Contacts of the helix formed by residues 118 - 146 (chain B) 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 GLU 118 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.8 34.1 + - + +
115B GLY* 3.7 3.9 - - - -
117B ALA* 1.3 74.1 - - + +
119B GLU* 1.3 60.4 + - - +
120B THR* 3.4 10.4 + - + +
121B ALA 3.5 1.6 + - - +
122B ARG* 3.0 28.8 + - - +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 4.1 1.2 + - - -
118B GLU* 1.3 70.2 - - - +
120B THR* 1.3 65.5 + - - +
122B ARG* 3.0 43.1 + - - +
123B GLY* 3.1 23.4 + - - -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B HIS* 5.4 6.5 - - + -
58B LEU* 5.4 13.5 - - + +
62B ARG* 5.2 7.4 + - - -
111B PHE* 6.3 0.2 - - + -
114B GLU* 4.5 8.3 - - - +
118B GLU* 4.9 7.4 - - + -
119B GLU* 1.3 78.7 - - - +
121B ALA* 1.3 81.3 + - + +
123B GLY* 3.5 1.2 + - - -
124B GLU* 3.4 24.7 + - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 5.7 1.8 - - - -
61B LEU* 5.5 0.2 - - - -
111B PHE* 3.7 23.3 - - + +
114B GLU* 3.6 35.7 - - + +
115B GLY* 4.0 9.2 - - - +
118B GLU 3.5 3.2 + - - +
120B THR* 1.3 80.1 - - + +
122B ARG* 1.3 66.0 + - - +
124B GLU* 3.2 10.0 + - - +
125B ILE* 3.0 28.8 + - - +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE 4.8 3.8 - - - -
175A LEU* 2.7 53.1 + - + +
177A PRO* 4.0 16.4 - - - +
115B GLY* 3.5 23.7 - - - +
118B GLU 3.0 18.6 + - - +
119B GLU* 3.0 41.7 + - - +
120B THR 3.3 0.2 - - - -
121B ALA* 1.3 77.6 - - - +
123B GLY* 1.3 60.6 + - - +
125B ILE* 3.4 6.4 + - - +
126B ALA* 2.9 38.4 + - - +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 3.1 17.3 + - - -
120B THR 3.5 2.2 + - - -
121B ALA 3.2 0.2 - - - -
122B ARG* 1.3 83.4 - - - +
124B GLU* 1.3 59.8 + - - +
126B ALA* 3.8 7.1 - - - +
127B ALA* 3.1 26.5 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.5 14.4 - - + +
61B LEU* 3.9 17.3 - - + -
62B ARG* 2.3 56.5 + - - +
108B PHE* 5.0 1.2 - - - -
120B THR* 3.4 14.7 + - - +
121B ALA* 3.2 8.4 + - - +
123B GLY* 1.3 73.9 - - - +
125B ILE* 1.3 67.4 - - - +
127B ALA* 3.4 7.5 + - - +
128B PHE* 3.1 23.0 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.1 18.8 - - + -
61B LEU* 4.2 5.2 - - + -
108B PHE* 3.6 29.4 - - + -
111B PHE* 4.0 31.9 - - + +
112B TYR* 3.7 33.2 - - + -
115B GLY* 5.5 0.2 - - - -
121B ALA 3.0 19.0 + - - +
122B ARG* 3.6 9.4 - - - +
124B GLU* 1.3 76.8 - - - +
126B ALA* 1.3 63.8 + - - +
128B PHE* 3.3 6.8 + - - +
129B LEU* 3.0 38.7 + - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU 4.7 3.6 + - - +
176A ASP* 4.6 16.8 - - - +
177A PRO* 5.8 0.7 - - + -
122B ARG* 2.9 35.2 + - - +
123B GLY* 3.9 7.2 - - - +
124B GLU 3.3 0.2 - - - -
125B ILE* 1.3 77.2 - - - +
127B ALA* 1.3 55.9 + - - +
129B LEU* 3.3 6.7 + - - +
130B ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLY 3.1 18.8 + - - +
124B GLU* 3.8 9.4 - - - +
125B ILE 3.3 0.2 - - - -
126B ALA* 1.3 70.8 - - - +
128B PHE* 1.3 61.9 + - - +
130B ALA* 3.3 6.3 + - - +
131B ARG* 2.9 30.7 + - - +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 4.0 18.6 - - - -
68B GLN* 4.0 20.9 - - + -
