Contacts of the helix formed by residues 114 - 139 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR 5.6 0.2 - - - +
112A THR 4.4 2.7 - - - +
113A ILE* 1.4 87.9 - - + +
115A PRO* 1.3 63.3 - - + -
116A GLU* 3.0 23.6 - - - +
117A ARG* 2.7 63.8 + - + +
118A VAL 3.4 2.4 + - - -
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Residues in contact with PRO 115 (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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103A PRO* 3.6 37.0 - - + +
106A LEU* 4.0 23.6 - - + +
109A TYR 6.0 0.4 - - - +
111A THR* 4.0 14.4 - - - +
113A ILE 3.5 0.4 - - - +
114A PRO* 1.3 82.5 - - + +
116A GLU* 1.3 65.3 + - - +
118A VAL* 3.2 8.4 + - + +
119A THR* 3.0 31.0 + - - -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 4.3 17.4 - - + +
114A PRO* 2.8 22.9 + - - +
115A PRO* 1.3 91.5 - - - +
117A ARG* 1.3 57.6 + - + +
119A THR* 3.3 9.2 + - - +
120A GLU* 2.9 37.1 + - + +
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.6 28.2 - - + +
114A PRO* 2.7 46.0 + - + +
116A GLU* 1.3 71.2 - - + +
118A VAL* 1.3 53.8 + - - +
120A GLU* 3.6 8.2 - - + +
121A LYS* 2.7 59.3 + - - +
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Residues in contact with VAL 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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101A PRO* 6.3 0.9 - - + -
106A LEU* 3.5 26.7 - - + -
111A THR* 5.0 3.4 - - + -
113A ILE* 3.8 34.3 - - + +
114A PRO 3.4 1.2 + - - +
115A PRO* 3.2 10.0 + - + +
117A ARG* 1.3 77.4 - - - +
119A THR* 1.3 58.4 + - - +
121A LYS* 3.2 6.6 + - - +
122A ILE* 2.9 43.4 + - + +
136D LEU* 4.2 10.0 - - + +
139D SER* 5.4 0.2 - - - -
141D VAL* 3.7 34.5 - - + -
145D VAL* 5.5 0.2 - - + -
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Residues in contact with THR 119 (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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100A ILE* 3.5 16.5 - - + +
101A PRO* 2.7 30.8 + - - +
102A SER* 3.6 1.8 + - - -
103A PRO* 3.6 20.2 - - + +
106A LEU* 5.2 0.9 - - - +
115A PRO 3.0 13.8 + - - -
116A GLU* 3.3 13.0 + - - +
118A VAL* 1.3 79.3 - - - +
120A GLU* 1.3 60.3 + - + +
122A ILE* 3.4 5.6 + - - +
123A SER* 3.1 30.8 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 2.9 34.0 + - + +
117A ARG* 3.6 9.2 - - + +
118A VAL 3.2 0.2 - - - -
119A THR* 1.3 74.3 - - + +
121A LYS* 1.3 70.7 + - - +
123A SER* 3.2 8.8 + - - -
124A GLU* 3.0 31.7 + - + +
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Residues in contact with LYS 121 (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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113A ILE* 3.8 19.3 - - + -
117A ARG* 2.7 56.6 + - - +
118A VAL 3.5 4.3 - - - +
120A GLU* 1.3 77.4 - - - +
122A ILE* 1.3 61.1 + - - +
124A GLU* 3.4 6.2 + - - +
125A ILE* 3.3 23.7 + - - +
132D THR* 4.2 12.4 - - + +
135D GLU* 4.1 27.6 - - - +
136D LEU* 4.2 16.2 - - + -
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Residues in contact with ILE 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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100A ILE* 4.2 9.0 - - + -
101A PRO* 3.6 33.0 - - + -
118A VAL* 2.9 33.8 + - + +
119A THR* 3.7 9.4 - - - +
121A LYS* 1.3 75.8 - - - +
123A SER* 1.3 63.1 + - - +
125A ILE* 3.3 7.4 - - - +
126A VAL* 3.0 29.6 + - + +
153A ASN* 3.7 25.4 - - - +
136D LEU* 4.1 21.1 - - + -
145D VAL* 4.5 9.4 - - + +
148D ILE* 4.4 8.3 - - + -
