Residues in contact with ASN 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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102B LEU 2.8 22.9 + - - +
103B GLN* 3.8 6.1 - - - +
105B LEU* 1.3 75.6 - - - +
107B GLN* 1.3 57.5 + - - +
109B TRP* 3.4 21.7 + - - +
110B ASN* 3.0 49.2 + - - +
185B ASN* 3.4 46.0 - - + +
186B ALA* 5.0 0.5 + - - -
189B MSE 5.6 1.8 - - - +
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Residues in contact with GLN 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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47B LYS* 5.8 1.1 - - - -
103B GLN* 2.9 25.0 + - + +
104B THR* 3.6 8.3 - - + +
105B LEU 3.1 0.2 - - - -
106B ASN* 1.3 79.2 - - - +
108B ALA* 1.3 62.5 + - - +
110B ASN* 3.4 10.5 + - - +
111B ASP* 3.0 53.4 + - - +
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Residues in contact with ALA 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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89B VAL* 3.8 28.4 - - + +
92B ASP* 6.2 1.6 - - + -
93B VAL* 4.1 13.7 - - + -
104B THR* 3.0 13.0 + - + +
105B LEU 3.0 7.2 + - - +
107B GLN* 1.3 79.4 - - - +
109B TRP* 1.3 56.1 + - - +
111B ASP* 3.4 8.8 + - - +
112B HIS* 3.1 30.8 + - - +
147B PHE* 3.8 8.1 - - + -
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Residues in contact with TRP 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 LEU 2.9 15.0 + - - +
106B ASN* 3.5 22.9 - - - +
108B ALA* 1.3 74.0 - - - +
110B ASN* 1.3 68.5 + - - +
112B HIS* 3.4 7.0 + - - -
113B GLN* 3.0 65.9 + - + +
144B LEU* 3.6 32.3 - - + -
147B PHE* 3.8 27.3 - + + -
185B ASN 5.0 1.7 + - - -
188B GLN* 5.6 2.2 - - - +
189B MSE 3.5 42.6 - - + +
192B ILE* 3.9 30.2 - - + +
193B LEU* 3.8 18.6 - - + -
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Residues in contact with ASN 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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106B ASN* 3.0 37.1 + - - +
107B GLN* 3.9 13.0 + - - +
108B ALA 3.4 0.2 - - - -
109B TRP* 1.3 84.3 - - - +
111B ASP* 1.3 62.0 + - - +
113B GLN* 3.2 18.6 - - - +
114B THR* 3.0 34.0 + - + +
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Residues in contact with ASP 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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47B LYS* 3.1 38.5 + - - -
107B GLN* 3.0 43.8 + - - +
108B ALA* 3.7 7.9 - - - +
109B TRP 3.3 0.2 - - - -
110B ASN* 1.3 78.8 - - - +
112B HIS* 1.3 60.4 + - + +
114B THR* 2.7 22.8 + - - +
115B ALA* 3.0 16.5 + - - +
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Residues in contact with HIS 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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81B VAL* 5.0 2.4 - - + +
84B HIS* 6.0 4.0 - + + -
85B LEU* 3.9 29.9 - - + +
89B VAL* 5.9 2.0 - - + -
108B ALA 3.1 17.9 + - - +
109B TRP* 3.9 9.9 - - - +
110B ASN 3.2 0.2 - - - -
111B ASP* 1.3 77.2 - - - +
113B GLN* 1.3 63.4 + - - +
115B ALA* 3.1 7.2 + - + +
116B MSE 2.9 63.8 + - + +
143B GLY* 3.2 33.5 + - - -
144B LEU* 4.3 12.3 - - + -
147B PHE* 3.7 28.5 - + + +
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Residues in contact with GLN 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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109B TRP* 3.0 61.2 + - + +
110B ASN* 3.2 27.5 - - - +
112B HIS* 1.3 79.0 + - - +
114B THR* 1.3 63.9 + - + +
116B MSE 3.5 3.2 + - - +
117B VAL* 3.1 29.6 + - + +
140B TYR* 3.5 25.4 + - - +
144B LEU* 5.5 0.2 - - + -
192B ILE* 4.7 9.1 - - - +
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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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47B LYS* 6.0 1.6 - - - +
110B ASN* 3.0 17.5 + - + +
111B ASP* 2.7 24.9 + - - +
113B GLN* 1.3 76.2 - - + +
115B ALA* 1.3 61.4 + - - +
117B VAL* 3.4 7.6 + - - +
118B MSE 3.3 31.9 + - - +
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Residues in contact with ALA 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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44B ILE* 4.2 25.8 - - + +
45B GLN* 4.8 12.3 - - + +
84B HIS* 6.1 2.2 - - + -
111B ASP 3.0 17.9 + - - +
112B HIS* 3.1 8.7 + - + +
114B THR* 1.3 77.0 + - - +
