Contacts of the helix formed by residues 101 - 128 (chain F) 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 THR 101 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F VAL* 4.4 0.2 - - - -
43F VAL* 3.7 9.9 - - + +
100F ASP* 1.3 92.3 + - - +
102F VAL* 1.3 57.5 + - - +
103F GLN* 3.6 11.5 + - - +
104F ALA* 2.8 35.3 + - - +
105F HIS* 3.1 16.9 + - - -
157J GLU* 3.8 29.6 - - - +
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Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F VAL* 4.0 9.9 - - + -
43F VAL 3.7 15.1 + - - +
44F GLY* 4.3 6.5 - - - -
45F PRO* 4.5 4.5 - - + -
46F ASN* 3.9 28.9 - - - +
47F PHE* 3.9 18.2 - - + +
50F VAL* 3.4 26.2 - - + -
101F THR* 1.3 72.4 - - - +
103F GLN* 1.3 65.0 + - + +
105F HIS* 3.6 0.5 + - - +
106F LEU* 3.1 42.6 + - + +
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Residues in contact with GLN 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F THR* 3.6 8.9 + - - +
102F VAL* 1.3 78.7 - - + +
104F ALA* 1.3 56.9 + - - +
106F LEU* 3.9 5.0 - - - +
107F ALA* 2.8 32.8 + - - +
155F HIS* 5.1 14.0 - - + -
156F LEU* 3.1 36.2 - - + +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F VAL* 4.3 7.8 - - + +
100F ASP* 3.1 40.4 - - + +
101F THR* 2.8 14.4 + - - +
103F GLN* 1.3 79.5 - - - +
105F HIS* 1.3 61.6 + - - +
107F ALA* 3.2 7.2 - - - +
108F ALA* 3.1 21.8 + - - +
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Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL* 3.7 36.8 - - + +
41F ASN* 3.5 16.6 + - + -
42F VAL* 3.6 23.6 - - + -
95F TYR* 3.1 25.4 + + - +
97F VAL* 3.4 19.9 - - + +
98F GLU 3.2 27.4 + - - -
100F ASP* 3.7 9.2 + - + +
101F THR 3.1 21.7 + - - +
102F VAL 4.3 1.3 - - - +
104F ALA* 1.3 71.1 - - - +
106F LEU* 1.3 61.9 + - + +
107F ALA 2.7 2.5 + - - -
108F ALA 2.8 1.7 + - - -
109F LEU* 2.5 38.6 + - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 3.9 27.4 - - + -
53F MET* 3.9 22.7 - - - -
102F VAL* 3.1 38.7 + - + +
103F GLN* 4.2 3.6 - - - +
105F HIS* 1.3 77.7 - - + +
107F ALA* 1.3 60.3 + - - +
109F LEU* 4.0 13.9 - - + -
110F ASP* 3.2 23.2 + - - +
152F VAL* 3.4 24.2 - - + +
154F ALA 6.1 0.2 - - - +
155F HIS* 4.3 30.6 + - + -
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Residues in contact with ALA 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLN 2.8 22.8 + - - +
104F ALA* 3.2 9.2 - - - +
105F HIS 2.7 4.6 + - - -
106F LEU* 1.3 76.4 - - - +
108F ALA* 1.3 62.0 + - - +
110F ASP* 3.3 16.0 - - - +
111F LEU* 3.5 12.5 + - - +
155F HIS* 5.2 8.4 + - + +
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F TYR* 4.2 8.3 - - + -
97F VAL* 3.8 28.5 - - + -
104F ALA 3.1 3.7 + - - +
105F HIS 2.8 4.2 + - - +
107F ALA* 1.3 72.6 - - - +
109F LEU* 1.3 55.0 + - - +
110F ASP 3.1 2.2 - - - -
111F LEU* 3.0 19.6 + - + +
112F VAL* 2.8 38.4 + - + +
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F THR* 5.0 4.7 - - + -
35F LEU* 4.0 26.2 - - + -
38F VAL* 3.6 35.7 - - + -
53F MET* 6.1 0.4 - - + -
54F ILE* 3.9 13.9 - - + -
95F TYR* 4.0 11.9 + - - +
105F HIS 2.5 27.3 + - - +
106F LEU* 4.0 17.9 - - + +
108F ALA* 1.3 72.2 - - - +
110F ASP* 1.3 61.5 + - - +
112F VAL* 3.4 10.6 + - + +
113F TYR* 3.2 41.6 + - + -
148F PHE* 5.2 6.1 - - + -
152F VAL* 4.4 7.4 - - + -
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Residues in contact with ASP 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU 3.2 13.2 + - - +
