Contacts of the helix formed by residues 101 - 133 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 1.3 80.0 - - + +
102A GLU* 1.3 67.7 + - - +
103A TYR* 2.9 29.5 + - + +
104A GLU* 3.0 28.6 + - - +
105A GLN* 2.9 35.7 + - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.5 30.9 - - - +
101A ASN* 1.3 80.4 - - - +
103A TYR* 1.3 73.0 + - + +
105A GLN* 3.7 10.0 - - - +
106A LEU* 3.0 38.1 + - + +
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 2.9 17.1 + - - +
102A GLU* 1.3 83.6 - - + +
104A GLU* 1.3 64.3 + - + +
106A LEU* 3.4 4.7 + - - +
107A ASN* 3.1 36.0 + - - +
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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
----------------------------------------------------------
98A ASN 3.8 10.8 - - - +
99A VAL* 3.8 9.2 - - + -
100A LYS* 2.7 38.7 + - - +
101A ASN* 3.0 31.1 + - - +
103A TYR* 1.3 75.8 - - + +
105A GLN* 1.3 61.0 + - - +
107A ASN* 4.0 4.2 - - - +
108A TYR* 2.9 32.6 + - - +
74B GLN 5.7 2.7 - - - +
77B TYR* 3.5 23.3 + - - +
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Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 2.8 27.0 + - - +
35A SER* 3.5 21.4 + - - +
36A ASN 3.7 1.6 + - - -
37A ASN* 3.5 32.9 - - - +
40A PHE* 3.7 25.0 - - + +
99A VAL* 3.3 20.4 - - + +
100A LYS 3.9 8.3 - - - +
101A ASN* 2.9 27.4 + - - +
102A GLU* 3.3 8.3 + - - +
104A GLU* 1.3 76.8 - - - +
106A LEU* 1.3 56.5 + - - +
108A TYR* 3.5 1.7 + - - +
109A ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.8 29.6 - - + +
35A SER* 3.9 25.6 - - - +
102A GLU* 3.0 26.5 + - + +
103A TYR* 4.1 3.6 - - - +
105A GLN* 1.3 73.2 - - - +
107A ASN* 1.3 67.2 + - - +
109A ALA* 3.5 5.5 + - + +
110A LYS* 3.4 19.4 + - - +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.1 30.1 + - - +
104A GLU* 4.0 5.6 - - - +
106A LEU* 1.3 74.4 - - - +
108A TYR* 1.3 66.0 + - - +
110A LYS* 3.3 16.0 + - - +
111A GLN* 3.5 16.6 + - - +
75B THR* 3.5 30.1 + - - +
77B TYR* 4.4 5.8 - - + +
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.5 22.4 - + + -
44A LEU* 3.5 22.3 - - + +
91A LEU* 2.7 51.6 + - + +
92A PHE* 3.4 11.1 - - - -
94A LYS* 4.5 0.4 - - + -
95A GLY* 3.4 20.7 - - - -
99A VAL* 4.0 9.6 - - + -
104A GLU 2.9 19.9 + - - +
105A GLN 3.7 3.1 - - - +
107A ASN* 1.3 75.6 - - - +
109A ALA* 1.3 52.0 + - - +
111A GLN* 3.1 5.6 + - + +
112A LEU* 2.8 51.0 + - + +
77B TYR* 3.4 44.3 - + + -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.3 41.1 - - + -
105A GLN 2.9 18.8 + - - +
106A LEU* 3.6 9.6 - - + +
107A ASN 3.2 0.2 - - - -
108A TYR* 1.3 78.4 - - - +
110A LYS* 1.3 62.8 + - - +
112A LEU* 3.6 7.1 - - - +
113A LYS* 3.0 37.3 + - - +
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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
----------------------------------------------------------
106A LEU 3.4 8.2 + - - +
107A ASN* 3.3 12.0 + - - +
108A TYR 3.2 0.4 - - - -
109A ALA* 1.3 78.5 - - - +
111A GLN* 1.3 64.7 + - + +
113A LYS* 3.9 7.6 - - - +
114A GLU* 3.1 49.5 + - + +
133B VAL* 6.2 2.2 - - - +
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 5.3 3.1 - - + -
107A ASN* 3.5 11.3 + - - +
108A TYR* 3.1 7.4 + - - +
110A LYS* 1.3 78.3 - - + +
112A LEU* 1.3 64.9 + - - +
114A GLU* 3.4 13.9 + - - +
115A ARG* 3.0 26.3 + - - +
75B THR* 2.5 31.3 + - - -
76B ILE* 3.7 7.3 - - - +
77B TYR* 2.7 40.0 + - + -
78B ASN* 3.5 15.3 + - + +
79B VAL 4.8 0.9 + - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.3 3.8 - - + -
34A PHE* 4.0 27.6 - - + -
40A PHE* 5.7 0.4 - - + -
