Contacts of the helix formed by residues 102 - 127 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.5 24.0 - - + -
43D VAL 3.8 8.3 + - - +
45D PRO* 5.4 6.0 - - + +
46D ASN 5.9 0.2 - - - +
47D PHE* 4.0 23.8 - - - +
50D VAL* 3.6 14.6 - - + -
101D THR* 1.3 69.8 - - - +
103D GLN* 1.3 73.0 + - - +
105D HIS* 3.1 2.3 - - - +
106D LEU* 2.6 62.7 + - + +
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Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PRO* 5.0 12.5 - - - +
101D THR* 3.5 26.1 - - + +
102D VAL* 1.3 82.9 + - - +
104D ALA* 1.3 56.0 + - + +
105D HIS 2.7 4.2 + - - -
106D LEU* 4.6 3.8 - - - -
107D ALA* 2.7 38.9 + - - +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 4.1 4.6 - - - +
100D ASP* 3.6 24.4 - - - +
101D THR* 2.6 32.7 + - - +
103D GLN* 1.3 72.5 - - + +
105D HIS* 1.3 60.7 + - - +
107D ALA* 4.4 6.5 - - - -
108D ALA* 5.1 2.0 - - - +
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Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS* 5.4 0.2 - + - -
38D VAL* 3.2 42.9 - - + +
41D ASN* 3.0 26.4 + - + -
42D VAL* 4.2 5.4 - - + -
95D TYR* 2.8 30.9 + + - -
97D VAL* 3.5 22.4 - - + -
98D GLU 2.9 22.0 + - - -
100D ASP* 3.6 6.5 - - + -
101D THR 2.9 21.3 - - - +
102D VAL* 3.1 4.7 - - - +
103D GLN 2.7 4.4 + - - -
104D ALA* 1.3 69.7 - - - +
106D LEU* 1.3 56.7 + - - +
107D ALA 3.1 1.8 - - - +
108D ALA* 3.6 8.7 - - - +
109D LEU* 2.6 34.8 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 5.5 1.7 - - + +
50D VAL* 3.9 21.5 - - + -
53D MET* 3.5 35.0 - - + -
54D ILE* 5.8 0.2 - - + -
102D VAL* 2.6 40.4 + - + +
103D GLN* 3.8 3.8 - - - +
105D HIS* 1.3 72.2 - - - +
107D ALA* 1.3 57.1 + - - +
109D LEU* 3.2 12.0 + - + +
110D ASP 2.9 23.4 + - - -
152D VAL* 3.6 35.1 - - + +
154D ALA* 4.4 16.2 - - + +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLN 2.7 25.5 + - - +
104D ALA* 4.4 3.6 - - - -
105D HIS 4.3 0.9 - - - +
106D LEU* 1.3 72.0 - - - +
108D ALA* 1.3 55.2 + - - +
110D ASP* 2.7 36.6 + - - +
111D LEU* 3.1 7.5 + - - +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TYR* 3.6 20.0 - - + +
97D VAL* 3.6 24.0 - - + -
104D ALA* 5.1 1.1 - - - +
105D HIS* 3.2 8.0 + - - +
107D ALA* 1.3 77.6 - - - +
109D LEU* 1.3 59.2 + - - +
110D ASP 3.4 0.2 - - - -
111D LEU* 3.2 33.9 - - + +
112D VAL* 3.3 12.3 + - - +
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 5.9 1.3 - - + -
34D THR* 4.4 10.8 - - + -
35D LEU* 3.8 29.6 - - + -
38D VAL* 3.8 25.6 - - + -
53D MET* 4.8 1.1 - - + -
54D ILE* 4.4 16.8 - - + -
95D TYR* 3.6 10.1 + - + -
105D HIS 2.6 21.0 + - - +
106D LEU* 3.3 18.2 - - + +
108D ALA* 1.3 72.3 - - - +
110D ASP* 1.3 64.6 + - - +
111D LEU 3.2 0.2 - - - -
112D VAL* 3.2 20.6 + - + +
113D TYR* 3.3 24.0 + - + -
148D PHE* 4.6 11.7 - - + -
152D VAL* 5.0 5.2 - - + -
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU 2.9 12.0 + - - +
107D ALA* 2.7 21.4 + - - +
109D LEU* 1.3 70.2 - - - +
111D LEU* 1.3 60.6 + - - +
113D TYR* 3.2 12.8 + - - +
114D ASN* 3.0 16.7 + - - -