107F ALA* 3.3 12.4 - - - +
109F LEU* 1.3 76.0 - - - +
111F LEU* 1.3 73.1 + - - +
113F TYR* 3.0 14.3 + - - +
114F ASN* 3.1 14.2 + - - -
149F GLN* 2.9 33.8 + - - +
152F VAL* 4.0 14.1 - - + +
153F ARG* 3.0 33.7 + - + +
155F HIS* 6.0 3.3 - - + -
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ALA 3.5 11.0 + - - +
108F ALA* 3.0 21.4 + - + +
110F ASP* 1.3 88.4 - - - +
112F VAL* 1.3 65.3 + - + +
114F ASN* 2.9 29.9 + - - +
115F GLY 3.5 3.8 + - - -
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ASP* 5.8 3.6 - - - +
31F LEU* 3.7 30.7 - - + -
34F THR* 5.1 7.2 - - + +
94F ASP 5.5 3.6 - - - +
95F TYR* 4.1 27.6 - - + -
108F ALA* 2.8 20.5 + - + +
109F LEU* 3.5 14.6 - - + +
110F ASP 3.2 0.2 - - - -
111F LEU* 1.3 73.8 - - - +
113F TYR* 1.3 57.6 + - + +
115F GLY* 3.8 0.7 + - - -
116F VAL* 3.0 37.9 + - + +
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Residues in contact with TYR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.7 35.8 - - + +
35F LEU* 4.1 2.5 - - + +
57F GLN* 2.5 46.6 + - - +
109F LEU* 3.2 32.1 + - + +
110F ASP* 3.0 10.8 + - - +
112F VAL* 1.3 75.9 - - + +
114F ASN* 1.3 59.6 + - - +
116F VAL* 4.0 9.2 - - + -
117F ILE* 3.0 34.5 + - + +
145F LEU* 3.4 36.8 - - + -
148F PHE* 3.3 27.5 - + - -
149F GLN* 3.8 19.1 - - + +
152F VAL* 5.2 1.6 - - + -
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Residues in contact with ASN 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ASP* 3.1 16.6 + - - -
111F LEU* 2.9 22.4 + - + +
113F TYR* 1.3 74.5 - - - +
115F GLY* 1.3 54.6 - - - +
117F ILE* 3.0 5.8 + - - +
118F GLU* 2.7 50.2 + - - +
149F GLN* 3.2 21.0 + - - +
153F ARG* 3.2 28.6 + - - +
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Residues in contact with GLY 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F TRP* 6.3 2.2 - - - -
111F LEU 3.5 5.9 + - - -
112F VAL 4.4 0.9 - - - -
114F ASN* 1.3 78.0 - - - +
116F VAL* 1.3 54.1 + - - +
118F GLU* 3.2 18.6 - - - +
119F ASP* 2.7 42.7 + - - +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F THR* 4.1 28.8 - - + +
28F TYR* 5.6 1.3 - - + -
31F LEU* 4.6 18.8 - - + -
92F TRP* 6.0 10.8 - - + -
112F VAL* 3.0 36.1 + - + +
113F TYR* 4.0 11.2 - - + +
114F ASN 3.1 0.6 - - - -
115F GLY* 1.3 75.3 - - - +
117F ILE* 1.3 53.6 + - + +
119F ASP* 3.6 6.3 - - - +
120F THR* 2.5 34.1 + - - -
145F LEU* 4.0 25.6 - - + -
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F TYR* 3.0 19.5 + - - +
114F ASN* 3.0 4.7 + - - +
116F VAL* 1.3 74.4 - - + +
118F GLU* 1.3 56.8 + - - +
120F THR* 3.7 8.5 - - - -
121F ARG* 2.6 63.5 + - + +
142F ALA* 4.7 6.7 - - + +
145F LEU* 3.3 48.0 - - + +
146F GLU* 3.6 25.6 - - + +
149F GLN* 4.0 14.8 - - - +
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Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ASN* 2.7 31.7 + - + +
115F GLY* 3.2 20.9 + - - +
117F ILE* 1.3 73.0 - - - +
119F ASP* 1.3 64.0 + - - +
121F ARG* 3.2 8.5 + - - +
122F LYS* 3.1 39.2 + - - +
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Residues in contact with ASP 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LYS* 6.0 2.3 - - - +
24F GLN* 4.8 6.4 + - - +
27F THR* 4.6 9.8 + - - +
91F THR* 4.3 17.5 - - - +
92F TRP* 4.1 23.2 - - + -
115F GLY* 2.7 25.7 + - - +
116F VAL* 3.6 6.5 - - - +
118F GLU* 1.3 71.8 - - - +
