Contacts of the helix formed by residues 114 - 138 (chain X) in PDB entry 6CP3
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 HIS 114 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98 PHE* 6.3 1.4 - - - -
128 GLN* 3.2 44.3 + - - +
29X PHE* 4.3 8.9 - + + +
109X PHE* 3.5 32.8 - + - -
110X ALA* 3.7 18.9 + - + +
111X LEU 4.0 10.3 - - - +
112X SER 3.2 1.2 - - - -
113X ALA* 1.3 75.2 - - - +
115X LEU* 1.3 64.4 + - - +
116X VAL* 3.2 3.8 - - + +
117X PHE* 3.2 11.9 + - + +
118X ILE* 3.1 25.7 + - - +
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Residues in contact with LEU 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S MET* 5.3 0.7 - - + -
113X ALA 3.0 26.1 + - - +
114X HIS* 1.3 68.9 - - - +
116X VAL* 1.3 62.0 + - + +
118X ILE* 4.5 4.9 - - + +
119X ILE* 2.9 61.2 + - + +
174X GLY 3.9 10.3 - - - +
175X LEU* 4.1 2.0 - - + -
178X GLY* 3.5 25.4 - - - +
179X SER* 3.3 37.0 - - - +
182X LEU* 3.9 18.4 - - + -
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Residues in contact with VAL 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 PHE* 3.6 61.2 - - + +
128 GLN* 5.7 1.8 - - - +
138 LEU* 5.8 2.2 - - + -
27J MET* 4.6 14.8 - - + -
114X HIS* 3.2 3.7 - - + -
115X LEU* 1.3 78.2 - - + +
117X PHE* 1.3 57.7 + - - +
119X ILE* 4.4 1.4 - - - +
120X SER* 2.9 32.7 + - - -
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Residues in contact with PHE 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128 GLN* 3.6 35.8 + - + +
138 LEU* 3.9 18.6 - - + +
168 GLY* 3.6 28.9 - - - -
178 PHE* 4.5 9.4 - + - -
208 MET* 4.9 7.6 - - + -
29X PHE* 4.2 20.0 - + + -
95X PHE* 3.7 35.2 - + - -
111X LEU 5.3 1.8 - - - -
114X HIS* 3.2 19.1 + - + +
116X VAL* 1.3 81.3 - - - +
118X ILE* 1.3 71.3 + - + +
120X SER* 3.3 6.4 + - - -
121X LEU* 2.9 32.0 + - + +
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Residues in contact with ILE 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X PHE* 4.8 11.2 - - + -
96X ILE* 6.0 5.2 - - + -
111X LEU 5.6 0.2 - - - +
112X SER* 3.3 42.0 - - - +
114X HIS 3.1 13.7 + - - +
115X LEU* 4.3 4.7 - - - +
117X PHE* 1.3 96.6 - - + +
119X ILE* 1.3 62.0 + - - +
121X LEU* 3.2 14.5 + - + +
122X SER* 2.9 25.6 + - - -
174X GLY* 4.2 23.8 - - - +
177X LEU* 5.1 8.1 - - + -
178X GLY* 4.8 7.6 - - - +
234X TRP* 4.5 11.3 - - + -
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Residues in contact with ILE 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115X LEU* 2.9 37.7 + - + +
116X VAL* 4.4 1.1 - - - +
118X ILE* 1.3 71.9 - - - +
120X SER* 1.3 59.3 + - - +
122X SER* 3.2 7.7 + - - -
123X ILE* 2.8 44.8 + - + +
171X ILE* 4.5 15.9 - - + +
174X GLY* 3.7 4.7 - - - +
175X LEU* 3.5 54.1 - - + +
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Residues in contact with SER 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 LEU* 3.4 28.9 - - - +
178 PHE* 3.9 6.7 - - - -
23J VAL* 3.5 14.3 - - - +
27J MET* 4.9 7.2 - - - -
116X VAL 2.9 21.5 + - - -
117X PHE* 3.4 9.0 - - - -
119X ILE* 1.3 76.3 - - - +
121X LEU* 1.3 56.3 + - - +
123X ILE* 3.2 12.2 + - - +
124X VAL* 3.0 31.0 + - - +
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Residues in contact with LEU 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178 PHE* 4.9 12.0 - - + -
208 MET* 3.7 42.0 - - + -
92X LEU* 4.6 8.1 - - + -
95X PHE* 4.5 12.6 - - + -
96X ILE* 4.8 9.0 - - + -
117X PHE* 2.9 19.8 + - + +
118X ILE* 3.2 17.9 + - + +
