Contacts of the helix formed by residues 117 - 142 (chain A) in PDB entry 1SGM
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 SER 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 2.6 29.4 + - - -
113A THR* 3.6 3.7 - - - +
116A ILE* 1.3 84.6 - - - +
118A GLU* 1.3 61.8 + - - +
119A PRO* 3.4 5.0 - - - +
120A LEU* 2.8 34.6 + - - +
121A ARG* 3.2 15.9 + - - +
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Residues in contact with GLU 118 (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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114A ALA 4.1 3.3 - - - +
115A LEU 5.9 0.3 - - - -
116A ILE 3.5 1.4 + - - +
117A SER* 1.3 70.7 - - - +
119A PRO* 1.3 63.6 - - + +
121A ARG* 2.8 45.4 + - - +
122A THR* 2.5 41.8 + - - +
171B LYS* 3.0 19.0 + - - -
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Residues in contact with PRO 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 4.4 13.7 - - - +
56A ILE* 3.9 20.2 - - + -
117A SER* 3.2 12.6 - - - +
118A GLU* 1.3 96.0 - - + +
120A LEU* 1.3 59.0 + - - +
122A THR* 3.3 5.5 + - - +
123A VAL* 3.0 33.6 + - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 4.2 17.7 - - + +
52A GLU* 3.3 24.0 - - + +
55A ALA* 3.8 24.0 - - + -
56A ILE* 3.6 26.9 - - + +
59A VAL* 5.1 2.2 - - + -
109A LEU* 4.3 10.8 - - + -
113A THR* 3.5 28.7 - - + +
117A SER* 2.8 33.0 + - - +
119A PRO* 1.3 73.9 - - - +
121A ARG* 1.3 67.3 + - - +
122A THR 3.3 0.2 + - - -
123A VAL* 3.4 4.6 + - + +
124A CYS* 3.1 28.9 + - - -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 5.6 1.6 - - - +
113A THR* 4.4 4.1 + - - -
114A ALA* 3.6 32.3 - - - +
117A SER 3.2 14.6 + - - +
118A GLU* 2.8 40.1 + - - +
120A LEU* 1.3 79.0 - - - +
122A THR* 1.3 60.0 + - - +
124A CYS* 3.3 6.7 + - - +
125A MET* 2.9 56.1 + - - +
168B LEU 4.2 2.0 - - - -
169B THR* 2.9 42.2 + - + +
170B ASN 3.8 5.9 + - - -
171B LYS* 3.6 31.1 - - - +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 2.5 33.4 + - - +
119A PRO* 3.5 7.5 - - - +
121A ARG* 1.3 82.1 + - - +
123A VAL* 1.3 65.4 + - + +
125A MET* 3.3 21.1 + - + +
126A LYS* 3.0 38.5 + - + +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.4 42.2 - - + +
59A VAL* 4.3 12.8 - - + -
60A THR* 3.5 24.7 - - - +
119A PRO 3.0 17.8 + - - +
120A LEU* 3.9 4.3 - - + +
122A THR* 1.3 78.5 - - + +
124A CYS* 1.3 57.9 + - - +
126A LYS* 3.4 16.5 + - + +
127A VAL* 2.9 31.1 + - + +
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Residues in contact with CYS 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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59A VAL* 4.0 10.8 - - - -
106A VAL* 3.7 22.6 - - + +
109A LEU* 3.8 17.9 - - - -
110A ALA* 3.6 40.8 - - + -
120A LEU 3.1 21.6 + - - +
121A ARG* 3.6 5.4 - - - +
123A VAL* 1.3 73.6 - - - +
125A MET* 1.3 64.9 + - - +
127A VAL* 3.3 1.6 + - - +
128A PHE* 3.0 28.1 + - + -
169B THR* 4.0 5.6 - - + -
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Residues in contact with MET 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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121A ARG* 2.9 45.0 + - - +
122A THR* 3.3 23.5 + - + +
124A CYS* 1.3 75.2 - - - +
126A LYS* 1.3 59.3 + - + +
128A PHE* 3.5 4.1 + - - +
129A LYS* 3.1 44.3 + - + +
169B THR* 3.8 11.9 - - + +
170B ASN* 3.2 34.4 - - - +
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Residues in contact with LYS 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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60A THR* 5.6 1.6 + - - -
122A THR* 3.0 34.6 + - + +
123A VAL* 3.7 17.3 + - + +
124A CYS 3.2 0.2 - - - -
125A MET* 1.3 79.1 - - + +
127A VAL* 1.3 66.5 + - - +
129A LYS* 3.2 10.0 + - + +
130A SER* 3.0 21.3 + - - -
