Contacts of the helix formed by residues 112 - 137 (chain D) in PDB entry 3BUW
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 112 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D THR 3.4 10.2 + - - +
109D LEU* 3.1 19.3 + - + +
111D GLU* 1.3 74.0 - - - +
113D GLU* 1.3 65.6 + - - +
114D TYR* 2.9 13.4 + - - +
115D PHE* 2.8 33.7 + - + +
116D ARG* 3.0 26.0 + - - +
169D PHE* 4.6 2.4 - - - -
174D PHE* 3.4 48.1 - - - +
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PRO* 4.2 24.7 - - + +
48D PRO* 5.2 0.3 - - - +
111D GLU 3.2 6.6 + - - +
112D ASN* 1.3 72.2 + - - +
114D TYR* 1.3 64.0 + - - +
116D ARG* 3.4 14.9 + - - +
117D VAL* 3.1 30.3 + - + +
197D LYS* 4.9 17.3 + - - +
198D THR 5.3 1.2 + - - -
199D ILE* 3.7 32.2 + - + +
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Residues in contact with TYR 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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112D ASN* 2.9 10.5 + - - +
113D GLU* 1.3 75.0 - - - +
115D PHE* 1.3 61.2 + - - +
117D VAL* 3.2 3.3 + - - +
118D PHE* 2.9 49.1 + + + +
164D GLU* 2.6 49.6 + - + +
165D LEU* 3.5 17.0 + - + -
168D ILE* 3.6 30.7 - - + -
169D PHE* 3.7 19.3 - + - -
174D PHE* 4.4 2.9 - - + -
198D THR* 3.9 33.0 - - + -
199D ILE* 4.0 26.4 - - + +
233D ASN* 6.3 0.4 - - - -
237D SER* 4.5 4.3 - - - -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 3.4 33.0 - - + -
56D VAL* 5.0 4.0 - - + -
95D LEU* 3.9 25.6 - - + -
98D ILE* 4.4 13.9 - - + -
99D LEU* 5.0 6.7 - - + -
106D MET* 6.2 0.2 - - + -
109D LEU* 3.6 41.3 - - + +
112D ASN* 2.8 30.2 + - + +
114D TYR* 1.3 77.4 - - - +
116D ARG* 1.3 57.9 + - - +
118D PHE* 3.3 3.6 + + - +
119D MET* 2.9 55.4 + - + +
165D LEU* 4.8 6.7 - - + -
169D PHE* 4.0 22.2 - + + -
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PRO* 4.2 20.9 + - - +
48D PRO* 3.3 31.3 + - + +
49D GLY* 3.2 24.5 - - - +
50D THR* 3.5 18.3 + - - +
51D VAL* 3.5 13.6 - - + +
110D GLY 3.2 28.0 - - - +
111D GLU* 3.4 22.0 + - - +
112D ASN 3.0 16.1 + - - +
113D GLU* 3.8 14.8 + - - +
114D TYR 3.3 0.2 - - - -
115D PHE* 1.3 74.6 - - - +
117D VAL* 1.3 62.6 + - - +
119D MET* 3.6 1.4 + - - +
120D GLU* 3.1 17.8 + - - +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PRO* 5.4 0.4 - - + -
48D PRO* 3.5 28.5 - - + -
113D GLU* 3.1 20.2 - - + +
114D TYR* 3.2 7.5 + - + +
116D ARG* 1.3 72.8 - - - +
118D PHE* 1.3 66.7 + - - +
120D GLU* 3.3 3.7 + - - +
121D ASN* 3.0 22.5 + - - +
199D ILE* 3.5 24.0 - - + -
233D ASN* 3.4 26.7 - - + +
235D TYR* 3.4 30.3 - - + -
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Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D THR* 4.5 11.7 - - + -
95D LEU* 4.4 3.6 - - + -
114D TYR* 2.9 44.5 + - + +
115D PHE* 3.6 6.3 - + - +
117D VAL* 1.3 78.2 - - - +
119D MET* 1.3 72.0 + - + +
121D ASN* 3.2 9.0 + - + +
122D LEU* 2.9 51.5 + - + +
161D MET* 3.4 44.2 - - + -
164D GLU* 3.9 6.7 - - - -
165D LEU* 3.9 38.6 - - + -
231D THR* 6.2 0.2 - - + -
233D ASN* 5.6 1.8 - - - +
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Residues in contact with MET 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 3.9 17.0 - - + -
55D MET* 4.4 2.5 - - - -
56D VAL* 4.0 24.9 - - + +
59D CYS* 3.8 34.3 - - + -
95D LEU* 4.0 18.4 - - + -
115D PHE* 2.9 51.7 + - + +
118D PHE* 1.3 91.5 - - - +
120D GLU* 1.3 61.9 + - - +
122D LEU* 3.3 4.1 + - - +
123D MET* 3.0 45.2 + - + +
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PRO* 3.1 37.6 - - + +
49D GLY 4.5 1.7 + - - -
55D MET* 5.6 1.7 - - - -
116D ARG 3.1 18.8 + - - +
117D VAL* 3.6 4.8 - - - +
