Contacts of the helix formed by residues 102 - 127 (chain A) in PDB entry 2YW7
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 VAL 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.7 20.6 - - + -
43A VAL 3.3 16.4 + - - +
44A GLY* 4.9 1.8 - - - -
46A ASN* 4.1 12.3 - - + +
47A PHE* 3.8 22.4 - - - +
50A VAL* 3.3 21.8 - - + -
101A THR* 1.3 68.5 - - - +
103A GLN* 1.3 71.0 + - + +
104A ALA 2.4 17.8 + - - -
105A HIS* 3.1 9.9 + - - -
106A LEU* 3.1 33.5 + - + +
155A HIS* 5.7 1.1 - - + -
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Residues in contact with GLN 103 (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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46A ASN* 5.7 4.5 - - - +
101A THR* 3.4 9.0 + - + +
102A VAL* 1.3 89.3 - - + +
104A ALA* 1.3 56.3 + - - +
106A LEU* 5.0 0.4 - - - +
107A ALA* 4.4 11.3 - - - +
155A HIS* 3.5 24.2 + - - +
156A LEU* 4.4 18.6 + - + +
45G PRO* 4.2 19.5 - - - +
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Residues in contact with ALA 104 (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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97A VAL* 4.9 5.9 - - + +
100A ASP* 4.1 17.3 - - + +
101A THR* 3.0 28.0 - - - +
102A VAL 2.4 7.3 + - - -
103A GLN* 1.3 74.3 - - - +
105A HIS* 1.3 64.1 + - - +
106A LEU 3.3 0.7 - - - -
107A ALA* 3.1 8.9 + - - +
108A ALA* 3.0 22.9 + - - +
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Residues in contact with HIS 105 (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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38A VAL* 3.7 18.1 - - + +
41A ASN* 3.7 18.3 - - + +
42A VAL* 3.4 28.0 - - + -
50A VAL* 5.6 1.3 - - + -
95A TYR* 3.1 27.2 + + - +
97A VAL* 3.5 20.6 - - + +
98A GLU 2.8 29.5 + - - -
100A ASP* 3.2 35.1 + - + +
101A THR 3.0 16.4 + - - +
102A VAL* 4.2 1.6 - - - +
104A ALA* 1.3 73.6 - - - +
106A LEU* 1.3 53.2 + - + +
108A ALA* 3.4 0.4 + - - -
109A LEU* 2.7 38.1 + - - +
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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
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50A VAL* 4.2 14.6 - - + -
53A MET* 3.8 31.0 - - + -
102A VAL* 3.1 40.3 + - + +
103A GLN* 5.0 0.7 - - - +
105A HIS* 1.3 76.6 - - + +
107A ALA* 1.3 54.0 + - - +
109A LEU* 4.0 9.9 - - + -
110A ASP* 2.6 32.1 + - - +
152A VAL* 3.2 32.4 - - + +
155A HIS* 3.7 33.2 - - + +
156A LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 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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103A GLN 4.4 6.3 - - - +
104A ALA* 3.1 20.4 + - - +
106A LEU* 1.3 77.6 - - - +
108A ALA* 1.3 61.6 + - - +
110A ASP* 3.2 19.5 - - - +
111A LEU* 3.3 13.2 + - - +
156A LEU* 4.0 20.6 - - + +
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Residues in contact with ALA 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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95A TYR* 3.6 24.5 - - + +
96A SER* 5.8 1.6 - - - +
97A VAL* 3.7 19.5 - - + -
104A ALA 3.0 9.2 + - - +
107A ALA* 1.3 76.7 - - - +
109A LEU* 1.3 57.5 + - - +
111A LEU* 3.3 13.0 + - - +
112A VAL* 3.0 29.1 + - - +
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Residues in contact with LEU 109 (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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31A LEU* 5.5 0.9 - - + -
34A THR* 4.5 7.6 - - + -
35A LEU* 3.7 32.3 - - + -
38A VAL* 4.0 30.3 - - + -
50A VAL* 5.8 0.4 - - + -
54A ILE* 4.8 5.4 - - + -
95A TYR* 4.0 7.6 + - + -
105A HIS* 2.7 23.1 + - + +
106A LEU* 3.7 13.0 - - + +
108A ALA* 1.3 71.3 - - - +
110A ASP* 1.3 66.0 + - - +
112A VAL* 3.5 10.2 + - + +
113A TYR* 3.2 39.9 + - + -
148A PHE* 4.2 18.8 - - + -
152A VAL* 4.4 7.9 - - + -
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Residues in contact with ASP 110 (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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106A LEU 2.6 17.9 + - - +
107A ALA* 3.2 12.1 - - - +
109A LEU* 1.3 75.7 - - - +
111A LEU* 1.3 63.5 + - - +
113A TYR* 3.3 6.0 + - - +