120F THR* 1.3 63.4 + - - +
122F LYS* 3.1 21.1 + - - +
123F SER* 3.0 24.7 + - - -
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Residues in contact with THR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F GLN* 3.1 30.4 + - - +
28F TYR* 4.8 1.3 - - - +
116F VAL* 2.5 23.7 + - - +
117F ILE* 3.1 12.7 + - - -
119F ASP* 1.3 76.3 - - - +
121F ARG* 1.3 58.1 + - - +
123F SER* 3.1 5.1 + - - +
124F ILE* 2.9 31.3 + - + +
138F LEU* 3.8 29.2 - - + +
142F ALA* 4.1 17.3 - - + +
145F LEU* 3.9 12.2 - - + +
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Residues in contact with ARG 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ILE* 2.6 47.3 + - + +
118F GLU* 3.5 7.6 - - - +
120F THR* 1.3 71.7 - - - +
122F LYS* 1.3 60.2 + - + +
124F ILE* 2.9 36.4 - - - +
125F GLU* 3.5 10.2 + - - +
139F ILE* 4.9 12.3 - - - +
142F ALA* 4.0 22.3 - - - +
146F GLU* 4.8 11.0 + - - -
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Residues in contact with LYS 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F GLU* 3.1 41.2 + - - +
119F ASP* 3.3 20.5 + - - +
120F THR 3.1 0.2 - - - -
121F ARG* 1.3 74.1 - - + +
123F SER* 1.3 54.2 + - - +
125F GLU* 2.8 17.6 + - + +
126F LYS* 2.5 51.0 + - + +
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Residues in contact with SER 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 4.2 23.8 + - - +
23F LYS* 5.6 4.0 - - - +
24F GLN* 4.2 11.6 + - - -
119F ASP 3.0 11.1 + - - -
120F THR 3.1 7.2 + - - -
122F LYS* 1.3 77.6 - - - +
124F ILE* 1.3 57.1 - - - +
126F LYS* 3.6 12.1 - - - +
127F LEU* 2.9 38.4 + - - +
138F LEU* 3.8 21.1 - - - -
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F THR* 2.9 21.1 + - + +
121F ARG* 2.9 52.3 - - - +
123F SER* 1.3 75.2 - - - +
125F GLU* 1.3 58.4 + - + +
127F LEU* 3.7 7.7 - - - +
128F GLU 3.4 2.1 + - - -
135F GLN* 2.8 79.1 + - + +
138F LEU* 4.6 5.2 - - + +
139F ILE* 3.5 34.8 - - + +
142F ALA* 5.7 0.4 - - + -
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F ARG 3.9 7.9 - - - +
122F LYS* 2.8 33.9 + - - +
124F ILE* 1.3 73.6 - - - +
126F LYS* 1.3 66.1 + - - +
127F LEU 2.9 11.4 + - - -
128F GLU* 3.1 22.9 + - + +
129F ASP 4.9 0.3 + - - -
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Residues in contact with LYS 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 3.9 32.6 - - + +
23F LYS* 5.2 9.0 - - - +
122F LYS* 2.5 36.5 + - + +
123F SER* 3.6 9.2 - - - +
125F GLU* 1.3 81.5 - - - +
127F LEU* 1.3 59.6 + - - +
130F LEU* 3.7 17.0 - - - +
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Residues in contact with LEU 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 4.1 21.3 - - + -
20F LEU* 3.8 20.4 - - + -
21F LEU* 5.2 2.0 - - + -
123F SER 2.9 26.7 + - - +
124F ILE* 3.7 5.6 - - - +
125F GLU 2.9 1.7 - - - -
126F LYS* 1.3 79.8 - - - +
128F GLU* 1.3 51.8 + - - +
129F ASP* 2.5 6.6 + - - +
130F LEU* 2.4 38.3 + - + +
131F ASP* 3.8 18.8 - - + +
134F SER* 3.4 29.6 - - - +
135F GLN* 3.6 21.3 - - + -
138F LEU* 4.1 16.6 - - + -
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ILE 3.4 1.1 + - - +
125F GLU* 3.1 17.3 + - - +
127F LEU* 1.3 72.5 - - - +
129F ASP* 1.3 74.1 + - - +
131F ASP 4.5 5.6 + - - +
132F LEU* 4.4 22.5 + - - +
135F GLN* 3.1 32.1 + - - +
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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