116B MSE 1.3 59.8 + - + +
118B MSE 3.0 21.9 + - - +
119B ILE* 3.0 28.6 + - + +
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Residues in contact with MSE 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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77B LEU* 5.3 1.3 - - + -
81B VAL* 4.2 17.7 - - + -
112B HIS* 2.9 49.9 + - + +
113B GLN* 3.9 0.4 - - - +
115B ALA* 1.3 73.8 - - + +
117B VAL* 1.3 60.3 + - - +
119B ILE* 3.9 22.0 - - + -
120B ARG* 3.0 32.2 + - - +
139B VAL* 3.5 44.0 - - + +
140B TYR* 3.7 26.3 - - + +
143B GLY* 3.7 17.9 - - - -
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Residues in contact with VAL 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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231A HIS* 3.9 18.3 - - + +
113B GLN* 3.1 22.1 + - + +
114B THR* 3.7 7.6 - - - +
115B ALA 3.2 0.4 - - - -
116B MSE 1.3 78.0 - - - +
118B MSE 1.3 62.6 + - - +
120B ARG* 3.4 28.9 - - - +
121B ASP* 3.4 25.8 + - - +
140B TYR* 3.9 12.8 - - + +
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Residues in contact with MSE 118 (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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231A HIS* 3.4 34.0 + - + +
232A GLU 5.5 0.7 - - - -
233A MET* 4.1 13.5 - - + -
44B ILE* 3.6 33.0 - - + +
47B LYS* 5.8 0.7 - - - -
49B ASN* 3.6 46.4 - - - +
54B PHE* 4.6 0.9 - - - -
114B THR* 3.3 23.4 + - - +
115B ALA* 3.0 9.8 + - - +
117B VAL* 1.3 77.7 - - - +
119B ILE* 1.3 56.5 - - - +
121B ASP* 3.5 4.3 + - - +
122B ILE* 3.1 33.7 + - - +
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Residues in contact with ILE 119 (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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41B ILE* 4.1 29.2 - - + -
44B ILE* 4.3 24.0 - - + -
45B GLN* 4.8 7.0 - - + +
77B LEU* 3.9 26.5 - - + -
81B VAL* 4.7 6.1 - - + -
115B ALA* 3.0 25.7 + - + +
116B MSE 4.0 20.2 - - + +
118B MSE 1.3 73.2 - - - +
120B ARG* 1.3 66.9 + - - +
121B ASP 3.1 1.3 - - - -
122B ILE* 3.0 8.8 + - - +
123B LEU* 3.0 30.6 + - + +
139B VAL* 4.3 5.4 - - + -
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Residues in contact with ARG 120 (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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116B MSE 3.0 16.9 + - - +
117B VAL* 3.4 37.1 - - - +
119B ILE* 1.3 77.2 - - - +
121B ASP* 1.3 83.2 + - - +
123B LEU* 3.2 4.7 - - - +
124B MSE 3.0 27.4 + - + +
127B ASP* 4.4 11.6 - - - +
139B VAL* 3.7 29.3 - - + +
140B TYR* 4.3 25.5 - - - +
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Residues in contact with ASP 121 (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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227A ALA* 3.8 13.8 - - + +
230A GLU* 5.6 1.6 - - - +
231A HIS* 3.0 23.5 + - - +
54B PHE* 3.3 15.4 - - + -
58B TYR* 4.0 1.2 - - - -
117B VAL* 3.4 16.9 + - - +
118B MSE 3.5 5.1 + - - +
119B ILE 3.1 0.6 - - - -
120B ARG* 1.3 107.0 + - - +
122B ILE* 1.3 65.3 + - - +
124B MSE 2.9 44.2 - - + +
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Residues in contact with ILE 122 (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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233A MET* 3.6 26.2 - - + -
37B LEU* 4.9 4.7 - - + -
41B ILE* 6.1 6.3 - - + -
44B ILE* 3.7 18.4 - - + -
54B PHE* 3.5 24.2 - - + -
57B LEU* 3.5 42.4 - - + +
58B TYR* 3.5 17.4 - - - +
61B ALA* 3.5 14.4 - - + +
118B MSE 3.1 18.9 + - - +
119B ILE* 3.0 8.5 + - - +
121B ASP* 1.3 78.3 - - - +
123B LEU* 1.3 66.1 + - + +
124B MSE 3.3 0.4 + - - -
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Residues in contact with LEU 123 (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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37B LEU* 4.7 4.5 - - + -
41B ILE* 5.2 8.3 - - + -
61B ALA* 3.6 26.2 - - + -
73B LEU* 4.1 20.4 - - + -
77B LEU* 3.8 33.9 - - + -
119B ILE* 3.0 21.8 + - + +
120B ARG 3.2 5.8 - - - +
122B ILE* 1.3 81.2 - - + +
124B MSE 1.3 63.3 + - - +
125B TYR 3.3 3.1 - - - -
126B MSE 3.2 41.7 + - + +
127B ASP* 3.3 6.2 + - - +
139B VAL* 4.1 11.7 - - + +
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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