114A ASN* 2.5 31.2 + - - +
149A GLN* 2.4 39.5 + - - +
152A VAL* 3.8 15.5 - - + +
153A ARG* 3.4 22.0 + - - +
156A LEU* 4.3 11.7 - - + +
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Residues in contact with LEU 111 (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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107A ALA 3.3 12.8 + - - +
108A ALA* 3.5 12.6 - - - +
109A LEU 3.2 0.4 - - - -
110A ASP* 1.3 84.4 - - - +
112A VAL* 1.3 68.6 + - - +
114A ASN* 2.8 34.0 + - + +
115A GLY 3.7 1.9 + - - -
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Residues in contact with VAL 112 (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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30A ASP* 5.7 4.7 - - - +
31A LEU* 4.6 16.8 - - + -
34A THR* 4.9 8.1 - - + -
92A TRP* 6.2 3.8 - - + -
95A TYR* 3.7 29.2 - - + -
108A ALA 3.0 17.4 + - - +
109A LEU* 3.6 12.6 - - + +
110A ASP 3.4 0.2 - - - -
111A LEU* 1.3 76.4 - - - +
113A TYR* 1.3 63.0 + - + +
115A GLY* 3.3 4.7 + - - -
116A VAL* 3.3 28.6 + - + +
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Residues in contact with TYR 113 (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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31A LEU* 3.6 24.0 - - + +
35A LEU* 3.4 12.1 - - + +
57A GLN* 2.7 39.7 + - - +
109A LEU* 3.2 30.1 + - + +
110A ASP* 3.5 9.4 - - - +
111A LEU 2.9 1.8 + - - -
112A VAL* 1.3 79.7 - - + +
114A ASN* 1.3 55.1 + - - +
116A VAL* 3.1 10.1 + - + +
117A ILE* 2.7 42.2 + - + +
145A LEU* 3.8 36.3 - - + -
148A PHE* 3.2 32.9 - + - -
149A GLN* 4.0 17.7 - - + +
152A VAL* 5.2 2.0 - - + -
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Residues in contact with ASN 114 (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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110A ASP* 2.5 24.1 + - - +
111A LEU* 2.8 25.0 + - + +
113A TYR* 1.3 70.4 - - - +
115A GLY* 1.3 50.8 - - - +
117A ILE* 3.2 4.0 + - - +
118A GLU* 2.5 51.4 + - + +
149A GLN* 2.4 39.7 + - - +
153A ARG* 4.1 9.9 + - - -
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Residues in contact with GLY 115 (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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111A LEU 3.7 2.0 + - - -
112A VAL 3.3 7.5 + - - -
113A TYR 3.3 0.4 - - - -
114A ASN* 1.3 75.2 - - - +
116A VAL* 1.3 59.8 + - - +
118A GLU* 3.9 13.2 + - - -
119A ASP* 2.9 43.1 + - - -
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Residues in contact with VAL 116 (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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27A THR* 4.3 27.2 - - + +
28A TYR* 5.2 4.0 - - + -
31A LEU* 4.3 20.4 - - + -
112A VAL* 3.3 27.5 + - + +
113A TYR* 3.1 17.0 + - + +
115A GLY* 1.3 77.3 - - - +
117A ILE* 1.3 56.1 + - + +
119A ASP* 3.8 1.7 - - - +
120A THR* 2.6 42.5 + - - +
145A LEU* 4.2 27.1 - - + -
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Residues in contact with ILE 117 (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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113A TYR* 2.7 25.2 + - + +
114A ASN* 3.6 3.8 - - - +
116A VAL* 1.3 70.0 - - - +
118A GLU* 1.3 61.1 + - - +
120A THR* 3.2 6.5 + - - -
121A ARG* 2.8 37.7 + - + +
142A ALA* 6.0 0.9 - - + +
145A LEU* 4.3 10.8 - - + +
146A GLU* 3.3 62.1 - - + +
149A GLN* 2.8 34.3 - - + +
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Residues in contact with GLU 118 (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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114A ASN* 2.5 34.9 + - + +
115A GLY* 3.5 13.2 + - - +
116A VAL 3.3 0.2 - - - -
117A ILE* 1.3 74.5 - - - +
119A ASP* 1.3 63.2 + - - +
121A ARG* 3.2 8.3 + - - +
122A LYS* 3.0 45.5 + - - +
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Residues in contact with ASP 119 (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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24A GLN* 4.4 7.0 - - - +
27A THR* 5.0 10.5 + - + +
91A THR* 4.0 16.1 + - - +
92A TRP* 4.6 12.6 - - - -
115A GLY* 2.9 24.1 + - - +
