Contacts of the helix formed by residues 114 - 139 (chain D) in PDB entry 3G4C
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 PRO 114 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D THR 4.6 1.1 - - - +
113D ILE* 1.3 91.3 - - + +
115D PRO* 1.3 67.0 - - + +
116D GLU* 3.6 16.4 - - + +
117D ARG* 2.9 32.1 + - + +
118D VAL* 3.1 10.7 + - - +
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Residues in contact with PRO 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PRO* 3.4 34.9 - - + +
106D LEU* 4.1 18.9 - - + +
109D TYR 6.0 0.7 - - - +
111D THR* 4.3 10.1 - - - +
113D ILE 3.5 3.5 - - - +
114D PRO* 1.3 82.3 - - + +
116D GLU* 1.3 66.5 + - - +
118D VAL* 3.3 14.8 + - + +
119D THR* 3.0 30.0 + - - -
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PRO* 3.7 29.3 - - + +
114D PRO* 3.6 11.2 - - + +
115D PRO* 1.3 89.6 - - - +
117D ARG* 1.3 56.4 + - - +
119D THR* 3.5 9.9 - - - +
120D GLU* 3.2 24.7 + - - +
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ILE* 3.8 24.1 - - + +
114D PRO* 2.9 30.5 + - + +
116D GLU* 1.3 77.8 - - - +
118D VAL* 1.3 58.2 + - - +
120D GLU* 3.1 39.8 + - - +
121D LYS* 2.9 58.8 + - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.9 22.2 - - + -
141A VAL* 3.8 23.8 - - + -
145A VAL* 5.1 0.7 - - + -
101D PRO* 6.3 1.1 - - + -
106D LEU* 3.4 32.8 - - + -
111D THR* 5.0 2.7 - - - +
113D ILE* 3.9 18.1 - - + +
114D PRO 3.1 14.6 + - - +
115D PRO* 3.4 8.1 - - + +
117D ARG* 1.3 74.1 - - - +
119D THR* 1.3 64.3 + - - +
121D LYS* 3.3 3.2 + - - +
122D ILE* 3.0 39.8 + - + +
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ILE* 3.7 14.1 - - + +
101D PRO* 2.8 29.0 + - - +
102D SER 3.8 1.7 + - - -
103D PRO* 3.8 17.7 - - + +
106D LEU* 6.0 0.2 - - - +
115D PRO 3.0 10.8 + - - -
116D GLU* 3.5 14.6 - - - +
118D VAL* 1.3 82.7 - - - +
120D GLU* 1.3 56.6 + - - +
122D ILE* 3.3 11.1 + - - +
123D SER* 2.8 31.2 + - - +
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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
----------------------------------------------------------
116D GLU 3.2 11.4 + - - +
117D ARG* 3.1 45.3 + - - +
119D THR* 1.3 78.9 - - - +
121D LYS* 1.3 61.0 + - + +
123D SER* 3.2 9.2 + - - -
124D GLU* 2.9 29.8 + - + +
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 4.3 15.8 - - + +
135A GLU* 3.9 35.0 + - - +
136A LEU* 4.2 11.4 - - + -
113D ILE* 3.5 36.8 - - + -
117D ARG* 2.9 53.8 + - - +
118D VAL 3.7 4.9 - - - +
120D GLU* 1.3 73.1 - - + +
122D ILE* 1.3 62.1 + - - +
124D GLU* 3.5 15.0 + - - +
125D ILE* 3.3 27.2 + - - +
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 4.1 12.3 - - + -
145A VAL* 4.3 11.9 - - + +
148A ILE* 4.4 7.2 - - + -
149A VAL* 3.9 24.7 - - + +
100D ILE* 3.9 10.1 - - + -
101D PRO* 3.8 32.3 - - + -
118D VAL* 3.0 35.8 + - + +
119D THR* 3.5 8.7 - - - +
120D GLU 3.2 0.2 - - - -
121D LYS* 1.3 77.0 - - - +
123D SER* 1.3 61.7 + - - +
124D GLU 3.4 0.2 + - - -
125D ILE* 3.5 2.9 + - - +
126D VAL* 3.1 21.8 + - - +
153D ASN* 3.8 23.8 - - - +
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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
----------------------------------------------------------
96D TYR* 4.7 0.7 + - - -
100D ILE* 3.6 28.3 - - - +
119D THR* 2.8 20.3 + - - +
120D GLU* 3.2 8.1 + - - -
122D ILE* 1.3 72.8 - - - +
124D GLU* 1.3 60.5 + - - +
126D VAL* 3.4 5.6 + - - +
127D ASP* 2.8 31.0 + - - +