72B TYR* 4.3 6.2 + + - -
94B ILE* 4.0 19.5 - - + -
104B MSE 4.1 11.7 - - + -
108B PHE* 3.3 50.3 - + + -
112B TYR* 5.4 2.5 - + - -
124B GLU 3.1 11.2 + - - +
125B ILE 3.5 8.1 - - - +
127B ALA* 1.3 77.2 - - - +
129B LEU* 1.3 69.8 + - + +
131B ARG* 3.4 10.8 + - - +
132B TRP* 3.1 51.7 + + - +
167B ASP* 6.0 0.4 - - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLN* 3.7 44.2 - - + +
175A LEU* 5.5 0.4 - - + -
176A ASP* 3.8 29.8 - - + +
112B TYR* 3.7 17.9 - - + +
125B ILE* 3.0 37.7 + - + +
126B ALA 3.9 1.1 - - - +
128B PHE* 1.3 82.0 - - + +
130B ALA* 1.3 58.7 + - - +
132B TRP* 3.3 25.2 + - + +
133B ARG* 2.8 41.2 + - - +
163B VAL* 4.4 3.3 - - + +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 3.0 17.2 + - - +
127B ALA* 3.8 6.7 - - - +
129B LEU* 1.3 75.3 - - - +
131B ARG* 1.3 66.2 + - - +
133B ARG* 3.9 17.2 - - - +
134B GLY* 2.9 20.8 + - - -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY 3.8 14.7 + - - -
66B ASP* 4.6 10.3 + - - +
69B GLY* 3.4 35.5 + - - -
70B ASP* 5.6 1.0 + - - -
72B TYR* 4.2 20.0 - - + -
127B ALA 2.9 17.4 + - - +
128B PHE* 3.7 10.8 - - - +
129B LEU 3.3 0.2 - - - -
130B ALA* 1.3 76.6 - - - +
132B TRP* 1.3 62.6 + - - +
134B GLY* 3.2 3.0 + - - -
135B VAL* 3.1 28.0 + - + +
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Residues in contact with TRP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.2 29.4 + + - +
90B ILE* 4.0 16.1 - - + +
91B THR* 5.6 1.6 + - - +
94B ILE* 3.6 35.2 - - + +
128B PHE* 3.1 37.0 + + - +
129B LEU* 3.6 13.9 - - + +
130B ALA 3.2 0.2 - - - -
131B ARG* 1.3 74.5 - - - +
133B ARG* 1.3 65.8 + - - +
134B GLY 3.2 0.2 + - - -
135B VAL* 3.2 3.3 - - - +
136B VAL* 3.0 35.7 + - + +
162B LEU* 6.2 0.4 - - - +
163B VAL* 3.5 45.9 - - + +
166B THR* 3.7 20.4 + - + -
167B ASP* 3.7 28.0 - - + -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLN* 4.4 6.1 + - - -
176A ASP* 2.8 30.5 + - - -
178A VAL* 3.6 33.0 - - - +
179A VAL* 3.5 18.4 - - - +
129B LEU* 2.8 28.6 + - - +
130B ALA* 4.0 21.4 - - - +
132B TRP* 1.3 75.5 - - - +
134B GLY* 1.3 53.6 + - - +
137B ARG* 2.7 38.4 + - - +
159B THR* 3.3 22.9 - - + +
160B VAL* 4.1 27.1 - - - +
163B VAL* 3.9 19.1 - - + +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 2.9 15.3 + - - -
131B ARG* 3.2 4.5 + - - -
132B TRP 3.2 0.4 - - - -
133B ARG* 1.3 77.9 - - - +
135B VAL* 1.3 60.9 + - - +
137B ARG* 3.5 5.8 + - - +
138B GLU* 3.2 24.5 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.9 45.1 - - + -
76B LEU* 3.9 27.8 - - + +
90B ILE* 4.1 17.1 - - + +
131B ARG* 3.1 15.7 + - + +
132B TRP 3.2 13.5 - - - +
134B GLY* 1.3 72.4 - - - +
136B VAL* 1.3 67.2 + - - +
138B GLU* 3.5 11.6 + - - +
139B SER* 3.4 21.0 + - - -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.6 21.9 - - + +
90B ILE* 3.9 15.9 - - + -
91B THR* 5.7 0.2 - - - +
132B TRP* 3.0 43.8 + - + +
133B ARG* 3.8 3.4 - - - +
135B VAL* 1.3 77.2 - - - +
137B ARG* 1.3 63.3 + - - +
139B SER* 3.1 5.2 + - - -
140B VAL* 2.9 25.8 + - + +
159B THR* 3.8 28.5 - - + +
162B LEU* 3.9 20.6 - - + -
