Contacts of the helix formed by residues 122 - 146 (chain A) in PDB entry 2GFN
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 ARG 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLY* 4.2 26.9 + - - -
120A THR* 2.9 28.6 - - - +
121A ALA* 1.3 70.2 - - - +
123A GLY* 1.3 62.4 + - - +
124A GLU 3.4 0.4 - - - -
125A ILE* 3.6 15.9 - - + +
126A ALA* 2.9 33.0 + - - +
175B LEU* 2.7 46.2 + - + +
177B PRO* 5.7 0.8 - - - +
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 3.2 22.8 - - - +
121A ALA 3.1 1.0 - - - -
122A ARG* 1.3 80.5 - - - +
124A GLU* 1.3 59.1 + - - +
126A ALA* 3.5 6.2 + - - +
127A ALA* 3.0 28.1 + - - +
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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
----------------------------------------------------------
58A LEU* 4.7 0.9 - - + -
61A LEU* 3.8 17.6 - - + +
62A ARG* 3.5 48.6 + - + +
65A GLY* 6.0 1.2 - - - -
108A PHE* 4.4 5.2 - - + -
121A ALA* 3.5 28.8 - - + +
122A ARG 3.4 0.4 - - - -
123A GLY* 1.3 72.3 - - - +
125A ILE* 1.3 66.5 + - - +
127A ALA* 3.4 9.0 + - - +
128A PHE* 2.9 24.3 + - - +
131A ARG* 5.3 5.7 + - - -
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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
----------------------------------------------------------
61A LEU* 5.0 1.3 - - + -
108A PHE* 4.5 10.1 - - + -
111A PHE* 3.1 43.3 - - + +
112A TYR* 3.5 32.1 - - + +
115A GLY* 5.2 1.3 - - - -
121A ALA 3.8 15.0 - - - +
122A ARG* 3.4 16.7 + - + +
123A GLY 3.3 0.2 - - - -
124A GLU* 1.3 77.5 - - - +
126A ALA* 1.3 63.6 + - - +
128A PHE* 3.1 8.5 + - - +
129A LEU* 2.9 41.8 + - + +
175B LEU* 5.0 14.6 - - + -
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Residues in contact with ALA 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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122A ARG* 2.9 23.0 + - - +
123A GLY* 3.7 7.2 - - - +
125A ILE* 1.3 78.9 - - - +
127A ALA* 1.3 56.4 - - - +
129A LEU* 3.4 7.5 + - - +
130A ALA* 2.8 32.9 + - - +
133A ARG* 5.6 0.3 + - - -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 3.0 18.3 + - - +
124A GLU* 3.6 12.1 - - - +
126A ALA* 1.3 73.6 - - - +
128A PHE* 1.3 65.0 + - - +
130A ALA* 4.0 4.0 - - - -
131A ARG* 2.9 57.7 + - - +
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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
----------------------------------------------------------
65A GLY* 4.3 11.0 - - - -
68A GLN* 3.8 24.7 - - + -
72A TYR* 4.5 5.0 + + - -
94A ILE* 3.8 22.2 - - + -
104A MSE 4.0 15.3 - - + -
108A PHE* 3.3 48.7 - + + -
112A TYR* 4.9 5.2 - - - -
124A GLU 2.9 14.9 + - - +
125A ILE 3.1 7.6 + - - +
127A ALA* 1.3 76.7 - - - +
129A LEU* 1.3 70.4 + - + +
131A ARG* 3.9 6.6 - - - +
132A TRP* 3.1 50.9 + + - +
167A ASP* 6.0 0.2 - - - -
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Residues in contact with LEU 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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112A TYR* 3.7 23.3 - - + +
125A ILE* 2.9 37.3 + - + +
126A ALA* 3.8 6.3 - - - +
128A PHE* 1.3 80.0 - - + +
130A ALA* 1.3 55.8 + - - +
132A TRP* 3.3 29.1 + - + +
133A ARG* 2.9 50.1 + - - +
163A VAL* 4.6 2.9 - - + -
172B GLN* 4.1 26.7 - - + +
175B LEU* 6.0 5.2 - - + -
176B ASP* 4.7 17.0 - - + +
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Residues in contact with ALA 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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126A ALA 2.8 22.6 + - - +
127A ALA* 4.0 5.4 - - - +
128A PHE 3.3 0.2 - - - -