149D VAL* 3.9 12.1 - - + -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.4 2.6 + - - -
100A ILE* 3.5 30.4 - - - +
119A THR* 3.1 17.4 + - - +
120A GLU* 3.2 11.8 + - - -
122A ILE* 1.3 76.6 - - - +
124A GLU* 1.3 58.5 + - - +
126A VAL* 3.6 3.3 - - - +
127A ASP* 3.0 28.9 + - - +
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Residues in contact with GLU 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 GLU* 3.0 22.1 + - + +
121A LYS* 3.9 7.0 - - - +
122A ILE 3.2 0.2 - - - -
123A SER* 1.3 76.9 - - - +
125A ILE* 1.3 60.5 + - - +
127A ASP* 3.3 6.2 + - - +
128A LYS* 2.9 29.6 + - - +
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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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121A LYS 3.3 11.4 + - - +
122A ILE 3.3 11.2 - - - +
124A GLU* 1.3 77.6 - - - +
126A VAL* 1.3 57.7 + - + +
128A LYS* 3.2 14.7 + - + +
129A ALA* 2.8 36.6 + - + +
151A PRO* 5.8 0.9 - - + -
125D ILE* 5.0 3.6 - - + +
128D LYS* 3.6 18.8 - - + -
129D ALA* 3.6 41.3 - - + +
132D THR* 3.7 18.6 - - + +
149D VAL* 3.7 33.2 - - + +
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Residues in contact with VAL 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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96A TYR* 4.8 5.4 - - + +
98A PHE* 3.2 43.3 - - + -
100A ILE* 4.3 6.1 - - + -
122A ILE* 3.0 21.5 - - + +
123A SER* 3.6 6.1 - - - +
125A ILE* 1.3 78.6 - - + +
127A ASP* 1.3 60.8 + - - +
129A ALA* 3.3 6.9 + - - +
130A TYR* 2.9 28.8 + - - +
151A PRO* 4.2 9.0 - - + -
153A ASN* 3.5 35.4 - - - +
149D VAL* 5.2 1.3 - - + -
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Residues in contact with ASP 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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96A TYR* 3.0 39.4 + - - +
123A SER 3.0 17.8 + - - +
124A GLU* 3.6 6.9 - - - +
126A VAL* 1.3 75.4 - - - +
128A LYS* 1.3 63.9 + - - +
130A TYR* 3.3 1.7 + - - +
131A ARG* 2.5 64.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 17.6 + - - +
125A ILE* 3.5 13.5 - - + +
127A ASP* 1.3 77.6 - - - +
129A ALA* 1.3 62.6 + - - +
131A ARG* 3.4 28.0 + - + +
132A THR* 3.1 34.7 + - - +
124D GLU* 2.7 38.7 + - - -
125D ILE* 3.3 26.5 - - + -
128D LYS* 4.2 14.8 - - + +
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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* 2.8 21.2 + - + +
126A VAL 3.7 4.0 - - - +
128A LYS* 1.3 75.1 - - - +
130A TYR* 1.3 57.3 + - - +
132A THR* 3.3 4.5 + - - -
133A TYR* 3.0 26.7 + - - +
149A VAL* 3.5 28.3 - - - +
150A LEU* 4.2 1.6 - - - -
151A PRO* 4.0 18.4 - - + -
125D ILE* 3.7 17.9 - - + -
129D ALA* 6.4 0.4 - - + -
149D VAL 6.1 0.2 - - - +
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Residues in contact with TYR 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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93A LYS* 5.2 1.7 - - - +
94A LEU* 2.5 31.2 + - + -
95A SER* 3.8 11.5 - - - -
96A TYR* 3.3 44.2 + + + +
98A PHE* 3.6 26.0 - + + -
126A VAL 2.9 17.7 + - - +
127A ASP 3.8 3.6 - - - +
129A ALA* 1.3 75.8 - - - +
131A ARG* 1.3 62.3 + - + +
133A TYR* 3.3 13.5 + + - +
134A LEU* 2.9 68.3 + - + +
150A LEU* 3.9 16.1 - - + +
154A LEU* 5.4 0.2 - - + -
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Residues in contact with ARG 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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96A TYR* 5.7 0.7 - - + -
