Contacts of the helix formed by residues 101 - 133 (chain B) in PDB entry 3U9J
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 101 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 1.3 80.8 - - + +
102B GLU* 1.3 68.3 + - - +
103B TYR* 3.0 28.4 + - + +
104B GLU* 2.9 31.0 + - - +
105B GLN* 2.9 36.3 + - - +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.5 31.6 - - - +
101B ASN* 1.3 81.0 - - - +
103B TYR* 1.3 70.2 + - + +
105B GLN* 3.7 10.3 - - - +
106B LEU* 3.0 39.2 + - + +
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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
----------------------------------------------------------
101B ASN* 3.0 16.4 + - - +
102B GLU* 1.3 82.6 - - + +
104B GLU* 1.3 60.2 + - + +
106B LEU* 3.9 4.8 - - - +
107B ASN* 3.0 42.4 + - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN 6.1 0.2 - - - +
77A TYR* 3.7 22.9 + - - +
98B ASN 4.1 9.8 - - - +
99B VAL* 3.8 11.2 - - + -
100B LYS* 2.6 37.4 + - - +
101B ASN* 2.9 30.2 + - - +
103B TYR* 1.3 77.7 - - + +
105B GLN* 1.3 57.5 + - - +
107B ASN* 3.9 3.8 - - - +
108B TYR* 2.9 32.2 + - - +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 2.8 26.5 + - - +
35B SER* 3.4 22.6 + - - +
36B ASN 3.8 1.6 + - - -
37B ASN* 2.8 41.8 + - - +
40B PHE* 3.7 22.1 - - + +
99B VAL* 3.4 20.6 - - + -
100B LYS 4.0 2.1 - - - +
101B ASN* 2.9 27.5 + - - +
102B GLU* 3.7 8.5 + - - +
103B TYR 3.3 0.2 - - - -
104B GLU* 1.3 76.8 - - - +
106B LEU* 1.3 56.6 + - - +
108B TYR* 3.5 2.1 + - - +
109B ALA* 2.9 29.0 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.8 29.4 - - + +
35B SER* 3.9 25.1 - - - +
102B GLU* 3.0 26.1 + - + +
103B TYR* 4.1 3.6 - - - +
105B GLN* 1.3 73.6 - - - +
107B ASN* 1.3 66.1 + - - +
109B ALA* 3.3 5.9 + - + +
110B LYS* 3.3 20.4 + - - +
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.5 27.5 + - - +
77A TYR* 4.3 5.6 - - + -
103B TYR* 3.0 34.3 + - - +
104B GLU* 3.9 5.2 - - - +
106B LEU* 1.3 78.3 - - - +
108B TYR* 1.3 64.3 + - - +
110B LYS* 3.4 12.4 + - - +
111B GLN* 3.6 9.7 + - - +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 3.4 41.8 - + + -
40B PHE* 3.5 22.7 - + + -
44B LEU* 3.6 24.0 - - + +
91B LEU* 2.7 52.0 + - + +
92B PHE* 3.4 10.6 - - - -
94B LYS* 4.6 0.4 - - + -
95B GLY* 3.5 20.3 - - - -
99B VAL* 4.0 9.4 - - + -
104B GLU 2.9 19.7 + - - +
105B GLN 3.6 3.1 - - - +
107B ASN* 1.3 75.8 - - - +
109B ALA* 1.3 57.9 + - - +
111B GLN* 3.0 6.0 + - - +
112B LEU* 2.8 43.3 + - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.3 41.3 - - + -
105B GLN 2.9 18.3 + - - +
106B LEU* 3.5 9.6 - - + +
107B ASN 3.2 0.2 - - - -
108B TYR* 1.3 77.8 - - - +
110B LYS* 1.3 62.6 + - - +
112B LEU* 3.6 7.1 - - - +
113B LYS* 3.0 36.5 + - - +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 3.3 8.5 + - - +
107B ASN* 3.7 10.8 - - - +
108B TYR 3.3 0.4 - - - -
109B ALA* 1.3 79.3 - - - +
111B GLN* 1.3 63.5 + - - +
113B LYS* 3.9 8.1 - - - +
114B GLU* 3.1 48.5 + - + +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 5.9 2.9 - - - +
77A TYR* 4.7 12.6 - - + +
78A ASN* 2.6 57.9 + - - +
79A VAL* 5.1 2.4 + - - +
129A GLU* 4.5 12.6 + - - +
91B LEU* 5.3 1.1 - - + -
107B ASN 3.6 7.0 + - - +
108B TYR* 3.0 11.1 + - - +
110B LYS* 1.3 80.7 - - - +
112B LEU* 1.3 64.0 + - - +
114B GLU* 3.3 25.6 + - - +
115B ARG* 3.0 27.8 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.3 5.8 - - + -
34B PHE* 4.0 13.5 - - + -