118D PHE 3.2 0.2 - - - -
119D MET* 1.3 76.5 - - - +
121D ASN* 1.3 63.4 + - - +
123D MET* 3.5 6.6 + - - +
124D LYS* 3.1 24.1 + - + +
235D TYR* 4.8 9.0 + - - -
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Residues in contact with ASN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D VAL 3.0 17.0 + - - +
118D PHE* 3.2 8.5 + - + +
120D GLU* 1.3 76.5 - - - +
122D LEU* 1.3 53.8 + - - +
124D LYS* 3.2 5.9 + - - +
125D LYS* 2.7 66.3 + - - +
161D MET* 3.6 23.4 - - - +
231D THR* 3.0 27.5 + - - -
233D ASN* 3.5 28.0 - - + +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D CYS* 3.0 31.9 - - - -
63D MET* 3.9 15.7 - - + -
88D LEU* 5.1 0.2 - - + -
91D THR* 4.3 6.5 - - + -
95D LEU* 3.8 22.7 - - + -
118D PHE* 2.9 37.6 + - + +
119D MET* 3.7 7.9 - - - +
120D GLU 3.3 0.2 - - - -
121D ASN* 1.3 77.4 - - - +
123D MET* 1.3 59.4 + - - +
125D LYS* 3.9 3.1 - - - +
126D THR* 2.9 48.5 + - + +
158D PHE* 4.0 18.4 - - + -
161D MET* 5.2 7.1 - - + -
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Residues in contact with MET 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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55D MET* 3.7 42.2 - - + +
58D LYS* 5.3 4.5 - - + -
59D CYS* 3.0 41.7 - - - +
62D LEU* 3.9 16.6 - - + -
119D MET* 3.0 44.3 + - + +
120D GLU* 3.8 6.1 - - - +
122D LEU* 1.3 75.6 - - - +
124D LYS* 1.3 64.1 + - - +
126D THR* 3.0 16.9 + - - -
127D LYS* 3.1 28.4 + - - +
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Residues in contact with LYS 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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120D GLU* 3.1 19.5 + - + +
121D ASN* 3.2 12.1 + - - +
123D MET* 1.3 78.5 - - - +
125D LYS* 1.3 59.3 + - - +
127D LYS* 3.4 6.7 + - + +
128D GLN* 2.8 74.0 + - + +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ASN* 2.7 52.2 + - - +
122D LEU 4.0 2.0 - - - +
124D LYS* 1.3 75.6 - - - +
126D THR* 1.3 56.5 + - - +
128D GLN* 3.3 26.9 + - - +
129D THR* 2.9 32.6 + - - -
154D LEU* 3.9 20.8 - - + +
157D ILE* 3.9 12.1 - - + -
158D PHE* 3.9 21.3 - - + -
161D MET* 4.0 9.6 - - + -
231D THR 3.6 16.4 - - - -
232D CYS* 2.9 28.9 + - - +
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Residues in contact with THR 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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59D CYS* 5.2 0.8 - - - +
62D LEU* 3.4 25.1 - - + +
63D MET* 3.8 33.0 - - + +
66D VAL* 3.8 10.5 - - + +
88D LEU* 4.9 0.9 - - + -
122D LEU* 2.9 31.1 + - + +
123D MET* 3.0 12.1 + - - -
125D LYS* 1.3 72.4 - - - +
127D LYS* 1.3 59.9 + - - +
129D THR* 3.2 3.0 + - - -
130D ILE* 2.9 36.3 + - - +
158D PHE* 4.0 14.6 - - + -
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Residues in contact with LYS 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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58D LYS* 4.6 11.1 - - - +
62D LEU* 4.1 28.9 - - + -
123D MET* 3.1 32.0 + - + +
124D LYS* 3.7 6.5 - - + +
126D THR* 1.3 76.6 + - - +
128D GLN* 1.3 58.9 + - + +
130D ILE* 3.2 9.1 + - + +
131D SER* 2.9 36.3 + - - +
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Residues in contact with GLN 128 (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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124D LYS* 2.8 65.4 + - + +
125D LYS* 3.4 38.2 + - - +
127D LYS* 1.3 77.8 - - + +
129D THR* 1.3 56.8 + - - +
131D SER* 3.4 6.1 + - - -
132D LEU* 2.9 28.8 + - - +
154D LEU* 3.9 17.4 - - + +