127A ASP* 2.5 65.0 + - - +
128A LYS* 3.7 30.7 - - - +
130A TYR* 1.3 80.1 - - + +
132A THR* 1.3 57.4 + - - +
134A LEU* 3.4 11.6 + - + +
135A GLU* 2.9 29.7 + - - +
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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 LYS* 3.1 24.4 + - - -
129A ALA 3.6 8.3 - - - -
130A TYR 3.3 0.2 - - - -
131A ARG* 1.3 73.8 - - - +
133A TYR* 1.3 66.7 + - - +
135A GLU* 3.2 14.3 + - - +
136A LEU* 2.9 42.6 + - + +
149A VAL* 4.5 6.1 - - + -
121D LYS* 4.3 20.0 - - + +
124D GLU* 4.9 1.8 + - - +
125D ILE* 3.4 28.9 - - + +
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Residues in contact with TYR 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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92A SER 3.7 6.2 + - - -
93A LYS* 3.6 11.8 - - + +
94A LEU* 3.0 47.2 + - + +
129A ALA 3.0 6.8 + - - +
130A TYR* 3.3 26.9 - + - +
132A THR* 1.3 76.7 - - - +
134A LEU* 1.3 76.1 + - + +
136A LEU* 3.3 4.4 + - - +
137A ILE* 3.0 44.8 + - + +
143A ARG* 4.4 7.7 - - - +
146A ALA* 3.6 22.4 - - + +
147A ARG* 3.6 28.0 - - + -
149A VAL* 3.9 9.4 - - + +
150A LEU* 3.6 25.1 - - + -
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Residues in contact with LEU 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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93A LYS* 5.0 10.3 - - + -
130A TYR* 2.9 59.8 + - + +
131A ARG* 3.6 11.9 - - + +
133A TYR* 1.3 85.7 - - + +
135A GLU* 1.3 57.1 + - - +
137A ILE* 3.3 8.6 + - + +
138A GLU* 2.9 47.1 + - + +
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Residues in contact with GLU 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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131A ARG 2.9 16.4 + - - +
132A THR* 3.2 15.2 + - - +
134A LEU* 1.3 77.0 - - - +
136A LEU* 1.3 58.3 + - + +
138A GLU* 3.3 13.2 + - - +
139A SER* 2.8 37.4 + - - +
113D ILE* 5.5 2.3 - - + +
121D LYS* 3.9 38.9 + - + +
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Residues in contact with LEU 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* 2.9 33.7 + - + +
133A TYR 3.7 4.3 - - - +
135A GLU* 1.3 75.2 - - - +
137A ILE* 1.3 62.5 + - - +
139A SER* 3.2 8.1 + - - -
141A VAL* 3.0 42.4 + - + +
146A ALA* 4.0 25.8 - - + +
149A VAL* 4.7 1.3 - - + -
113D ILE* 4.3 7.0 - - + -
118D VAL* 3.9 32.8 - - + -
121D LYS* 4.2 20.0 - - + -
122D ILE* 4.1 27.8 - - + -
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Residues in contact with ILE 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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93A LYS* 5.1 10.8 - - + -
133A TYR* 3.0 36.4 + - + +
134A LEU* 3.6 11.7 - - + +
136A LEU* 1.3 75.3 - - - +
138A GLU* 1.3 64.2 + - + +
140A GLY* 3.1 14.7 + - - -
141A VAL 3.4 14.4 + - - +
143A ARG* 3.3 43.1 - - + +
146A ALA* 3.4 23.6 - - + -
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 2.9 37.7 + - + +
135A GLU* 3.3 9.5 + - - +
137A ILE* 1.3 77.9 - - + +
139A SER* 1.3 60.4 + - - +
140A GLY* 3.2 1.1 + - - -
112D THR* 4.6 4.7 + - - -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 2.8 22.1 + - - +
136A LEU* 3.4 13.0 - - - -
137A ILE 3.2 0.6 - - - -
138A GLU* 1.3 75.9 - - - +
140A GLY* 1.3 57.7 + - - +
141A VAL* 3.5 4.9 - - - -
110D LYS 4.2 0.7 - - - +
111D THR* 3.1 8.5 - - - -
112D THR* 2.7 50.2 + - - +
113D ILE* 4.1 29.2 - - - +
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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