Contacts of the helix formed by residues 101 - 128 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D HIS 6.1 1.3 - - - +
42E VAL* 4.6 0.7 - - - -
43E VAL* 3.4 11.0 - - + +
44E GLY* 5.9 1.6 - - - -
45E PRO* 6.4 1.1 - - - -
100E ASP* 1.3 91.3 + - - +
102E VAL* 1.3 60.5 + - - +
103E GLN* 3.6 9.1 + - - +
104E ALA* 3.2 20.6 + - - +
105E HIS* 3.0 34.4 + - - -
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E VAL* 4.1 16.4 - - + -
43E VAL 3.8 13.7 - - - +
45E PRO* 4.5 14.4 - - + -
46E ASN* 4.8 12.3 - - - +
47E PHE* 4.1 17.9 - - + +
50E VAL* 3.5 13.7 - - + -
101E THR* 1.3 70.1 - - - +
103E GLN* 1.3 72.9 + - + +
104E ALA 2.9 4.8 + - - -
105E HIS 3.3 0.3 + - - -
106E LEU* 2.9 62.1 + - + +
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Residues in contact with GLN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ASN* 5.8 3.6 + - - +
101E THR* 3.5 8.6 + - - +
102E VAL* 1.3 89.4 - - + +
104E ALA* 1.3 56.8 + - - +
106E LEU* 4.8 5.8 - - - +
107E ALA* 3.1 22.8 - - - +
154E ALA 4.9 2.9 + - - +
155E HIS* 4.0 23.7 - - - +
45H PRO* 5.1 15.6 - - - +
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Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E VAL* 4.0 7.8 - - + +
100E ASP* 3.5 31.4 - - + +
101E THR* 3.2 22.9 + - - +
102E VAL 2.9 0.6 - - - -
103E GLN* 1.3 78.0 - - - +
105E HIS* 1.3 65.9 + - - +
107E ALA* 3.5 4.8 - - - +
108E ALA* 3.4 18.9 + - - +
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Residues in contact with HIS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E VAL* 3.7 18.6 - - + +
41E ASN* 3.2 23.1 + - + -
42E VAL* 3.5 30.3 - - + -
95E TYR* 2.9 29.3 + + - +
97E VAL* 3.5 24.6 - - + +
98E GLU 2.9 29.5 + - - -
100E ASP 3.7 4.5 + - - -
101E THR 3.0 26.9 + - - +
102E VAL 4.2 1.1 - - - +
104E ALA* 1.3 73.9 - - - +
106E LEU* 1.3 57.8 + - + +
108E ALA* 2.8 5.0 + - - -
109E LEU* 2.6 36.3 + - - +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E VAL* 4.4 8.5 - - + -
53E MET* 3.5 34.3 - - + -
102E VAL* 2.9 44.4 + - + +
103E GLN* 4.8 4.7 - - - +
105E HIS* 1.3 76.6 - - - +
107E ALA* 1.3 62.6 + - - +
109E LEU* 4.1 16.6 - - + -
110E ASP* 3.0 24.1 + - - +
152E VAL* 3.5 38.2 - - + +
154E ALA* 5.2 9.4 - - + +
155E HIS 5.1 9.4 - - - +
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Residues in contact with ALA 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E GLN 3.1 25.2 + - - +
104E ALA* 3.5 7.8 + - - +
105E HIS 3.1 0.4 - - - -
106E LEU* 1.3 76.5 - - - +
108E ALA* 1.3 62.3 + - - +
110E ASP* 3.2 20.0 - - - +
111E LEU* 3.6 11.7 + - - +
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Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 4.0 11.2 - - + -
96E SER* 6.2 1.3 - - - +
97E VAL* 3.9 20.0 - - + -
104E ALA 3.4 9.1 + - - +
105E HIS 2.8 11.7 + - - +
107E ALA* 1.3 73.9 - - - +
109E LEU* 1.3 58.3 + - - +
111E LEU* 2.9 21.0 + - + +
112E VAL* 2.9 29.3 + - + +
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 5.5 0.2 - - + -
34E THR* 4.9 3.6 - - + -
35E LEU* 3.9 24.5 - - + -
38E VAL* 4.2 31.0 - - + -
54E ILE* 4.6 7.4 - - + -
95E TYR* 4.2 4.4 - - + +
105E HIS 2.6 19.8 + - - +
106E LEU* 3.9 22.4 - - + +
108E ALA* 1.3 69.7 - - - +
110E ASP* 1.3 67.1 + - - +
112E VAL* 3.3 17.9 - - + +
113E TYR* 3.1 40.9 + - + -
148E PHE* 4.1 22.2 - - + -
152E VAL* 4.5 4.0 - - + -
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Residues in contact with ASP 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU 3.0 13.7 + - - +