163B VAL* 4.0 5.2 - - + -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG 2.7 21.6 + - - +
134B GLY* 3.9 6.1 - - - +
135B VAL 3.3 0.2 - - - -
136B VAL* 1.3 73.6 - - - +
138B GLU* 1.3 64.0 + - - +
139B SER 3.2 0.2 + - - -
140B VAL* 3.2 2.6 + - - +
141B VAL* 2.9 54.6 + - + +
155B ALA* 4.4 13.6 - - + +
156B ASP* 2.8 35.4 + - - +
159B THR* 3.3 21.5 - - + +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 4.1 32.5 - - - +
134B GLY 3.2 17.9 + - - +
135B VAL* 3.6 8.2 - - - +
137B ARG* 1.3 76.5 - - - +
139B SER* 1.3 56.9 + - - +
141B VAL* 3.3 11.1 - - + +
142B ALA* 3.0 28.6 + - + +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.9 12.8 - - - +
83B PRO* 3.4 17.4 - - - +
86B LYS* 3.8 23.5 - - - +
87B LEU* 3.7 24.4 - - - +
90B ILE* 4.5 1.8 - - - +
135B VAL 3.4 8.6 + - - -
136B VAL 3.1 7.7 + - - -
138B GLU* 1.3 78.4 - - - +
140B VAL* 1.3 60.3 + - - +
142B ALA* 4.2 5.4 - - - -
143B ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.0 24.5 - - + -
136B VAL* 2.9 26.9 + - + +
137B ARG* 3.6 9.4 - - - +
139B SER* 1.3 76.7 - - - +
141B VAL* 1.3 63.4 + - - +
143B ALA* 3.3 5.6 + - - +
144B GLN* 3.0 30.9 + - + +
149B VAL* 4.6 6.6 - - + +
155B ALA* 3.9 24.9 - - + +
158B VAL* 3.8 34.5 - - + -
159B THR* 4.0 3.8 - - - +
162B LEU* 5.5 1.1 - - + -
197B VAL* 5.1 1.6 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 2.9 45.4 + - - +
138B GLU* 3.3 17.7 - - + +
140B VAL* 1.3 71.5 - - - +
142B ALA* 1.3 64.5 - - + +
144B GLN* 3.2 12.4 + - - +
145B ARG* 2.8 60.6 + - - +
155B ALA* 3.5 22.7 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 3.9 15.7 - - + -
138B GLU* 3.0 20.0 + - + +
139B SER* 3.7 7.6 - - - +
141B VAL* 1.3 76.8 - - + +
143B ALA* 1.3 61.6 + - - +
145B ARG* 3.3 10.7 + - - +
146B GLU* 3.1 27.8 + - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 3.6 17.4 - - + +
84B ILE* 4.2 7.9 - - + -
87B LEU* 5.4 0.9 - - + -
139B SER 2.9 20.9 + - - +
140B VAL* 3.6 3.8 - - - +
141B VAL 3.3 0.2 - - - -
142B ALA* 1.3 72.9 - - - +
144B GLN* 1.3 63.7 + - - +
146B GLU* 3.2 3.0 + - - -
147B GLY 3.1 4.3 + - - -
148B THR* 3.0 36.6 + - - +
149B VAL* 3.5 28.5 - - + -
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 3.0 21.3 + - - +
141B VAL* 3.6 14.3 - - - +
143B ALA* 1.3 74.5 - - - +
145B ARG* 1.3 59.4 + - + +
147B GLY* 3.1 18.4 + - - -
149B VAL* 3.5 32.1 - - + +
150B SER 3.0 15.9 + - - +
151B THR* 4.2 14.8 + - - +
153B LEU* 2.9 34.0 + - - +
155B ALA* 3.8 21.3 - - - +
158B VAL* 5.6 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 2.8 44.8 + - - +
142B ALA* 3.7 8.5 - - - +
143B ALA 3.2 0.2 - - - -
144B GLN* 1.3 78.8 - - + +
146B GLU* 1.3 58.5 + - + +
147B GLY 3.3 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 3.5 36.7 - - - +
142B ALA* 3.1 13.5 + - - +
143B ALA 3.2 6.2 + - - +
145B ARG* 1.3 74.8 - - - +
147B GLY* 1.3 59.8 + - - +
148B THR* 3.4 18.9 + - + +
----------------------------------------------------------
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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