116A VAL* 3.9 3.6 - - - +
118A GLU* 1.3 77.5 - - - +
120A THR* 1.3 53.4 + - - +
122A LYS* 3.4 21.8 - - - +
123A SER* 2.7 40.0 + - - +
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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
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24A GLN* 2.9 29.9 + - - +
27A THR* 5.5 1.4 - - - +
28A TYR* 4.9 1.6 - - - +
116A VAL* 2.6 32.6 + - - +
117A ILE* 3.6 8.1 - - - -
119A ASP* 1.3 73.8 - - - +
121A ARG* 1.3 64.3 + - - +
123A SER* 3.7 1.6 + - - -
124A ILE* 3.1 25.6 + - + +
138A LEU* 4.0 14.5 - - + +
142A ALA* 3.9 31.9 - - + +
145A LEU* 4.4 8.8 - - + +
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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
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117A ILE* 2.8 28.3 + - + +
118A GLU* 3.3 9.2 - - - +
120A THR* 1.3 73.9 - - - +
122A LYS* 1.3 65.3 + - - +
124A ILE* 2.9 16.0 + - - +
125A GLU* 2.9 23.5 + - - +
142A ALA* 5.8 0.9 - - + -
146A GLU* 3.3 34.0 + - - +
71B ARG* 3.8 12.9 - - - +
75B LEU* 5.0 5.5 - - - +
131B ASP* 3.8 17.1 + - - +
132B LEU* 4.4 8.1 - - - +
133B VAL* 3.3 25.0 - - - +
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Residues in contact with LYS 122 (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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118A GLU* 3.0 32.2 + - - +
119A ASP* 3.3 30.5 + - - +
121A ARG* 1.3 75.1 - - - +
123A SER* 1.3 59.3 + - - +
124A ILE 3.1 0.2 + - - -
125A GLU* 3.2 17.3 + - - +
126A LYS* 2.8 48.3 + - + +
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Residues in contact with SER 123 (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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20A LEU* 3.3 34.4 + - - +
23A LYS* 5.4 2.6 + - - +
24A GLN* 3.3 23.7 + - - -
119A ASP* 2.7 22.2 + - - +
120A THR 4.0 1.1 - - - -
122A LYS* 1.3 73.2 - - - +
124A ILE* 1.3 60.7 + - - +
126A LYS* 3.7 1.9 + - - +
127A LEU* 3.1 32.6 + - - +
138A LEU* 3.8 13.7 - - - -
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Residues in contact with ILE 124 (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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120A THR 3.1 19.3 + - - +
121A ARG* 2.9 17.7 + - - +
123A SER* 1.3 74.1 - - - +
125A GLU* 1.3 58.5 + - + +
127A LEU* 2.8 24.0 + - - +
135A GLN* 2.6 44.8 + - + +
138A LEU* 3.9 22.4 - - + +
139A ILE* 3.6 33.7 - - + +
142A ALA* 4.3 11.7 - - + -
132B LEU* 3.8 22.2 - - + -
133B VAL* 5.1 4.9 - - + -
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Residues in contact with GLU 125 (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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121A ARG 2.9 11.4 + - - +
122A LYS* 3.7 17.8 - - - +
124A ILE* 1.3 77.4 - - + +
126A LYS* 1.3 64.2 + - + +
128A GLU* 3.0 29.9 + - - +
135A GLN* 4.5 2.5 - - - +
132B LEU* 6.3 0.2 - - - -
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Residues in contact with LYS 126 (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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20A LEU* 4.0 26.2 - - + +
23A LYS* 5.1 10.9 - - - +
122A LYS* 2.8 35.0 + - + +
123A SER* 3.8 5.8 - - - +
125A GLU* 1.3 83.3 - - + +
127A LEU* 1.3 59.0 + - - +
128A GLU* 3.3 0.8 + - - -
129A ASP 4.8 1.0 + - - -
130A LEU* 3.2 25.3 - - + +
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Residues in contact with LEU 127 (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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17A VAL* 3.8 28.0 - - + -
20A LEU* 3.8 22.4 - - + -
21A LEU* 4.8 4.3 - - + -
123A SER* 3.1 20.2 + - - +
124A ILE* 2.8 12.3 + - - +
126A LYS* 1.3 78.3 - - - +
128A GLU* 1.3 67.8 + - - +
129A ASP 3.5 0.9 - - - -
130A LEU* 3.0 24.1 + - + -
131A ASP 3.0 17.7 + - - +
134A SER* 3.8 15.3 - - - +
135A GLN* 3.7 35.2 - - + +
138A LEU* 4.3 15.7 - - + -
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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
------------------------------------------------------------
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