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Residues in contact with GLU 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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128A LYS* 2.7 39.0 + - - -
132A THR* 4.9 1.7 + - - -
120D GLU* 2.9 15.8 + - + +
121D LYS* 3.6 20.8 - - - +
122D ILE 3.3 0.2 - - - -
123D SER* 1.3 76.3 - - - +
125D ILE* 1.3 57.4 + - - +
127D ASP* 3.0 7.2 + - - +
128D LYS* 2.8 60.4 + - + +
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Residues in contact with ILE 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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125A ILE* 5.2 2.9 - - + +
128A LYS* 3.3 38.8 - - + -
129A ALA* 3.7 17.3 - - + -
132A THR* 3.4 32.5 - - + +
149A VAL* 3.8 35.7 - - + +
121D LYS 3.3 9.0 + - - +
122D ILE 3.8 6.7 - - - +
124D GLU* 1.3 74.8 - - - +
126D VAL* 1.3 61.5 + - + +
127D ASP 3.2 0.2 + - - -
128D LYS* 3.9 4.4 - - + +
129D ALA* 2.7 44.7 + - + +
151D PRO* 4.9 2.9 - - + -
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Residues in contact with VAL 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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149A VAL* 6.2 0.7 - - + -
96D TYR* 3.8 15.5 - - + +
98D PHE* 3.5 47.8 - - + -
100D ILE* 4.1 5.8 - - + -
122D ILE* 3.1 12.6 + - + +
123D SER* 3.4 13.9 - - - +
125D ILE* 1.3 78.2 - - + +
127D ASP* 1.3 60.1 + - - +
129D ALA* 3.8 1.0 - - - +
130D TYR* 2.9 30.0 + - - +
151D PRO* 3.9 10.3 - - + -
153D ASN* 3.3 33.0 - - - +
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TYR* 2.6 33.4 + - - +
123D SER 2.8 17.7 + - - +
124D GLU* 3.4 7.0 - - - +
126D VAL* 1.3 78.3 - - - +
128D LYS* 1.3 56.4 + - - +
130D TYR* 3.5 1.2 + - - +
131D ARG* 2.9 70.8 + - - +
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Residues in contact with LYS 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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125A ILE* 3.6 15.7 - - + -
128A LYS* 4.2 18.2 - - + +
124D GLU* 2.8 57.5 + - + +
125D ILE* 3.9 3.8 - - + +
127D ASP* 1.3 68.5 - - - +
129D ALA* 1.3 57.2 + - - +
131D ARG* 3.4 38.2 + - - +
132D THR* 2.8 36.9 + - - -
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Residues in contact with ALA 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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125A ILE* 3.6 17.8 - - + +
129A ALA* 6.4 0.9 - - + -
125D ILE* 2.7 26.2 + - + +
126D VAL 3.8 0.7 - - - +
128D LYS* 1.3 70.3 - - - +
130D TYR* 1.3 59.5 + - - +
132D THR* 3.2 3.8 + - - -
133D TYR* 2.9 28.4 + - - +
149D VAL* 3.6 25.8 - - - +
150D LEU* 4.1 2.5 - - - -
151D PRO* 3.7 20.9 - - + -
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Residues in contact with TYR 130 (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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93D LYS* 4.7 4.2 - - - +
94D LEU* 2.6 31.6 + - + -
95D SER* 4.2 2.8 - - - -
96D TYR* 3.2 53.1 + + + +
98D PHE* 3.9 13.0 - + + -
126D VAL 2.9 21.4 + - - +
127D ASP 3.9 1.1 - - - +
129D ALA* 1.3 73.9 - - - +
131D ARG* 1.3 60.1 + - + +
133D TYR* 3.3 14.4 - + - +
134D LEU* 3.0 77.1 + - + +
150D LEU* 3.8 20.5 - - + +
154D LEU* 5.6 0.2 - - + -
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASP* 2.9 48.8 + - - +
128D LYS* 3.7 46.5 - - - +
130D TYR* 1.3 80.3 - - + +
132D THR* 1.3 56.0 + - - +
134D LEU* 3.3 14.5 + - + +
135D GLU* 2.9 31.5 + - - +