43B LEU* 4.0 26.5 - - + -
44B LEU* 4.1 7.6 - - + -
47B LEU* 4.1 5.4 - - + -
91B LEU* 4.1 15.9 - - + +
92B PHE* 3.6 35.9 - - + -
108B TYR* 2.8 40.3 + - + +
109B ALA* 3.6 3.8 - - - +
111B GLN* 1.3 77.4 - - - +
113B LYS* 1.3 55.7 + - - +
115B ARG* 3.3 1.2 + - - +
116B LEU* 2.9 43.7 + - + +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.3 29.5 - - + +
34B PHE* 3.6 33.5 - - + -
109B ALA* 3.0 25.9 + - - +
110B LYS* 3.9 7.2 - - - +
112B LEU* 1.3 77.8 - - - +
114B GLU* 1.3 61.7 + - + +
116B LEU* 4.0 4.7 - - - +
117B GLU* 3.0 28.5 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 5.1 4.5 - - - +
110B LYS* 3.1 40.6 + - + +
111B GLN* 3.3 34.5 + - - +
113B LYS* 1.3 77.6 - - + +
115B ARG* 1.3 59.2 + - + +
117B GLU* 3.5 8.4 + - - +
118B ALA* 3.1 27.4 + - - +
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Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 2.8 46.2 - - - +
81A SER* 6.1 1.6 - - - -
83B ASN 5.9 0.2 + - - -
84B LYS* 4.6 26.8 - - - +
87B GLU* 4.8 12.1 - - - +
88B MSE 3.3 34.6 - - + +
91B LEU* 4.0 15.5 - - + -
111B GLN* 3.0 14.5 + - - +
112B LEU 3.8 2.7 - - - +
114B GLU* 1.3 75.7 - - - +
116B LEU* 1.3 59.8 + - - +
118B ALA* 3.3 12.3 + - - +
119B PHE* 2.8 41.8 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 4.2 18.4 - - + +
29B LEU* 4.1 27.8 - - + -
47B LEU* 4.0 18.2 - - + -
51B PHE* 3.6 26.2 - - + -
88B MSE 3.6 20.4 - - + -
92B PHE* 4.2 5.6 - - + -
112B LEU* 2.9 42.3 + - + +
113B LYS* 4.0 3.6 - - - +
115B ARG* 1.3 72.5 - - - +
117B GLU* 1.3 61.5 + - - +
119B PHE* 3.6 2.9 - - + +
120B THR* 2.8 36.6 + - - -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LYS* 3.0 20.8 + - - +
114B GLU* 3.6 7.7 - - - +
116B LEU* 1.3 77.4 - - - +
118B ALA* 1.3 56.8 + - - +
120B THR* 4.0 4.6 - - - -
121B ARG* 3.0 49.9 + - + +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU 3.1 17.5 + - - +
115B ARG* 3.6 20.4 - - - +
117B GLU* 1.3 75.1 - - - +
119B PHE* 1.3 65.1 + - - +
121B ARG* 3.4 28.4 + - - +
122B ASP* 3.2 26.0 + - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.6 14.8 - - - -
51B PHE* 3.5 31.9 - + - -
54B PHE* 3.7 19.7 - + - -
83B ASN* 3.6 30.7 - - + -
85B LEU* 3.6 22.9 - - + -
88B MSE 4.1 13.0 - - + -
115B ARG* 2.8 27.6 + - - +
116B LEU* 3.6 5.8 - - - +
118B ALA* 1.3 76.8 - - - +
120B THR* 1.3 61.3 - - - +
122B ASP* 3.0 7.9 + - + +
123B PHE* 2.8 62.0 + + + +
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.7 27.6 - - + -
25B TYR* 2.7 25.6 + - - +
26B CYS* 5.0 6.8 - - - -
116B LEU 2.8 20.0 + - - -
117B GLU* 4.1 4.9 - - - -
119B PHE* 1.3 77.6 - - - +
121B ARG* 1.3 62.3 + - - +
122B ASP 3.3 0.5 + - - -
123B PHE* 4.2 3.6 - - - -
124B LEU* 3.4 41.1 + - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU 5.5 0.2 + - - -
117B GLU* 3.0 51.2 + - + +
118B ALA* 3.6 28.9 + - - +
119B PHE 3.1 0.2 - - - -
120B THR* 1.3 78.5 - - - +
122B ASP* 1.3 65.1 + - - +
124B LEU* 5.0 1.3 - - - +
125B PRO* 3.1 22.5 - - - +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 4.9 10.6 + - - -
121A ARG* 6.0 0.2 + - - -
122A ASP* 4.1 18.6 - - - +
83B ASN* 4.4 7.1 - - - +
84B LYS* 5.3 4.5 + - - -
118B ALA 3.2 12.4 + - - +
119B PHE* 3.0 9.6 + - + +
121B ARG* 1.3 89.9 + - - +
123B PHE* 1.3 63.6 + - - +
124B LEU 3.4 0.4 - - - -
125B PRO* 3.3 5.4 - - - +
126B HIS* 3.2 22.3 + - - +
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MSE 4.0 16.4 - - + -