107E ALA* 3.2 14.9 - - - +
109E LEU* 1.3 72.7 - - - +
111E LEU* 1.3 55.9 + - + +
113E TYR* 2.8 26.9 + - - +
114E ASN* 2.7 26.9 + - - +
149E GLN* 2.4 37.2 + - - +
152E VAL* 4.0 12.0 - - + +
153E ARG* 3.0 23.9 + - + +
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ALA 3.9 13.2 - - - +
108E ALA* 2.9 17.9 + - + +
110E ASP* 1.3 78.0 - - + +
112E VAL* 1.3 64.4 + - + +
114E ASN* 3.1 21.8 - - + +
115E GLY* 3.0 17.7 + - - -
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Residues in contact with VAL 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASP* 5.6 5.6 - - - +
31E LEU* 5.1 7.6 - - + -
34E THR* 4.8 11.9 - - + -
92E TRP* 6.0 4.0 - - + +
95E TYR* 3.8 23.3 - - + -
108E ALA* 2.9 21.7 + - + +
109E LEU* 3.3 24.0 - - + +
111E LEU* 1.3 73.9 - - + +
113E TYR* 1.3 64.1 + - + +
115E GLY* 2.8 19.6 + - - -
116E VAL* 3.0 22.7 + - + +
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Residues in contact with TYR 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.5 31.0 - - + +
35E LEU* 3.7 1.1 - - + +
57E GLN* 2.7 43.8 + - - +
109E LEU* 3.1 29.1 + - + +
110E ASP* 2.8 10.1 + - - +
112E VAL* 1.3 76.8 - - + +
114E ASN* 1.3 59.8 + - - +
116E VAL* 2.9 9.1 + - + -
117E ILE* 2.8 39.6 + - + +
145E LEU* 3.5 36.3 - - + -
148E PHE* 3.1 35.1 - + - -
149E GLN* 3.3 21.8 - - + -
152E VAL* 5.3 1.1 - - + -
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Residues in contact with ASN 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ASP* 2.7 44.9 + - - +
111E LEU* 3.1 25.0 - - + +
113E TYR* 1.3 72.7 - - - +
115E GLY* 1.3 64.2 + - - +
117E ILE* 5.0 1.6 - - - -
118E GLU* 3.1 34.5 + - - +
149E GLN* 3.3 12.5 + - - +
153E ARG* 4.1 10.5 - - - +
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Residues in contact with GLY 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E THR* 5.7 0.7 - - - -
111E LEU 3.0 7.7 + - - -
112E VAL 2.8 10.9 + - - -
114E ASN* 1.3 77.3 - - - +
116E VAL* 1.3 63.4 + - - +
118E GLU* 4.2 7.1 - - - +
119E ASP* 3.2 27.1 + - - +
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLN* 5.4 0.2 - - - +
27E THR* 4.1 27.4 - - + +
28E TYR* 5.1 5.6 - - + -
31E LEU* 3.9 33.4 - - + -
112E VAL* 3.0 19.0 + - + +
113E TYR* 2.9 18.5 + - + +
115E GLY* 1.3 75.1 - - - +
117E ILE* 1.3 50.6 + - - +
119E ASP* 3.1 6.2 + - - +
120E THR* 2.7 44.9 + - - +
145E LEU* 4.0 22.9 - - + -
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Residues in contact with ILE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E TYR* 2.8 21.2 + - + +
114E ASN* 4.5 1.3 - - - +
116E VAL* 1.3 67.6 - - - +
118E GLU* 1.3 67.9 + - - +
120E THR* 2.8 21.6 + - - -
121E ARG* 2.8 22.0 + - + +
142E ALA* 5.9 1.3 - - + -
145E LEU* 4.3 11.4 - - + +
146E GLU* 3.3 53.6 - - + +
149E GLN* 3.0 48.0 - - + +
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Residues in contact with GLU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E ASN* 3.1 24.3 + - - +
115E GLY* 4.2 5.4 - - - +
117E ILE* 1.3 79.1 - - - +
119E ASP* 1.3 61.3 + - - +
121E ARG* 3.8 7.9 - - - +
122E LYS* 3.3 32.6 + - + +
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Residues in contact with ASP 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLN* 4.9 6.6 + - - +
27E THR* 5.4 8.5 - - + +
91E THR* 5.1 11.1 - - - +
92E TRP* 5.4 5.2 - - - -
115E GLY 3.2 19.7 + - - +
116E VAL* 3.1 4.9 + - - +
117E ILE 3.0 0.4 - - - -
118E GLU* 1.3 79.5 - - - +
120E THR* 1.3 65.1 + - - +
122E LYS* 3.2 22.9 + - - +
123E SER* 3.2 27.8 + - - -