43A LEU* 4.0 15.3 - - + -
44A LEU* 4.2 4.0 - - + -
47A LEU* 4.0 9.0 - - + -
91A LEU* 4.3 14.5 - - + +
92A PHE* 3.7 32.5 - - + -
108A TYR* 2.8 44.8 + - + +
109A ALA 3.3 4.5 + - - +
111A GLN* 1.3 73.4 - - - +
113A LYS* 1.3 57.1 + - - +
115A ARG* 3.2 1.7 + - - +
116A LEU* 2.9 46.7 + - + +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.3 29.3 - - + +
34A PHE* 3.6 34.3 - - + -
109A ALA* 3.0 26.5 + - - +
110A LYS* 3.9 7.1 - - - +
112A LEU* 1.3 78.6 - - - +
114A GLU* 1.3 62.4 + - + +
116A LEU* 3.4 4.4 + - - +
117A GLU* 3.0 39.9 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 3.1 44.7 + - + +
111A GLN* 3.7 13.5 - - - +
113A LYS* 1.3 77.9 - - + +
115A ARG* 1.3 58.8 + - - +
117A GLU* 3.5 14.4 + - - +
118A ALA* 3.1 28.1 + - - +
129B GLU* 4.5 13.0 - - - +
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN 5.0 1.0 + - - -
84A LYS* 3.4 29.6 - - - +
87A GLU* 3.0 22.2 + - - -
88A MSE 3.6 26.9 - - + +
91A LEU* 3.9 13.5 - - + -
111A GLN 3.0 18.0 + - - +
112A LEU 3.7 3.4 - - - +
114A GLU* 1.3 77.0 - - - +
116A LEU* 1.3 58.6 + - - +
118A ALA* 3.4 13.3 + - - +
119A PHE* 2.9 37.3 + - - +
78B ASN* 2.9 36.7 - - + +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 4.1 19.3 - - + +
29A LEU* 4.1 26.9 - - + -
47A LEU* 4.1 16.8 - - + -
51A PHE* 3.6 34.5 - - + -
88A MSE 3.7 12.3 - - + -
92A PHE* 4.3 5.6 - - + -
112A LEU* 2.9 43.3 + - + +
113A LYS* 3.9 4.0 - - - +
115A ARG* 1.3 74.7 - - - +
117A GLU* 1.3 65.1 + - - +
119A PHE* 3.2 2.2 + - + +
120A THR* 2.9 31.3 + - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 6.3 2.0 - - + -
113A LYS* 3.0 35.4 + - + +
114A GLU* 3.6 13.7 - - - +
116A LEU* 1.3 75.3 - - + +
118A ALA* 1.3 57.9 + - - +
120A THR* 3.0 20.2 + - - -
121A ARG* 3.0 30.6 + - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU 3.1 17.5 + - - +
115A ARG* 3.6 21.5 - - - +
116A LEU 3.2 0.2 - - - -
117A GLU* 1.3 74.3 - - - +
119A PHE* 1.3 64.7 + - - +
121A ARG* 3.4 26.9 + - - +
122A ASP* 3.3 26.0 + - - +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.7 16.4 - - - -
51A PHE* 3.6 31.6 - + - -
54A PHE* 3.7 20.4 - + - -
83A ASN* 3.6 28.3 - - + -
85A LEU* 3.5 22.7 - - + -
88A MSE 4.1 15.0 - - + -
115A ARG* 2.9 29.1 + - - +
116A LEU* 3.2 3.6 + - + +
118A ALA* 1.3 77.5 - - - +
120A THR* 1.3 54.9 + - + +
122A ASP* 3.0 6.2 + - - +
123A PHE* 2.8 66.8 + + + +
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Residues in contact with THR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.6 9.0 - - + -
25A TYR* 2.7 37.9 - - + +
26A CYS* 5.1 5.2 - - - -
116A LEU* 2.9 18.1 + - + +
117A GLU* 3.0 14.5 + - - -
119A PHE* 1.3 79.1 - - + +
121A ARG* 1.3 64.4 + - - +
122A ASP 3.4 0.5 + - - -
123A PHE* 3.8 5.6 - - - -
124A LEU* 3.0 37.3 + - - +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU 5.6 0.2 + - - -
117A GLU* 3.0 38.4 + - - +
118A ALA* 3.6 27.8 + - - +
119A PHE 3.1 0.2 - - - -
120A THR* 1.3 82.6 + - - +
122A ASP* 1.3 65.3 + - - +
124A LEU* 5.1 0.6 - - - +
125A PRO* 3.2 21.7 - - - +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 4.8 7.4 - - - +
84A LYS* 5.7 1.9 + - - -
118A ALA 3.3 11.5 + - - +
119A PHE* 3.0 8.3 + - - +
121A ARG* 1.3 89.7 + - - +
123A PHE* 1.3 64.8 + - - +
124A LEU 3.3 2.2 - - - -
125A PRO* 3.2 6.6 - - - +
126A HIS* 3.2 22.3 + - - +
84B LYS* 4.3 15.5 + - - +
122B ASP* 4.1 17.1 - - - +
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MSE 4.0 16.4 - - + -
22A VAL* 4.1 12.3 - - + -
54A PHE* 4.0 34.5 - + + -
57A HIS* 4.9 2.7 - + - -
58A GLU* 3.6 24.5 - - - -