129A LEU* 1.3 74.8 - - - +
131A ARG* 1.3 59.7 + - + +
133A ARG* 3.6 13.5 + - - +
134A GLY* 2.9 24.4 + - - -
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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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65A GLY 5.6 4.6 + - - -
66A ASP* 5.5 5.9 + - - +
69A GLY* 6.1 4.8 - - - -
72A TYR* 4.3 13.3 - - + -
124A GLU* 5.3 6.1 + - - -
127A ALA* 2.9 42.2 + - - +
128A PHE* 3.9 5.8 - - - +
130A ALA* 1.3 76.7 - - + +
132A TRP* 1.3 64.0 + - - +
134A GLY* 3.4 2.4 + - - +
135A VAL* 3.2 28.9 + - - +
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Residues in contact with TRP 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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72A TYR* 3.6 20.8 - - - +
90A ILE* 4.0 15.6 + - + +
91A THR* 5.5 1.2 - - - +
94A ILE* 3.5 43.3 - - + +
112A TYR* 4.9 0.4 - - - -
128A PHE* 3.1 34.5 + + + +
129A LEU* 3.5 15.9 - - + +
131A ARG* 1.3 76.5 - - - +
133A ARG* 1.3 66.2 - - - +
135A VAL* 3.2 5.6 - - - +
136A VAL* 3.2 33.7 + - + +
162A LEU* 6.2 0.4 - - - +
163A VAL* 3.6 47.4 - - + +
166A THR* 3.7 22.5 + - - +
167A ASP* 3.7 26.2 - - + -
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Residues in contact with ARG 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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126A ALA 5.6 0.4 + - - -
129A LEU* 2.9 39.8 + - - +
130A ALA* 4.0 10.7 - - - +
132A TRP* 1.3 76.0 - - - +
134A GLY* 1.3 53.7 + - - +
137A ARG* 2.7 39.7 + - + +
159A THR* 3.5 25.3 - - + +
160A VAL* 4.5 20.9 - - - +
163A VAL* 3.8 22.5 - - + +
172B GLN* 3.9 21.0 + - - -
176B ASP* 2.4 32.6 + - - -
178B VAL* 4.2 10.7 - - - +
179B VAL* 4.0 10.1 - - - +
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Residues in contact with GLY 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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130A ALA 2.9 18.6 + - - -
131A ARG* 3.4 3.8 + - - -
132A TRP 3.1 0.6 - - - -
133A ARG* 1.3 77.6 - - - +
135A VAL* 1.3 62.0 + - - +
137A ARG* 3.9 4.9 - - - +
138A GLU* 3.2 32.6 + - - +
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Residues in contact with VAL 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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72A TYR* 4.1 33.4 - - + -
76A LEU* 4.0 27.2 - - + +
90A ILE* 4.0 27.3 - - + +
131A ARG 3.2 14.0 + - - +
132A TRP* 3.2 18.4 - - - +
134A GLY* 1.3 73.5 - - - +
136A VAL* 1.3 65.5 + - - +
138A GLU* 3.6 12.4 + - - +
139A SER* 3.3 22.9 + - - -
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Residues in contact with VAL 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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87A LEU* 3.5 25.1 - - + +
90A ILE* 3.7 26.0 - - + -
91A THR* 5.7 0.4 - - - +
132A TRP* 3.2 29.3 + - + +
133A ARG* 3.7 2.9 - - - +
135A VAL* 1.3 74.3 - - - +
137A ARG* 1.3 67.2 + - - +
139A SER 3.1 2.3 + - - -
140A VAL* 2.9 29.6 + - + +
159A THR* 3.6 32.5 - - + +
162A LEU* 4.0 17.9 - - + -
163A VAL* 4.1 5.4 - - + -
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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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133A ARG 2.7 23.3 + - - +
134A GLY* 3.9 5.6 - - - +
136A VAL* 1.3 73.5 - - - +
138A GLU* 1.3 63.4 + - + +
140A VAL* 3.2 2.9 + - - +
141A VAL* 2.9 48.3 + - + +
154A ASP* 5.8 0.4 + - - -
155A ALA* 4.6 10.4 - - + +
156A ASP* 2.8 39.2 + - - +
159A THR* 3.3 20.9 - - + +
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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