149D GLN* 3.1 9.8 + - - +
152D VAL* 4.2 15.4 - - + +
153D ARG* 2.8 48.2 + - + +
155D HIS* 5.8 0.3 + - - -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ALA 3.1 8.7 + - - +
108D ALA* 3.2 25.8 - - + +
109D LEU 3.2 0.2 - - - -
110D ASP* 1.3 76.9 - - - +
112D VAL* 1.3 63.9 + - - +
113D TYR 3.2 0.5 + - - -
114D ASN* 3.2 30.1 + - + +
115D GLY* 3.6 3.1 + - - -
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ASP* 5.8 2.5 - - - +
31D LEU* 4.7 12.3 - - + -
34D THR* 4.6 9.2 - - + -
95D TYR* 3.7 27.6 - - + -
108D ALA 3.3 12.5 + - - +
109D LEU* 3.2 17.3 + - + +
111D LEU* 1.3 76.0 - - + +
113D TYR* 1.3 71.7 + - + +
115D GLY* 3.2 5.7 + - - -
116D VAL* 3.1 36.4 + - + +
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.5 33.7 - - + +
35D LEU* 4.2 0.6 - - + +
57D GLN* 2.7 28.6 + - - +
109D LEU* 3.5 22.4 - - + +
110D ASP* 3.2 9.7 + - - +
111D LEU 3.2 0.8 - - - -
112D VAL* 1.3 82.7 - - + +
114D ASN* 1.3 66.8 + - - +
116D VAL* 2.8 6.7 + - + +
117D ILE* 2.8 31.5 + - + +
145D LEU* 3.2 48.6 - - + +
148D PHE* 3.1 30.8 - + + -
149D GLN* 3.8 26.5 - - + +
152D VAL* 5.4 1.6 - - + -
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Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP* 3.0 28.7 + - - -
111D LEU* 3.2 24.8 + - + +
113D TYR* 1.3 75.8 - - - +
115D GLY* 1.3 57.6 + - - +
117D ILE* 4.0 3.5 - - - +
118D GLU* 3.0 44.4 + - - +
149D GLN* 2.9 20.2 + - - +
153D ARG* 3.5 9.5 + - - +
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Residues in contact with GLY 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D TRP* 6.5 0.9 - - - -
111D LEU 3.6 3.4 + - - -
112D VAL 3.2 7.6 + - - -
113D TYR 3.1 0.8 - - - -
114D ASN* 1.3 80.8 - - - +
116D VAL* 1.3 55.8 + - - +
118D GLU* 4.0 7.6 - - - +
119D ASP* 3.0 36.9 + - - +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 3.5 32.6 - - + +
28D TYR* 4.7 4.9 - - + -
31D LEU* 3.9 27.8 - - + -
92D TRP* 6.2 2.0 - - + -
112D VAL* 3.1 32.3 - - + +
113D TYR* 2.8 11.2 + - + +
115D GLY* 1.3 77.4 - - - +
117D ILE* 1.3 56.6 + - + +
119D ASP* 4.0 2.7 - - - +
120D THR* 2.7 37.6 + - - +
145D LEU* 4.7 13.7 - - + -
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Residues in contact with ILE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 2.8 24.0 + - + +
114D ASN* 4.0 3.1 - - - +
116D VAL* 1.3 70.8 - - - +
118D GLU* 1.3 57.2 + - + +
120D THR* 3.0 7.0 + - - -
121D ARG* 2.8 57.5 + - + +
142D ALA* 5.7 2.9 - - + +
145D LEU* 4.0 18.6 - - + +
146D GLU* 3.3 52.3 - - + +
149D GLN* 3.1 36.1 - - + +
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASN* 3.0 29.7 + - + +
115D GLY* 4.0 6.1 - - - +
117D ILE* 1.3 76.3 - - + +
119D ASP* 1.3 62.1 + - - +
121D ARG* 3.5 17.5 + - - +
122D LYS* 3.1 40.0 + - - +
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Residues in contact with ASP 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LYS* 4.3 16.4 + - - -
24D GLN* 4.9 6.3 - - - +
27D THR* 4.8 8.6 + - + +
91D THR* 3.4 21.9 + - - +