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Residues in contact with THR 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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121A LYS* 4.2 28.0 - - + +
125A ILE* 3.7 27.0 - - + +
128D LYS 2.8 24.8 + - - -
129D ALA 3.2 4.7 + - - -
131D ARG* 1.3 74.1 - - - +
133D TYR* 1.3 56.0 + - - +
135D GLU* 3.4 16.2 + - - +
136D LEU* 2.9 51.6 + - + +
149D VAL* 4.6 2.5 - - + -
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Residues in contact with TYR 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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92D SER 3.8 9.4 + - - -
93D LYS* 3.8 2.3 - - + -
94D LEU* 3.1 39.3 + - + +
129D ALA 2.9 13.6 + - - +
130D TYR* 3.3 37.7 - + - +
132D THR* 1.3 76.3 - - - +
134D LEU* 1.3 64.7 + - + +
136D LEU* 3.3 4.9 + - - +
137D ILE* 2.9 59.7 + - + +
143D ARG* 4.3 7.4 - - - +
146D ALA* 3.5 24.9 - - + +
147D ARG* 3.6 26.7 - - + -
149D VAL* 4.0 10.2 - - + +
150D LEU* 3.8 15.3 - - + -
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Residues in contact with LEU 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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93D LYS* 5.2 7.0 - - + -
130D TYR* 3.0 64.3 + - + +
131D ARG* 3.7 11.7 - - + +
133D TYR* 1.3 83.1 - - + +
135D GLU* 1.3 60.0 - - - +
137D ILE* 3.3 11.1 + - + +
138D GLU* 2.9 50.3 + - - +
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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
----------------------------------------------------------
113A ILE* 5.4 4.3 - - + +
121A LYS* 4.1 33.5 - - - +
131D ARG 2.9 15.7 + - - +
132D THR* 3.4 17.1 + - - +
134D LEU* 1.3 76.9 - - - +
136D LEU* 1.3 57.5 + - + +
138D GLU* 3.4 10.9 + - - +
139D SER* 2.7 36.5 + - - +
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Residues in contact with LEU 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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113A ILE* 5.1 4.7 - - + -
118A VAL* 4.2 27.1 - - + +
121A LYS* 4.2 23.8 - - + -
122A ILE* 4.1 23.6 - - + -
132D THR* 2.9 33.3 + - + +
133D TYR 3.6 4.0 - - - +
134D LEU 3.2 0.2 - - - -
135D GLU* 1.3 77.2 - - + +
137D ILE* 1.3 64.0 + - - +
139D SER* 3.1 12.9 + - - +
141D VAL* 3.0 34.2 + - + +
146D ALA* 3.8 31.4 - - + +
149D VAL* 4.4 4.3 - - + -
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Residues in contact with ILE 137 (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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93D LYS* 4.9 9.9 - - + -
133D TYR* 2.9 59.7 + - + +
134D LEU* 3.5 14.8 - - + +
136D LEU* 1.3 74.4 - - - +
138D GLU* 1.3 61.5 + - + +
140D GLY* 2.9 21.1 + - - -
141D VAL 3.8 10.9 + - - +
143D ARG* 4.4 21.3 - - + -
146D ALA* 4.0 13.0 - - + +
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Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 4.4 6.3 + - - -
134D LEU* 2.9 40.6 + - - +
135D GLU* 3.8 8.7 - - - +
136D LEU 3.3 0.2 - - - -
137D ILE* 1.3 79.1 - - + +
139D SER* 1.3 59.0 + - - +
140D GLY 3.2 1.0 + - - -
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS 4.2 0.5 - - - +
111A THR* 3.2 8.5 - - - -
112A THR* 2.8 48.8 + - - +
113A ILE* 4.2 25.9 - - - +
118A VAL* 5.4 0.2 - - - -
135D GLU* 2.7 23.8 + - - +
136D LEU* 3.4 13.2 - - - +
137D ILE 3.1 0.4 - - - -
138D GLU* 1.3 77.2 - - - +
140D GLY* 1.3 55.7 + - - +
141D VAL* 4.6 6.3 - - - -
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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