Contacts of the helix formed by residues 115 - 141 (chain A) in PDB entry 4G1U
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 ALA 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 1.3 75.0 - - - +
116A LEU* 1.3 63.0 + - + +
117A TYR 3.0 1.1 - - - -
118A SER* 2.5 32.9 + - - +
119A HIS* 2.8 20.7 + - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU 4.3 3.5 - - - +
115A ALA* 1.3 79.3 - - + +
117A TYR* 1.3 58.3 + - + +
119A HIS* 3.4 20.2 + - + +
120A MET* 2.8 39.0 + - + +
192A SER* 4.0 15.7 - - - +
193A THR* 3.7 48.7 - - + +
196A VAL* 4.6 15.7 - - + -
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Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.2 44.5 + - + +
115A ALA 3.0 0.6 - - - -
116A LEU* 1.3 78.1 - - + +
118A SER* 1.3 58.8 + - - +
119A HIS 3.2 0.4 - - - -
120A MET* 4.0 11.2 - - + -
121A VAL* 2.9 44.1 + - + +
196A VAL* 4.2 31.0 - - + +
199A SER* 5.3 3.1 + - - -
200A LEU* 5.6 10.6 - - + +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 3.6 30.1 - - - +
114A LEU 2.8 13.7 + - - -
115A ALA* 2.5 22.7 + - - -
117A TYR* 1.3 75.9 - - - +
119A HIS* 1.3 62.6 + - - +
121A VAL* 4.4 2.8 - - - +
122A GLY* 2.9 26.0 + - - -
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL* 3.9 30.9 - - + +
103A ILE* 5.2 5.9 + - + +
104A ILE* 4.2 17.4 - - + +
115A ALA* 2.8 39.6 + - + -
116A LEU* 3.5 22.2 - - + +
117A TYR 3.2 0.2 - - - -
118A SER* 1.3 80.9 + - - +
120A MET* 1.3 61.4 + - + +
122A GLY* 5.0 0.2 - - - -
123A ALA* 2.9 34.2 + - - +
181A TRP* 6.2 0.2 - + - -
252A ALA* 3.5 20.4 - - + +
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Residues in contact with MET 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 2.8 29.9 + - + +
117A TYR* 3.7 15.0 - - + +
118A SER 3.4 0.2 - - - -
119A HIS* 1.3 77.7 - - + +
121A VAL* 1.3 59.4 + - + +
123A ALA* 3.8 1.2 - - - +
124A PHE* 2.9 32.3 + - - +
196A VAL* 4.2 18.6 - - + -
197A ALA* 5.0 3.8 - - + +
200A LEU* 3.6 32.8 - - + -
248A GLY 5.0 2.6 - - - -
249A ALA* 3.9 18.6 - - - +
252A ALA* 3.5 33.0 - - + +
253A VAL* 3.5 26.2 - - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 2.9 31.0 + - + +
118A SER* 4.4 2.9 - - - +
120A MET* 1.3 78.9 - - + +
122A GLY* 1.3 57.0 + - - +
124A PHE* 3.8 11.0 - - + +
125A ILE* 2.9 40.7 + - + +
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Residues in contact with GLY 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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99A CYS* 3.2 16.4 - - - +
100A VAL* 5.8 0.4 - - - -
103A ILE* 4.3 18.4 - - - -
118A SER 2.9 20.3 + - - -
119A HIS* 3.9 0.4 - - - -
121A VAL* 1.3 77.6 - - - +
123A ALA* 1.3 56.2 + - - +
125A ILE* 3.0 8.8 + - - +
126A GLY 3.0 23.9 + - - -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.2 34.5 + - + +
99A CYS* 4.3 0.2 - - - +
100A VAL* 3.9 7.1 - - + +
119A HIS 2.9 22.7 + - - +
120A MET 4.1 0.7 - - - +
122A GLY* 1.3 72.1 - - - -
124A PHE* 1.3 55.9 + - - +
127A SER* 2.9 30.5 + - - -
248A GLY* 3.6 24.2 - - - +
252A ALA* 3.6 10.5 - - + +
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Residues in contact with PHE 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 MET 2.9 20.4 + - - +
121A VAL* 3.8 13.0 - - + +
123A ALA* 1.3 75.4 - - - +
125A ILE* 1.3 73.9 + - + +
127A SER* 4.2 3.8 - - - -
128A LEU* 2.9 59.8 + - + +
241A LEU* 4.4 11.0 - - + -
244A ALA* 4.0 17.0 - - + -
245A ILE* 3.7 33.9 - - + +
248A GLY* 4.1 7.6 - - - -
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Residues in contact with ILE 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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99A CYS* 4.5 7.9 - - - -
121A VAL* 2.9 32.4 + - + +