92D TRP* 4.1 12.5 - - - -
115D GLY 3.0 20.3 + - - +
116D VAL* 4.0 5.6 - - - +
118D GLU* 1.3 76.2 - - - +
120D THR* 1.3 57.0 + - - +
122D LYS* 3.2 26.2 + - - +
123D SER* 3.0 28.6 + - - -
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 2.7 36.2 + - - +
28D TYR* 4.6 1.8 + - - +
116D VAL* 2.7 25.7 + - - +
117D ILE* 3.0 7.4 + - - -
119D ASP* 1.3 73.5 - - - +
121D ARG* 1.3 57.3 + - - +
122D LYS 3.0 1.6 - - - -
123D SER* 2.8 5.6 + - - +
124D ILE* 2.6 56.3 + - + +
138D LEU* 4.3 9.9 - - + +
141D HIS* 5.6 0.2 - - + -
142D ALA* 4.3 16.8 - - + +
145D LEU* 5.8 3.4 - - + +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 5.5 5.1 + - - -
71A ARG* 5.3 0.6 - - - +
75A LEU* 5.2 10.5 - - - +
133A VAL* 6.1 2.9 - - + +
117D ILE* 2.8 41.5 + - + +
118D GLU* 3.7 14.8 - - - +
120D THR* 1.3 72.7 - - - +
122D LYS* 1.3 56.2 + - - +
124D ILE* 3.2 16.1 + - + +
125D GLU* 2.9 38.3 + - + +
142D ALA* 5.7 1.1 - - + -
146D GLU* 3.5 33.7 + - - +
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLU* 3.1 31.0 + - - +
119D ASP* 3.2 28.0 + - - +
120D THR 3.0 0.6 - - - -
121D ARG* 1.3 76.6 - - + +
123D SER* 1.3 57.6 + - - +
125D GLU* 2.9 14.0 + - - +
126D LYS* 2.9 51.3 + - - +
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 3.4 39.6 + - - +
23D LYS* 5.8 4.0 - - - +
24D GLN* 4.5 8.4 + - - -
119D ASP 3.0 10.7 + - - -
120D THR* 2.8 12.9 + - - -
122D LYS* 1.3 75.7 - - - +
124D ILE* 1.3 60.9 + - - +
126D LYS* 3.7 8.6 + - - +
127D LEU* 3.2 29.8 + - - +
138D LEU* 3.8 14.6 - - - -
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.9 20.9 - - + -
133A VAL* 4.9 5.6 - - + -
120D THR* 2.6 24.1 + - + +
121D ARG* 3.3 17.9 - - + +
123D SER* 1.3 70.7 - - - +
125D GLU* 1.3 63.7 + - - +
127D LEU 3.5 3.3 + - - -
135D GLN* 3.1 30.3 + - + +
138D LEU* 3.6 22.9 - - + -
139D ILE* 3.3 50.9 - - + +
142D ALA* 3.8 21.8 - - + -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 4.7 17.8 - - + +
121D ARG* 2.9 21.1 + - + +
122D LYS* 2.9 11.1 + - - +
124D ILE* 1.3 72.9 - - - +
126D LYS* 1.3 54.9 + - + +
127D LEU 2.8 5.1 + - - -
128D GLU* 2.7 36.1 + - - +
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Residues in contact with LYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 3.9 31.0 - - + +
23D LYS* 5.6 8.1 - - - +
122D LYS* 2.9 33.1 + - - +
123D SER* 3.9 10.8 + - - +
125D GLU* 1.3 76.1 - - + +
127D LEU* 1.3 59.1 + - - +
128D GLU 3.3 1.1 + - - -
129D ASP 5.1 1.2 + - - +
130D LEU* 3.4 21.7 - - + +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.8 35.2 - - + -
20D LEU* 4.0 17.9 - - + -
21D LEU* 4.8 2.7 - - + -
123D SER 3.2 22.1 + - - +
124D ILE 3.8 6.1 - - - +
125D GLU 2.8 1.2 + - - -
126D LYS* 1.3 78.7 - - - +
128D GLU* 1.3 68.5 + - - +
129D ASP 3.5 0.9 - - - -
130D LEU* 3.2 6.9 + - + -
131D ASP* 3.2 40.9 + - + +
134D SER* 3.7 30.5 - - - +
135D GLN* 3.5 10.2 + - + -
138D LEU* 3.8 15.0 - - + -
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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