22B VAL* 4.0 13.2 - - + -
54B PHE* 4.0 35.9 - + + -
57B HIS* 4.9 1.8 - + - -
58B GLU* 3.5 24.2 - - - -
83B ASN* 3.7 20.1 + - - -
85B LEU* 6.4 0.4 - - + -
119B PHE* 2.8 46.8 + + + +
120B THR* 3.4 5.6 + - - +
122B ASP* 1.3 73.2 - - - +
124B LEU* 1.3 64.3 + - + +
126B HIS* 3.2 8.6 + + - +
127B MSE 3.0 60.6 + - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 5.3 11.3 - - + +
22B VAL* 4.9 9.9 - - + -
120B THR* 3.4 33.1 + - + +
121B ARG* 5.7 0.7 - - - -
123B PHE* 1.3 84.0 - - + +
125B PRO* 1.3 64.6 - - + +
127B MSE 3.2 27.6 + - + +
128B LYS* 3.0 26.2 + - - +
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG 3.1 25.8 - - - +
122B ASP* 3.3 9.6 - - - +
124B LEU* 1.3 96.2 - - + +
126B HIS* 1.3 55.1 + - - +
128B LYS* 3.5 12.2 - - + +
129B GLU* 2.9 30.5 + - - +
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.4 5.5 + - - -
80B HIS* 3.5 11.2 - + - -
81B SER* 3.3 42.8 + - - -
83B ASN* 3.5 28.0 + - - +
122B ASP 3.2 13.1 + - - +
123B PHE* 3.2 12.1 + + - +
125B PRO* 1.3 80.0 - - - +
127B MSE 1.3 69.3 + - + +
129B GLU* 3.4 12.6 + - - +
130B GLU* 3.0 25.5 + - + +
202B FE 2.3 31.2 - - - -
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Residues in contact with MSE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.5 55.4 - - + +
18B MSE 4.0 9.6 - - + -
19B LYS* 3.9 25.6 - - + +
22B VAL* 5.2 0.4 - - + -
123B PHE* 3.0 60.7 + - + +
124B LEU* 3.2 27.8 + - + +
126B HIS* 1.3 74.5 - - + +
128B LYS* 1.3 65.7 + - - +
130B GLU* 3.2 3.8 + - - -
131B GLU* 3.2 29.5 + - - +
203B FE 4.2 2.5 - - - -
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 3.0 14.5 + - - +
125B PRO* 3.5 13.5 - - + +
127B MSE 1.3 77.0 - - - +
129B GLU* 1.3 58.8 + - - +
131B GLU* 3.3 12.6 + - - +
132B GLU* 2.8 71.4 + - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 4.5 13.0 - - - +
81B SER* 5.5 3.1 + - - -
125B PRO 2.9 16.1 + - - +
126B HIS* 3.7 12.8 + - - +
127B MSE 3.2 0.2 - - - -
128B LYS* 1.3 77.2 - - - +
130B GLU* 1.3 54.8 + - + +
132B GLU* 4.8 2.0 - - - -
133B VAL* 2.7 60.6 + - + +
134B PHE* 3.4 24.3 + - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.5 23.1 - - + -
15B HIS* 2.9 11.1 + - - -
61B GLU* 3.0 7.0 - - - +
66B ILE* 5.5 0.4 - - - +
80B HIS* 2.9 12.7 + - + -
126B HIS* 3.0 17.5 + - + +
127B MSE 3.2 7.0 + - - +
129B GLU* 1.3 76.8 - - + +
131B GLU* 1.3 58.7 + - - +
134B PHE* 3.1 33.9 + - + +
135B GLN 3.0 27.2 + - - -
202B FE 2.1 29.6 - - - -
203B FE 2.3 25.0 - - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.2 9.0 - - - -
11B PHE* 4.0 15.8 - - + +
12B THR* 4.9 11.6 - - - +
15B HIS* 2.6 37.5 + - - +
19B LYS* 4.3 14.6 + - - -
127B MSE 3.2 15.7 + - - +
128B LYS* 3.7 12.3 - - - +
130B GLU* 1.3 77.1 - - - +
132B GLU* 1.3 61.8 + - + +
135B GLN* 3.5 22.4 - - - +
136B PRO* 3.7 2.3 - - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS* 2.8 62.7 + - + +
129B GLU* 4.3 1.6 - - - +
131B GLU* 1.3 81.5 - - + +
133B VAL* 1.3 66.5 + - + +
136B PRO* 3.3 17.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 6.2 2.5 - - - +
129B GLU* 2.7 40.3 + - + +
132B GLU* 1.3 82.8 - - + +
134B PHE* 1.3 78.5 + - + +
135B GLN 3.5 0.4 - - - -
136B PRO* 3.3 9.9 - - - +
137B MSE 3.2 31.6 + - + +
----------------------------------------------------------
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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).
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