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Residues in contact with THR 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLN* 3.6 30.8 + - - +
28E TYR* 4.8 2.2 - - - +
116E VAL* 2.7 34.6 + - - +
117E ILE* 2.8 16.0 + - - -
119E ASP* 1.3 71.5 - - - +
121E ARG* 1.3 61.6 + - - -
123E SER* 3.2 5.4 + - - -
124E ILE* 3.0 27.4 + - + +
138E LEU* 4.2 16.3 - - + +
142E ALA* 4.0 32.5 - - + +
145E LEU* 5.0 5.1 - - + +
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Residues in contact with ARG 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 2.8 28.2 + - + +
118E GLU* 3.8 7.2 - - - +
120E THR* 1.3 74.0 - - - +
122E LYS* 1.3 66.0 + - - +
124E ILE* 3.0 30.7 + - - +
125E GLU* 3.1 29.0 + - - +
142E ALA* 5.5 0.9 - - + -
146E GLU* 2.8 27.6 + - - -
71J ARG* 3.1 24.9 - - - +
75J LEU* 4.4 7.1 - - - +
130J LEU 5.0 2.8 + - - -
131J ASP* 3.7 24.2 + - - +
132J LEU* 4.5 2.2 - - - +
133J VAL* 3.6 18.2 - - - +
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Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLU* 3.3 22.7 + - + +
119E ASP* 3.2 26.0 + - - +
121E ARG* 1.3 76.1 - - - +
123E SER* 1.3 58.6 + - - +
125E GLU* 3.6 7.2 + - - +
126E LYS* 3.0 53.6 + - - +
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Residues in contact with SER 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 4.9 19.3 + - - +
24E GLN* 4.3 12.6 + - - -
119E ASP* 3.2 14.3 + - - -
120E THR* 3.5 9.2 - - - -
121E ARG 3.1 0.8 - - - -
122E LYS* 1.3 74.8 - - - +
124E ILE* 1.3 57.3 + - - +
126E LYS* 2.9 8.6 + - - +
127E LEU* 2.8 42.7 + - - +
138E LEU* 4.1 17.3 - - - -
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Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E THR* 3.0 16.0 + - + +
121E ARG* 3.0 23.4 + - - +
123E SER* 1.3 72.8 - - - +
125E GLU* 1.3 65.8 + - + +
127E LEU* 3.0 16.9 + - - +
128E GLU 3.0 10.6 + - - -
135E GLN* 3.2 22.4 + - + +
138E LEU* 4.1 18.8 - - + +
139E ILE* 3.4 39.9 - - + +
142E ALA* 3.8 28.9 - - + -
132J LEU* 4.9 11.4 - - + -
133J VAL* 4.9 4.3 - - + -
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 3.1 22.1 + - + +
122E LYS* 3.9 8.7 + - - +
124E ILE* 1.3 84.2 - - + +
126E LYS* 1.3 59.5 + - - +
128E GLU* 3.4 32.2 - - - +
129E ASP* 4.8 1.6 + - - +
132J LEU* 5.5 7.0 - - + -
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Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 4.1 30.5 - - + +
122E LYS* 3.0 43.3 + - - +
123E SER* 2.9 9.4 + - - +
125E GLU* 1.3 76.9 - - - +
127E LEU* 1.3 53.1 + - - +
129E ASP* 4.4 2.7 + - - +
130E LEU* 2.7 31.3 - - + +
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 3.6 32.1 - - + -
20E LEU* 3.5 26.9 - - + -
21E LEU* 4.8 4.5 - - + -
123E SER* 2.8 16.5 + - - +
124E ILE 3.7 3.6 - - - +
126E LYS* 1.3 74.0 - - - +
128E GLU* 1.3 52.8 + - - +
129E ASP 2.6 8.6 + - - -
130E LEU* 2.6 37.0 + - + -
131E ASP 3.2 14.5 + - - +
132E LEU 4.5 0.7 + - - -
134E SER* 4.2 17.9 - - - -
135E GLN* 4.2 17.0 - - + +
138E LEU* 3.4 32.1 - - + -
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU* 5.9 3.1 - - - +
124E ILE 3.0 5.4 + - - +
125E GLU* 3.4 30.9 - - - +
126E LYS 3.5 0.4 - - - -
127E LEU* 1.3 75.1 - - - +
129E ASP* 1.3 67.7 + - + +
130E LEU 3.6 0.6 + - - -
132E LEU* 4.4 16.0 - - + +
135E GLN* 3.3 25.7 - - - +
128J GLU* 3.9 23.7 - - - +
132J LEU* 4.0 19.2 - - + +
----------------------------------------------------------
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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