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Residues in contact with VAL 127 (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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59A VAL* 3.8 24.2 - - + +
60A THR* 4.3 10.1 - - + +
63A GLY* 3.5 18.4 - - - -
106A VAL* 3.9 10.3 - - + -
123A VAL* 2.9 25.2 + - + +
124A CYS* 3.3 6.7 + - - +
126A LYS* 1.3 79.4 - - + +
128A PHE* 1.3 63.3 + - - +
130A SER* 2.4 26.7 + - - +
131A TRP* 3.1 36.3 + - + +
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Residues in contact with PHE 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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106A VAL* 4.1 10.5 - - + -
107A GLY* 3.8 16.8 - - - -
110A ALA* 4.4 5.4 - - + -
124A CYS 3.0 21.0 + - - +
125A MET* 3.7 5.6 - - - +
127A VAL* 1.3 75.8 - - - +
129A LYS* 1.3 57.7 + - + +
131A TRP* 3.0 31.6 + + - +
132A GLU* 2.9 39.2 + - - +
157A ASN* 3.5 20.8 - - - +
161A GLU* 3.4 35.9 - - + -
165B MET* 4.9 4.3 - - + -
166B LEU* 5.0 13.2 - - + -
169B THR* 3.7 35.0 - - + -
170B ASN* 5.2 3.6 - - - +
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Residues in contact with LYS 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 MET* 3.1 42.5 + - + +
126A LYS* 3.4 11.0 - - + +
127A VAL 3.2 0.2 - - - -
128A PHE* 1.3 75.9 - - - +
130A SER* 1.3 57.5 + - - +
132A GLU* 3.3 22.7 + - - +
133A ALA* 2.8 30.2 + - - +
154A THR* 6.2 0.6 - - - -
170B ASN* 4.4 17.5 - - - +
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Residues in contact with SER 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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63A GLY 4.9 1.7 + - - -
67A GLU* 4.2 23.0 + - - +
126A LYS 3.0 11.8 + - - -
127A VAL* 2.4 29.4 + - - +
129A LYS* 1.3 78.1 - - - +
131A TRP* 1.3 68.9 + - - +
133A ALA* 3.4 9.5 + - - +
134A VAL* 3.3 24.7 + - - +
137A ARG* 4.9 0.5 + - - -
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Residues in contact with TRP 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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63A GLY* 3.0 24.6 + - - -
66A VAL* 3.4 39.0 - - + +
67A GLU* 4.0 13.2 - - - -
70A ILE* 3.7 18.6 - - + +
105A PRO* 4.3 11.4 - - + -
106A VAL* 3.4 37.5 - - + -
127A VAL* 3.3 21.5 - - + +
128A PHE* 3.0 30.1 + + - +
130A SER* 1.3 83.4 + - - +
132A GLU* 1.3 67.7 + - - +
134A VAL* 3.0 21.6 + - - +
135A PHE* 3.4 14.4 + - + -
157A ASN* 3.6 22.7 - - - +
161A GLU* 4.1 12.3 - - - -
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Residues in contact with GLU 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 PHE* 2.9 26.3 + - - +
129A LYS* 3.6 24.6 + - + +
131A TRP* 1.3 75.8 - - - +
133A ALA* 1.3 57.8 + - - +
135A PHE* 3.2 9.7 + - - +
136A ALA* 2.9 27.9 + - - +
150A ASN* 4.7 4.0 - - - +
153A GLY* 3.5 28.4 - - - +
154A THR* 3.3 29.8 + - - +
157A ASN* 3.0 26.1 - - + +
166B LEU* 3.8 15.2 - - - +
170B ASN* 5.3 0.7 + - - -
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Residues in contact with ALA 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 LYS 2.8 17.6 + - - +
130A SER* 3.5 10.8 - - - +
131A TRP 3.1 0.4 - - - -
132A GLU* 1.3 77.2 - - - +
134A VAL* 1.3 56.6 + - - +
136A ALA* 3.6 8.5 - - - +
137A ARG* 2.8 47.8 + - - +
150A ASN* 5.1 2.7 - - - +
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Residues in contact with VAL 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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67A GLU* 3.8 28.0 - - + +
70A ILE* 3.4 24.5 - - + -
71A GLN* 3.3 36.2 - - + +
74A MET* 4.0 5.5 - - + +
130A SER 3.3 16.6 - - - +
131A TRP* 3.0 10.0 + - - +
133A ALA* 1.3 78.0 - - - +
135A PHE* 1.3 62.9 + - - +
137A ARG* 3.4 21.8 + - - +
138A LYS* 3.3 21.0 + - - +
