Contacts of the helix formed by residues 119 - 142 (chain B) in PDB entry 4GCK
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 ASP 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER 4.9 0.7 - - - +
29A SER* 3.1 39.8 + - - +
30A GLN* 3.8 20.0 + - - +
114B LEU 5.7 0.4 - - - +
117B GLU 3.4 6.8 + - - +
118B GLN* 1.3 70.1 - - - +
120B ARG* 1.3 62.2 + - - +
121B LEU 3.0 1.7 + - - -
122B GLN* 3.1 22.5 + - - +
123B GLY* 3.5 2.9 + - - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.6 19.2 - - - +
57B ARG* 4.2 11.9 - - - +
60B ASP* 2.4 45.8 + - - -
118B GLN* 3.9 18.4 + - + +
119B ASP* 1.3 77.4 - - - +
121B LEU* 1.3 66.7 + - + +
122B GLN 3.2 0.2 - - - -
123B GLY* 3.2 6.1 + - - +
124B ARG* 3.1 29.4 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.5 29.2 - - + -
59B PHE* 3.8 17.5 - - + -
60B ASP* 3.5 39.9 - - - +
63B ILE* 3.7 18.8 - - + +
114B LEU* 3.8 18.6 - - + -
117B GLU* 3.8 22.4 - - + -
118B GLN 2.9 17.4 + - - +
120B ARG* 1.3 82.1 - - - +
122B GLN* 1.3 60.7 + - - +
124B ARG* 3.1 10.1 + - - +
125B ILE* 3.1 22.9 + - - +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS* 5.7 0.3 - - - -
175A ARG* 3.5 24.3 - - + +
177A GLU* 5.9 3.1 - - - +
109B LEU 5.2 0.6 + - - -
110B THR 5.7 0.8 - - - -
111B GLY* 3.3 31.1 - - - +
114B LEU* 3.7 15.8 - - + +
118B GLN 4.3 0.4 + - - -
119B ASP* 3.1 13.0 + - - +
121B LEU* 1.3 75.8 - - - +
123B GLY* 1.3 61.2 + - - +
124B ARG 3.1 0.2 - - - -
125B ILE* 3.0 17.5 + - - +
126B ASN* 2.8 57.9 + - - +
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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
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119B ASP 3.5 5.2 + - - -
120B ARG* 3.2 10.0 + - - -
122B GLN* 1.3 79.5 - - - +
124B ARG* 1.3 56.7 + - - +
126B ASN* 3.5 12.8 + - - +
127B GLN* 3.1 35.7 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASP* 2.6 65.9 + - - +
63B ILE* 3.6 24.7 - - + +
64B GLU* 3.5 35.4 + - - +
67B GLU* 5.1 11.1 + - - +
120B ARG* 3.1 18.0 + - - +
121B LEU* 3.3 13.2 - - - +
122B GLN 3.1 0.2 - - - -
123B GLY* 1.3 78.0 - - - +
125B ILE* 1.3 62.9 + - - +
127B GLN* 3.3 18.0 + - + +
128B LEU* 3.2 18.5 + - - +
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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
----------------------------------------------------------
63B ILE* 4.0 20.6 - - + -
66B ILE* 4.8 5.8 - - + -
108B ILE* 3.9 31.0 - - + +
109B LEU* 3.5 27.4 - - + +
114B LEU* 4.0 9.0 - - + -
121B LEU 3.1 12.2 + - - +
122B GLN* 3.0 21.4 + - - +
124B ARG* 1.3 75.1 - - - +
126B ASN* 1.3 65.9 + - - +
128B LEU* 2.9 22.2 + - + +
129B PHE* 2.9 39.9 + - + -
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 2.8 59.8 + - - +
176A SER* 4.5 3.8 - - - +
177A GLU* 5.7 2.2 - - - +
122B GLN* 2.8 39.4 + - - +
123B GLY* 3.7 12.0 - - - +
124B ARG 3.3 0.2 - - - -
125B ILE* 1.3 76.4 - - - +
127B GLN* 1.3 59.0 + - + +
129B PHE* 3.3 2.3 + - - +