120X SER* 1.3 76.0 - - - +
122X SER* 1.3 56.9 + - - +
124X VAL* 3.2 11.7 + - + +
125X ILE* 2.9 50.5 + - + +
234X TRP* 4.5 14.1 - - + -
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Residues in contact with SER 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118X ILE 2.9 12.5 + - - -
119X ILE* 3.2 9.4 + - - -
121X LEU* 1.3 76.5 - - - +
123X ILE* 1.3 58.8 + - - +
125X ILE* 3.3 6.9 + - - +
126X TRP* 2.9 30.3 + - - +
170X ALA* 2.9 27.2 + - - -
173X LEU* 3.9 10.9 - - - +
174X GLY* 3.7 15.9 + - - -
234X TRP* 3.7 20.4 - - - -
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Residues in contact with ILE 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J VAL* 3.7 22.7 - - + -
119X ILE* 2.8 37.1 + - + +
120X SER* 3.6 9.0 - - - +
122X SER* 1.3 73.4 - - - +
124X VAL* 1.3 60.6 + - - +
126X TRP* 3.8 8.6 - - + +
127X LEU* 2.9 43.1 + - + +
170X ALA* 5.5 10.5 - - + +
171X ILE* 5.7 7.4 - - + -
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Residues in contact with VAL 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178 PHE* 3.6 30.1 - - + -
16J PHE* 3.4 29.0 - - + +
19J ALA* 3.3 9.3 - - - +
20J GLY* 3.6 13.7 - - - +
23J VAL* 3.7 21.5 - - + -
120X SER 3.0 18.5 + - - +
121X LEU* 3.2 13.9 + - + +
123X ILE* 1.3 75.9 - - - +
125X ILE* 1.3 59.5 + - + +
128X GLY* 2.9 25.5 + - - -
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Residues in contact with ILE 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J PHE* 3.1 19.7 - - + -
88X MET* 6.2 0.4 - - + -
92X LEU* 3.8 32.5 - - + -
121X LEU* 2.9 33.8 + - + +
122X SER* 3.3 5.8 + - - +
124X VAL* 1.3 77.5 - - + +
126X TRP* 1.3 53.3 + - - +
129X ASN* 2.7 49.7 + - - +
173X LEU* 5.6 5.6 - - + -
234X TRP* 3.6 33.0 - - + +
238X THR* 4.0 18.4 - - - +
241X TYR* 6.4 0.9 - - + -
242X LEU* 5.5 1.1 - - + -
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Residues in contact with TRP 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X SER 2.9 17.4 + - - +
123X ILE* 3.9 6.1 - - + +
125X ILE* 1.3 76.5 - - - +
127X LEU* 1.3 91.8 + - + +
129X ASN* 3.2 15.3 + - + +
130X THR* 3.0 42.4 + - + +
166X TYR* 3.0 61.7 + + - -
167X PHE* 4.0 13.5 - - + -
169X ARG* 4.4 16.3 - - + +
170X ALA* 3.5 36.6 - - + -
241X TYR* 6.3 0.7 - + - -
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Residues in contact with LEU 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ALA* 3.7 15.9 - - + +
22J ALA* 5.5 6.5 - - + -
23J VAL* 4.0 14.8 - - + -
123X ILE* 2.9 38.0 + - + +
126X TRP* 1.3 98.9 - - + +
128X GLY* 1.3 61.4 + - - +
130X THR* 2.5 27.0 + - + +
131X ILE* 2.9 20.3 + - + +
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Residues in contact with GLY 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J PRO* 3.6 30.0 - - - +
16J PHE* 3.7 23.1 - - - -
19J ALA* 3.5 1.0 - - - +
124X VAL 2.9 12.4 + - - -
127X LEU* 1.3 74.1 - - - +
129X ASN* 1.3 59.0 + - - +
131X ILE* 3.4 0.4 + - - -
132X LEU* 2.9 31.4 + - - +
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Residues in contact with ASN 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J PHE* 3.2 20.3 - - - -
125X ILE* 2.7 41.2 + - - +
126X TRP* 3.2 17.5 + - + +
128X GLY* 1.3 76.4 - - - +
130X THR* 1.3 58.1 + - + +
132X LEU* 3.4 5.8 + - - +
133X GLY* 3.0 26.3 + - - -
141X PHE* 4.6 1.0 - - - -
238X THR* 4.8 0.2 + - - -
241X TYR* 4.7 15.9 - - + +
242X LEU* 3.4 23.7 - - - +
245X ALA* 3.9 24.2 - - + +