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Residues in contact with THR 129 (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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66D VAL* 3.8 29.8 - - + -
125D LYS 2.9 15.4 + - - -
126D THR 3.6 6.7 - - - -
128D GLN* 1.3 74.8 - - - +
130D ILE* 1.3 65.5 + - - +
132D LEU* 3.2 24.1 + - + +
133D PHE* 3.2 18.9 + - + -
151D LEU* 3.9 27.4 - - + -
154D LEU* 3.9 11.9 - - + +
158D PHE* 3.6 17.7 - - + -
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 3.8 43.5 - - + +
65D LYS* 3.9 44.4 - - + +
66D VAL* 3.8 12.6 - - + -
69D LEU* 4.1 12.2 - - + +
126D THR 2.9 22.9 + - - +
127D LYS* 3.6 6.5 - - + +
129D THR* 1.3 75.8 - - - +
131D SER* 1.3 64.3 + - - +
133D PHE* 3.3 6.4 + - - +
134D LYS* 3.2 22.6 + - + +
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Residues in contact with SER 131 (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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127D LYS* 2.9 21.1 + - - +
128D GLN* 3.7 6.1 - - - -
130D ILE* 1.3 75.3 - - - +
132D LEU* 1.3 66.1 + - - +
134D LYS* 3.0 16.6 - - - +
135D GLU* 2.9 44.8 + - - +
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Residues in contact with LEU 132 (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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128D GLN 2.9 14.1 + - - +
129D THR* 3.2 15.0 - - + +
131D SER* 1.3 76.2 - - - +
133D PHE* 1.3 54.3 + - - +
135D GLU* 5.1 1.8 - - - -
136D GLY* 2.8 35.0 + - - +
140D MET* 3.8 10.4 - - + +
147D PRO* 3.4 34.8 - - + +
150D ASN* 3.9 24.0 - - + +
151D LEU* 3.6 32.5 - - + +
154D LEU* 5.3 4.7 - - + -
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Residues in contact with PHE 133 (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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69D LEU* 3.6 43.3 - - + -
70D CYS* 3.7 24.5 - - - -
72D ASN* 5.8 0.2 - - + -
75D LEU* 3.6 36.8 - - + -
129D THR* 3.2 24.7 + - + -
130D ILE 3.6 6.7 - - - +
131D SER 3.2 0.4 - - - -
132D LEU* 1.3 79.6 - - - +
134D LYS* 1.3 61.7 + - - +
137D LYS* 3.1 21.8 + - - +
140D MET* 3.8 40.3 - - + +
141D TYR* 5.2 7.9 - + - -
151D LEU* 4.1 12.8 - - + -
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Residues in contact with LYS 134 (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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130D ILE* 3.2 10.1 + - + +
131D SER* 3.0 32.3 - - - +
133D PHE* 1.3 79.7 - - - +
135D GLU* 1.3 75.1 + - + +
137D LYS* 3.5 24.3 + - - +
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Residues in contact with GLU 135 (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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131D SER* 2.9 35.4 + - - +
132D LEU* 4.4 1.6 - - - +
134D LYS* 1.3 91.5 - - + +
136D GLY* 1.3 65.1 + - - +
137D LYS* 3.3 15.3 - - - +
139D ARG* 5.5 2.6 + - - -
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Residues in contact with GLY 136 (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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132D LEU* 2.8 23.7 + - - -
135D GLU* 1.3 71.5 - - - +
137D LYS* 1.3 72.2 + - - +
138D GLU* 3.6 2.8 - - - +
139D ARG* 3.1 27.3 + - - +
140D MET* 4.2 4.3 - - - -
147D PRO* 4.3 23.3 - - - -
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE 3.1 15.2 + - - +
134D LYS 3.5 20.4 + - - +
135D GLU* 3.7 10.9 - - - +
136D GLY* 1.3 79.8 - - - +
138D GLU* 1.3 84.3 + - - +
139D ARG 3.2 0.9 + - - -
140D MET* 3.2 20.5 + - - +
141D TYR* 4.0 9.8 + - - -
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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