130B GLU* 2.8 35.7 + - + +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLU* 6.2 0.2 - - - +
123B GLY 3.1 19.4 + - - +
124B ARG* 3.4 21.3 - - + +
125B ILE 3.1 0.4 - - - -
126B ASN* 1.3 78.4 - - + +
128B LEU* 1.3 56.8 + - - +
130B GLU* 3.2 8.1 + - - +
131B ARG* 2.8 30.7 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 5.6 2.7 - - + +
66B ILE* 4.0 27.6 - - + +
67B GLU* 3.9 45.3 + - + +
70B LEU* 5.1 5.6 - - + -
71B ILE* 4.1 12.6 - - + -
109B LEU* 4.3 17.7 - - + -
124B ARG 3.2 11.4 + - - +
125B ILE* 2.9 17.2 + - + +
127B GLN* 1.3 75.3 - - - +
129B PHE* 1.3 57.9 + - + +
131B ARG* 3.1 5.1 + - + +
132B ILE* 2.9 51.7 + - + +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 3.7 43.1 - - - +
95B ILE* 5.9 4.7 - - + -
109B LEU* 3.3 48.5 - - + -
110B THR* 5.7 0.4 - - + -
125B ILE* 2.9 33.6 + - + -
126B ASN 3.6 6.1 - - - +
128B LEU* 1.3 76.8 - - + +
130B GLU* 1.3 57.5 + - - +
132B ILE* 3.3 13.0 + - + +
133B GLU* 2.8 30.8 + - - +
163B LEU* 3.5 28.8 - - + +
166B CYS* 6.2 0.7 - - + -
167B GLU* 3.8 26.0 - - + -
170B LEU* 5.3 9.9 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ARG* 4.9 6.1 + - - -
180A TYR* 2.4 36.0 + - - -
126B ASN* 2.8 24.2 + - + +
127B GLN* 3.2 8.0 + - - +
129B PHE* 1.3 72.9 - - - +
131B ARG* 1.3 62.0 + - - +
133B GLU* 3.7 14.6 - - - +
134B VAL* 2.8 41.2 + - + +
137B ARG* 4.9 12.6 + - - -
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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
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67B GLU* 2.7 38.9 + - - +
71B ILE* 3.6 45.1 - - + +
127B GLN 2.8 13.6 + - - +
128B LEU* 3.3 10.3 - - - +
130B GLU* 1.3 78.6 - - - +
132B ILE* 1.3 63.0 + - - +
134B VAL* 3.3 7.6 + - - +
135B GLN* 3.1 21.4 + - + +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 4.9 9.4 - - + -
71B ILE* 4.6 4.9 - - + -
74B ILE* 4.2 22.9 - - + -
91B ILE* 5.0 0.9 - - + -
95B ILE* 4.0 35.9 - - + -
109B LEU* 6.3 0.9 - - + -
128B LEU* 2.9 43.0 + - + +
129B PHE* 3.6 17.7 - - + +
131B ARG* 1.3 77.0 - - - +
133B GLU* 1.3 62.8 + - - +
135B GLN* 3.2 7.6 + - - +
136B LEU* 2.9 31.0 + - + +
163B LEU* 4.2 14.6 - - + -
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ARG* 3.1 39.6 + - - -
175A ARG* 4.9 1.2 + - - -
129B PHE 2.8 19.0 + - - +
130B GLU* 3.2 18.8 + - - +
132B ILE* 1.3 73.9 - - - +
134B VAL* 1.3 58.0 + - - +
136B LEU* 3.2 7.9 + - - +
137B ARG* 3.0 50.0 + - - +
156B THR* 4.4 5.2 - - - +
159B ALA* 4.0 17.9 - - + +
160B SER* 3.5 20.0 + - - -
163B LEU* 3.7 13.5 - - + +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.8 34.5 + - + +
131B ARG* 3.5 7.9 - - - +
133B GLU* 1.3 75.6 - - - +
135B GLN* 1.3 58.0 + - - +
137B ARG* 3.0 33.3 - - - +
138B GLN* 3.0 26.5 + - + +
141B ARG* 5.1 2.0 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 6.4 1.8 - - + -
74B ILE* 3.9 26.1 - - + +
75B ASN* 4.3 8.5 - - - +
78B LEU* 3.5 29.7 - - + +
91B ILE* 4.8 3.4 - - + -
131B ARG* 3.1 13.8 + - + +