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76A LEU* 4.3 18.0 - - - +
134A GLY 3.2 19.0 + - - +
135A VAL* 3.8 14.9 - - - +
136A VAL 3.3 0.2 - - - -
137A ARG* 1.3 75.9 - - - +
139A SER* 1.3 59.9 + - - +
141A VAL* 3.5 7.3 + - - +
142A ALA* 2.8 27.3 + - - +
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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
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76A LEU* 5.0 4.3 - - - +
83A PRO* 3.4 19.2 + - - +
86A LYS* 3.8 22.7 - - - +
87A LEU* 3.6 31.3 - - - +
90A ILE* 4.7 3.1 - - - +
135A VAL 3.3 8.9 + - - -
136A VAL 3.1 2.9 + - - -
138A GLU* 1.3 77.8 - - - +
140A VAL* 1.3 61.1 + - - +
142A ALA* 4.1 6.1 - - - +
143A ALA* 2.9 25.1 + - - +
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Residues in contact with VAL 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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87A LEU* 4.1 16.4 - - + -
136A VAL* 2.9 28.0 + - + +
137A ARG 3.6 6.5 - - - +
139A SER* 1.3 76.0 - - - +
141A VAL* 1.3 58.4 + - - +
143A ALA* 3.2 6.2 + - - +
144A GLN* 2.9 41.2 + - + +
149A VAL* 4.7 7.1 - - + +
155A ALA* 3.7 30.3 - - + -
158A VAL* 4.0 29.2 - - + -
159A THR* 3.9 13.9 - - - +
162A LEU* 5.6 0.9 - - + -
197A VAL* 5.1 2.7 - - + -
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Residues in contact with VAL 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 40.4 + - + +
138A GLU* 3.7 5.8 - - - +
140A VAL* 1.3 75.9 - - - +
142A ALA* 1.3 59.5 + - - +
144A GLN* 3.3 12.5 + - - +
145A ARG* 2.9 71.0 + - + +
155A ALA* 3.6 23.6 - - + -
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Residues in contact with ALA 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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83A PRO* 3.8 18.6 - - + -
138A GLU 2.8 18.8 + - - +
139A SER* 3.7 8.1 - - - +
140A VAL 3.3 0.2 - - - -
141A VAL* 1.3 77.0 - - - +
143A ALA* 1.3 57.2 + - - +
145A ARG* 3.2 12.0 + - - +
146A GLU* 2.9 32.5 + - + +
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Residues in contact with ALA 143 (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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83A PRO* 3.6 16.5 - - + +
84A ILE* 4.0 10.1 - - + -
87A LEU* 5.2 0.4 - - + -
139A SER 2.9 17.1 + - - +
140A VAL* 3.2 6.3 + - - +
142A ALA* 1.3 72.4 - - - +
144A GLN* 1.3 65.6 + - - +
146A GLU* 3.3 1.6 + - - -
147A GLY 3.0 4.0 + - - -
148A THR* 3.0 43.2 + - - +
149A VAL* 3.6 21.5 - - + -
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Residues in contact with GLN 144 (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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140A VAL* 2.9 19.3 + - - +
141A VAL* 3.5 14.9 - - - +
143A ALA* 1.3 77.2 - - - +
145A ARG* 1.3 58.4 + - + +
147A GLY* 2.9 20.4 + - - -
149A VAL* 3.4 30.7 - - + +
150A SER 3.1 14.9 + - - -
151A THR* 4.0 21.8 + - - +
153A LEU* 2.8 33.9 + - - +
155A ALA* 3.6 25.9 + - - +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 2.9 48.4 + - + +
142A ALA* 3.2 11.8 + - - +
144A GLN* 1.3 76.8 - - + +
146A GLU* 1.3 62.6 + - + +
147A GLY 3.5 0.5 + - - -
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 5.2 0.7 - - - -
83A PRO* 3.5 33.6 - - + +
142A ALA* 2.9 19.0 + - + +
143A ALA 3.7 4.9 - - - +
144A GLN 3.2 0.2 - - - -
145A ARG* 1.3 76.5 - - + +
147A GLY* 1.3 60.9 + - - +
148A THR* 3.3 20.4 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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