83A ASN* 3.7 19.9 + - - -
85A LEU* 6.5 0.4 - - + -
119A PHE* 2.8 46.6 + + + +
120A THR* 3.6 6.0 + - - +
122A ASP* 1.3 74.7 - - - +
124A LEU* 1.3 64.1 + - + +
126A HIS* 3.2 8.0 - + - +
127A MSE 3.0 59.7 + - + +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 4.3 19.7 - - + -
22A VAL* 5.1 11.7 - - + -
120A THR* 3.0 32.5 + - - +
121A ARG 5.1 0.2 - - - +
123A PHE* 1.3 85.7 - - + +
125A PRO* 1.3 65.6 - - + +
127A MSE 3.3 25.3 + - + +
128A LYS* 3.0 26.2 + - - +
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Residues in contact with PRO 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG 3.2 25.8 - - - +
122A ASP* 3.2 9.6 - - - +
124A LEU* 1.3 94.2 - - + +
126A HIS* 1.3 55.2 + - - +
128A LYS* 3.5 13.3 - - + +
129A GLU* 2.9 31.0 + - - +
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Residues in contact with HIS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.3 5.9 + - - -
80A HIS* 3.4 21.1 - + - -
81A SER* 3.2 39.6 + - - +
83A ASN* 3.4 28.8 + - - +
122A ASP 3.2 12.7 + - - +
123A PHE* 3.2 11.0 - + - +
124A LEU 3.2 0.2 - - - -
125A PRO* 1.3 79.7 - - - +
127A MSE 1.3 67.4 + - + +
129A GLU* 3.4 12.5 + - - +
130A GLU* 3.0 26.7 + - + +
200A FE 2.3 30.8 - - - -
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Residues in contact with MSE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 3.5 55.7 - - + +
18A MSE 4.0 9.4 - - + -
19A LYS* 4.0 21.3 - - + +
22A VAL* 5.3 1.1 - - + -
123A PHE* 3.0 63.0 + - + +
124A LEU* 3.3 29.1 + - + +
126A HIS* 1.3 75.9 - - + +
128A LYS* 1.3 65.6 + - - +
130A GLU* 3.2 4.0 + - - +
131A GLU* 3.2 29.5 + - - +
201A FE 4.2 2.2 - - - -
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU 3.0 14.1 + - - +
125A PRO* 3.5 13.7 - - + +
127A MSE 1.3 76.7 - - - +
129A GLU* 1.3 58.4 + - - +
131A GLU* 3.2 12.7 + - - +
132A GLU* 2.8 73.1 + - + +
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL 4.2 10.1 - - - +
81A SER* 4.8 7.8 + - - -
125A PRO 2.9 15.6 + - - +
126A HIS* 3.7 11.7 + - - +
127A MSE 3.3 0.2 - - - -
128A LYS* 1.3 75.6 - - - +
130A GLU* 1.3 61.3 + - - +
132A GLU* 4.5 1.8 - - - +
133A VAL* 2.7 57.3 + - + +
134A PHE* 3.4 26.1 + - + -
111B GLN* 4.5 15.1 + - - +
114B GLU* 5.1 4.4 - - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.4 23.5 - - + -
15A HIS* 2.9 10.2 + - - -
61A GLU* 3.0 7.1 - - - +
66A ILE* 5.6 0.6 - - + +
80A HIS* 2.8 13.2 + - + -
126A HIS* 3.0 15.3 + - + +
127A MSE 3.2 7.7 + - - +
129A GLU* 1.3 76.6 - - + +
131A GLU* 1.3 58.1 + - - +
134A PHE* 3.1 33.8 + - + +
135A GLN 3.0 27.5 + - - -
200A FE 2.1 29.3 - - - -
201A FE 2.2 25.7 - - - -
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.5 6.8 - - - -
11A PHE* 4.0 15.7 - - + +
12A THR* 4.9 11.1 - - - +
15A HIS* 2.7 36.0 + - - +
19A LYS* 4.7 12.5 + - - -
127A MSE 3.2 16.3 + - - +
128A LYS* 3.6 12.9 - - - +
130A GLU* 1.3 78.8 - - - +
132A GLU* 1.3 63.4 + - + +
135A GLN* 3.5 21.9 - - - +
136A PRO* 3.7 2.9 - - - +
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 2.8 58.3 + - + +
129A GLU* 4.4 1.4 - - - +
131A GLU* 1.3 80.9 - - + +
133A VAL* 1.3 68.2 + - + +
136A PRO* 3.2 17.7 - - - +
----------------------------------------------------------
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 2.7 40.6 + - + +
132A GLU* 1.3 83.1 - - + +
134A PHE* 1.3 78.2 + - + +
136A PRO* 3.3 10.0 - - - +
137A MSE 3.2 32.5 + - + +
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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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