132B ILE* 3.2 11.4 + - - +
134B VAL* 1.3 75.2 - - - +
136B LEU* 1.3 60.6 + - + +
138B GLN* 3.2 18.7 + - - +
139B VAL* 2.9 36.3 + - + +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 3.8 24.3 - - + +
91B ILE* 3.9 32.8 - - + -
92B VAL* 5.6 4.0 - - + -
95B ILE* 5.6 1.1 - - + -
132B ILE* 2.9 30.5 + - + +
133B GLU* 3.2 11.0 + - - +
135B GLN* 1.3 76.9 - - + +
137B ARG* 1.3 57.5 + - - +
139B VAL* 3.4 5.8 + - - +
140B MET* 3.1 37.0 + - + +
159B ALA* 3.8 27.6 - - + +
162B LEU* 4.1 19.3 - - + -
163B LEU* 4.5 12.1 - - + -
166B CYS* 6.4 0.7 - - - -
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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
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130B GLU* 4.9 7.3 + - - -
133B GLU* 3.0 41.9 + - - +
134B VAL* 3.0 49.4 - - - +
136B LEU* 1.3 75.6 - - - +
138B GLN* 1.3 66.2 + - - +
140B MET* 3.4 2.1 + - - +
141B ARG* 3.0 59.1 + - - +
155B GLU* 3.9 23.3 - - + +
156B THR* 3.8 33.3 + - - +
159B ALA* 4.1 6.0 - - - +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 3.0 15.3 + - + +
135B GLN* 3.2 22.0 + - - +
137B ARG* 1.3 77.8 - - - +
139B VAL* 1.3 63.5 + - - +
141B ARG* 3.3 25.6 + - - +
142B GLU* 2.9 53.0 + - - +
145B MET* 5.8 1.4 - - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU* 3.5 32.3 - - + -
84B THR* 4.0 22.4 + - + +
87B ARG* 4.1 22.5 + - + +
88B LEU* 3.6 28.7 - - + -
91B ILE* 4.4 11.0 - - + -
135B GLN* 2.9 22.1 + - - +
136B LEU 3.6 8.3 - - - +
137B ARG 3.3 0.2 - - - -
138B GLN* 1.3 75.9 - - - +
140B MET* 1.3 63.3 + - - +
142B GLU* 3.2 15.1 + - - +
143B LYS 3.6 6.4 + - - -
146B ARG* 5.6 0.2 - - - -
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR* 4.5 2.0 - - - -
88B LEU* 4.0 17.7 - - + -
136B LEU* 3.1 23.5 + - + +
137B ARG 3.8 1.3 - - - +
138B GLN 3.3 0.2 - - - -
139B VAL* 1.3 77.2 - - - +
141B ARG* 1.3 63.6 + - - +
143B LYS* 3.1 20.3 + - - +
144B LYS 4.7 0.3 + - - -
150B GLY* 5.5 0.5 - - - -
151B TYR* 3.6 31.3 + - + -
155B GLU* 3.6 25.0 - - + +
158B LEU* 3.6 28.5 - - + -
159B ALA* 3.5 33.0 - - + +
162B LEU* 3.8 24.5 - - + -
197B LEU* 4.6 2.5 - - + -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 5.1 2.2 + - - +
137B ARG* 3.0 61.8 + - - +
138B GLN* 3.3 31.3 + - - +
140B MET* 1.3 75.9 - - - +
142B GLU* 1.3 62.7 + - - +
143B LYS 3.2 1.1 + - - -
144B LYS* 3.4 27.5 - - - +
145B MET* 3.6 8.1 - - + +
155B GLU* 3.4 31.9 + - + +
156B THR* 4.7 5.5 + - - -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.7 8.2 + - - +
138B GLN* 2.9 43.6 + - - +
139B VAL* 3.2 10.1 + - - +
140B MET 3.2 1.2 - - - -
141B ARG* 1.3 76.0 - - - +
143B LYS* 1.3 64.5 + - - +
144B LYS 3.3 0.7 - - - -
145B MET* 3.3 20.8 + - + +
146B ARG* 2.9 65.7 + - + +
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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) + - + + + + + -
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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