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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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70A ILE* 3.6 30.7 - - + -
74A MET* 4.1 22.8 - - + +
84A ILE* 4.3 16.6 - - + +
87A PHE* 4.0 26.7 - + - -
131A TRP* 3.4 23.3 + - + -
132A GLU* 3.2 12.2 + - - +
134A VAL* 1.3 75.5 - - - +
136A ALA* 1.3 64.5 + - - +
138A LYS* 3.2 5.9 + - - +
139A LEU* 3.1 27.5 + - + +
153A GLY* 4.1 16.8 - - - +
156A ILE* 3.8 37.5 - - + -
157A ASN* 4.5 13.0 - - + -
160A ILE* 4.0 6.5 - - + -
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Residues in contact with ALA 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 GLU 2.9 15.9 + - - +
133A ALA* 3.6 7.0 - - - +
135A PHE* 1.3 77.7 - - - +
137A ARG* 1.3 57.3 + - - +
139A LEU* 3.1 3.6 + - - +
140A MET* 2.8 37.7 + - + +
149A ALA* 3.8 24.8 + - + +
150A ASN* 3.0 33.4 - - - +
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Residues in contact with ARG 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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67A GLU* 4.6 9.5 + - - -
71A GLN* 2.5 34.1 + - - +
130A SER 4.9 0.4 + - - -
133A ALA* 2.8 31.3 + - - +
134A VAL* 3.7 29.9 - - - +
135A PHE 3.3 0.2 - - - -
136A ALA* 1.3 72.2 - - + +
138A LYS* 1.3 57.5 - - - +
140A MET* 3.3 12.1 + - + +
141A GLU* 2.9 43.5 + - + +
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Residues in contact with LYS 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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74A MET* 2.7 61.0 + - + +
75A ASP* 4.7 4.6 + - - +
77A SER 2.8 19.9 + - - -
78A SER* 3.9 9.7 + - - +
80A PRO* 4.3 18.8 - - + -
83A ALA* 4.4 1.6 - - - -
84A ILE* 5.9 1.6 - - + -
134A VAL 3.3 5.9 + - - +
135A PHE 3.2 10.0 + - - +
137A ARG* 1.3 78.2 - - - +
139A LEU* 1.3 62.3 + - + +
141A GLU* 3.4 17.8 + - - +
142A ASN* 2.9 47.1 + - - +
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Residues in contact with LEU 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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80A PRO* 3.9 17.7 - - + -
84A ILE* 4.5 8.7 - - + -
135A PHE 3.1 19.5 + - - +
136A ALA 3.5 5.8 - - - +
138A LYS* 1.3 77.4 - - + +
140A MET* 1.3 61.9 + - - +
142A ASN* 2.9 13.7 + - - -
143A GLY 3.3 0.7 + - - -
144A PHE* 3.0 40.3 + - + +
149A ALA* 3.8 17.3 - - + +
152A LEU* 3.6 39.5 - - + -
153A GLY 4.9 0.7 - - - +
156A ILE* 4.9 8.1 - - + -
187A VAL* 3.4 29.4 - - + -
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Residues in contact with MET 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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136A ALA* 2.8 27.7 + - + +
137A ARG* 3.6 12.6 - - + +
139A LEU* 1.3 73.6 - - - +
141A GLU* 1.3 61.8 + - + +
142A ASN 3.1 0.9 + - - -
143A GLY* 3.1 11.8 + - - -
144A PHE 3.5 16.9 - - - +
146A GLU* 3.9 39.3 - - + +
149A ALA* 3.7 9.9 - - + -
150A ASN* 3.8 26.7 - - - +
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Residues in contact with GLU 141 (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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137A ARG* 2.9 35.4 + - + +
138A LYS* 3.7 24.2 + - - +
140A MET* 1.3 76.5 - - + +
142A ASN* 1.3 62.9 + - - +
143A GLY 3.8 0.3 + - - -
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Residues in contact with ASN 142 (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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78A SER 3.4 19.7 + - - +
80A PRO* 3.1 33.8 - - + +
138A LYS* 2.9 35.4 + - - +
139A LEU* 2.9 9.3 + - - +
141A GLU* 1.3 83.5 - - - +
143A GLY* 1.3 56.3 + - - +
144A PHE* 3.6 10.5 + - + -
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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