122A GLY* 3.0 10.7 + - - +
124A PHE* 1.3 91.6 - - + +
126A GLY* 1.3 60.4 + - - +
128A LEU* 3.9 7.7 - - + +
129A ALA* 2.9 32.4 + - + +
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Residues in contact with GLY 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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95A GLY* 3.9 8.5 - - - -
96A ALA 4.0 6.5 + - - -
99A CYS* 3.4 24.0 - - - -
122A GLY 3.0 11.5 + - - -
123A ALA 4.0 1.8 - - - -
125A ILE* 1.3 73.7 - - - +
127A SER* 1.3 64.9 + - - +
129A ALA* 3.3 5.2 + - - +
130A ILE* 3.0 30.7 + - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.2 30.1 - - - +
96A ALA* 4.0 6.7 - - - +
123A ALA 2.9 21.0 + - - -
124A PHE 3.8 2.2 - - - -
126A GLY* 1.3 75.5 - - - +
128A LEU* 1.3 57.2 + - - +
131A SER* 2.9 32.7 + - - -
244A ALA* 3.2 29.5 + - - -
247A ILE* 3.5 10.2 - - - +
248A GLY 4.1 5.4 - - - -
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Residues in contact with LEU 128 (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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124A PHE* 2.9 50.1 + - + +
125A ILE* 4.0 8.3 - - + +
127A SER* 1.3 72.6 - - - +
129A ALA* 1.3 62.2 + - - +
131A SER* 3.7 2.5 - - - -
132A THR* 2.9 39.9 + - + +
240A LEU* 5.3 6.6 - - + +
241A LEU* 3.9 26.7 - - + -
244A ALA* 3.9 17.4 - - + +
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Residues in contact with ALA 129 (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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125A ILE* 2.9 22.4 + - + +
126A GLY* 3.6 6.7 - - - +
127A SER 3.2 0.2 - - - -
128A LEU* 1.3 78.4 - - + +
130A ILE* 1.3 68.8 + - + +
132A THR* 3.0 11.6 + - - +
133A ILE* 3.0 24.9 + - + +
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Residues in contact with ILE 130 (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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90A LEU 4.2 0.2 - - - +
91A GLY 3.1 36.3 - - - +
92A ILE* 3.8 10.5 - - + +
95A GLY* 3.5 21.1 - - - -
126A GLY* 3.0 15.4 + - - +
129A ALA* 1.3 79.8 - - + +
131A SER* 1.3 58.0 + - - +
133A ILE* 3.2 12.6 + - + +
134A ILE* 2.9 33.6 + - + +
155A ILE* 3.5 38.4 - - + -
159A CYS* 5.7 0.4 - - - -
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Residues in contact with SER 131 (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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76A MET* 4.3 6.9 - - - -
80A PHE* 4.4 2.6 - - - -
92A ILE* 3.1 29.9 - - - +
127A SER 2.9 22.9 + - - -
128A LEU* 3.7 6.5 - - - -
130A ILE* 1.3 79.0 - - - +
132A THR* 1.3 56.0 + - - +
134A ILE* 3.5 2.2 + - - +
135A PHE* 2.9 30.0 + - - +
240A LEU* 3.3 24.5 + - - +
243A SER* 4.3 4.7 + - - -
244A ALA* 4.9 5.5 - - - +
247A ILE* 5.3 0.5 - - - +
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Residues in contact with THR 132 (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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128A LEU* 2.9 26.8 + - + +
129A ALA* 3.0 12.3 + - - +
131A SER* 1.3 73.6 - - - +
133A ILE* 1.3 68.6 + - + +
135A PHE* 3.8 3.3 - - - +
136A THR* 3.0 31.9 + - - +
240A LEU* 3.6 24.0 - - - +
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Residues in contact with ILE 133 (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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129A ALA 3.0 17.2 + - - +
130A ILE* 3.2 18.8 + - + +
132A THR* 1.3 82.0 - - + +
134A ILE* 1.3 75.7 + - + +
136A THR* 3.1 8.9 + - - -
137A LEU* 3.0 36.5 + - + +
155A ILE* 5.5 9.2 - - + -
322B LEU* 5.6 13.9 - - + -
326B LEU* 6.0 5.4 - - + -