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Residues in contact with THR 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X TRP* 3.0 38.0 + - + +
127X LEU* 2.5 33.9 + - + +
129X ASN* 1.3 77.7 - - + +
131X ILE* 1.3 59.7 + - - +
133X GLY 3.4 1.0 + - - -
134X LEU* 2.9 45.8 + - - +
141X PHE* 4.3 3.5 - - - -
166X TYR* 3.3 31.0 - - + +
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Residues in contact with ILE 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J TRP* 5.3 6.7 - - + +
15J PRO* 3.7 24.2 - - + +
18J VAL* 5.1 15.7 - - + -
19J ALA* 5.7 2.0 - - + -
127X LEU* 2.9 19.3 + - + +
128X GLY* 3.9 4.0 - - - +
130X THR* 1.3 84.9 + - - +
132X LEU* 1.3 58.4 + - - +
134X LEU* 4.0 11.3 - - + +
135X TYR* 2.9 31.9 + - + +
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Residues in contact with LEU 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL 4.9 2.5 - - - +
14J TRP* 4.8 15.0 - - + +
15J PRO* 3.8 22.9 - - + +
16J PHE* 4.3 16.6 - - + -
85X TYR* 3.3 43.1 - - + +
128X GLY 2.9 17.9 + - - +
129X ASN* 3.7 7.4 - - - +
130X THR 3.3 0.2 - - - -
131X ILE* 1.3 77.9 - - - +
133X GLY* 1.3 57.2 + - - +
135X TYR* 3.4 4.5 + - + +
136X LYS* 3.0 36.8 + - - +
242X LEU* 5.7 3.6 - - + -
245X ALA* 5.7 3.6 - - + +
246X VAL* 4.4 17.0 - - + -
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Residues in contact with GLY 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X ASN 3.0 12.0 + - - -
132X LEU* 1.3 76.0 - - - +
134X LEU* 1.3 56.7 + - - +
136X LYS* 3.4 4.0 + - - -
137X HIS* 2.9 34.7 + - - +
141X PHE* 3.5 19.8 - - - -
245X ALA 3.5 24.1 + - - -
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Residues in contact with LEU 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X THR* 2.9 31.4 + - - +
131X ILE* 4.0 12.6 - - + +
133X GLY* 1.3 73.9 - - - +
135X TYR* 1.3 61.5 + - - +
138X GLY* 2.9 48.2 + - - +
141X PHE* 3.6 24.5 - - + -
142X PHE* 3.6 25.6 - - + -
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Residues in contact with TYR 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J TRP* 3.9 36.6 - + + +
131X ILE* 2.9 20.9 + - + +
132X LEU* 3.9 5.4 - - + +
134X LEU* 1.3 78.3 - - - +
136X LYS* 1.3 64.0 + - - +
138X GLY 4.7 0.9 + - - -
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Residues in contact with LYS 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ASN* 5.8 3.4 - - - +
85X TYR* 5.4 6.2 + - - -
132X LEU* 3.0 26.2 + - - +
133X GLY* 4.3 0.7 - - - -
134X LEU 3.4 0.2 - - - -
135X TYR* 1.3 83.3 - - + +
137X HIS* 1.3 78.2 + - + +
245X ALA 5.3 0.4 - - - -
246X VAL* 3.3 53.2 - - + +
247X TYR* 5.5 2.6 - - + -
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Residues in contact with HIS 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X GLY 2.9 22.0 + - - +
136X LYS* 1.3 97.6 + - + +
138X GLY* 1.3 65.7 + - - +
139X TRP 3.2 4.0 + - - -
140X VAL* 3.4 24.5 + - + +
141X PHE* 3.5 25.1 - + + +
245X ALA 4.2 3.8 - - - -
246X VAL 2.9 26.8 + - - -
247X TYR* 5.0 1.3 - + - -
248X LEU* 3.4 36.4 - - + +
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Residues in contact with GLY 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X LEU* 2.9 45.9 + - - +
135X TYR 4.6 1.0 + - - -
136X LYS 3.8 0.6 - - - -
137X HIS* 1.3 76.0 - - - +
139X TRP* 1.3 64.1 + - - +
141X PHE 3.8 2.8 + - - -
142X PHE* 4.6 1.7 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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