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Residues in contact with ILE 134 (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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80A PHE* 4.1 5.8 - - + -
90A LEU* 3.7 55.0 - - + +
92A ILE* 4.9 1.6 - - + -
130A ILE* 2.9 25.7 + - + +
131A SER* 4.0 4.9 - - - +
133A ILE* 1.3 84.7 - - + +
135A PHE* 1.3 62.1 + - - +
137A LEU* 3.4 4.7 + - + +
138A SER* 3.0 23.0 + - - -
148A LEU* 3.6 28.0 - - + +
151A ALA* 3.6 32.3 - - + -
155A ILE* 5.0 2.2 - - + -
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Residues in contact with PHE 135 (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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79A LEU* 4.3 10.3 - - + -
80A PHE* 3.5 26.2 - + + -
131A SER 2.9 18.8 + - - +
132A THR* 3.8 7.4 - - - +
133A ILE 3.2 0.2 - - - -
134A ILE* 1.3 75.2 - - - +
136A THR* 1.3 73.2 + - - +
138A SER* 3.3 2.1 + - - -
139A ARG* 3.1 61.1 + - + +
140A TRP* 5.4 9.9 - + - -
236A LYS* 3.5 38.4 - - + -
237A LEU* 5.7 7.0 - - + -
240A LEU* 4.1 24.5 - - + -
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Residues in contact with THR 136 (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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132A THR* 3.0 21.2 + - - +
133A ILE* 3.4 5.8 - - + +
135A PHE* 1.3 85.6 - - - +
137A LEU* 1.3 73.6 + - + +
139A ARG* 3.4 0.4 + - - -
140A TRP* 3.0 61.6 + - + +
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Residues in contact with LEU 137 (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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133A ILE* 3.0 32.7 + - + +
134A ILE* 4.0 5.2 - - + +
135A PHE 3.3 0.2 - - - -
136A THR* 1.3 91.4 - - + +
138A SER* 1.3 60.2 + - - +
139A ARG 3.7 0.2 + - - -
140A TRP* 4.4 0.4 - - + -
141A GLY* 3.7 18.6 + - - +
144A ASN* 4.9 2.4 - - - +
147A ARG* 4.5 26.8 + - + +
148A LEU* 4.1 12.5 - - + +
151A ALA* 4.8 13.9 - - + -
322B LEU* 5.2 4.3 - - + -
325B ILE* 4.3 22.9 - - + -
326B LEU* 4.0 34.5 - - + -
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Residues in contact with SER 138 (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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80A PHE* 3.6 27.1 + - - +
134A ILE 3.0 16.8 + - - -
135A PHE 3.4 5.7 + - - -
137A LEU* 1.3 76.9 - - - +
139A ARG* 1.3 77.7 + - - +
141A GLY 3.5 8.5 - - - +
142A HIS 6.1 0.2 - - - -
143A GLY* 4.3 13.1 - - - -
144A ASN* 5.6 3.6 - - - +
148A LEU* 3.6 28.9 - - - +
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Residues in contact with ARG 139 (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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79A LEU* 2.3 52.5 + - - +
80A PHE* 5.0 1.1 - - - -
81A ARG* 2.8 25.9 - - - +
135A PHE* 3.1 44.5 + - + +
136A THR 3.9 2.2 - - - +
138A SER* 1.3 89.1 + - - +
140A TRP* 1.3 84.2 + - + +
141A GLY 3.1 11.8 - - - +
218A LEU* 5.5 3.4 - - - +
222A ASP* 2.5 35.1 + - - +
236A LYS* 3.3 22.1 - - - +
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Residues in contact with TRP 140 (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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135A PHE* 5.4 8.9 - + - -
136A THR* 3.0 51.4 + - + +
137A LEU* 6.5 0.2 - - + -
139A ARG* 1.3 95.9 - - + +
141A GLY* 1.3 60.9 + - - +
236A LYS* 5.3 9.6 - - - -
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Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.7 11.7 + - - +
138A SER 3.5 6.6 - - - +
139A ARG 3.1 15.3 - - - +
140A TRP* 1.3 78.4 - - - +
142A HIS* 1.3 67.8 + - - -
143A GLY 3.3 1.7 + - - -
147A ARG* 3.6 25.5 - - - +
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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