Contacts of the helix formed by residues 119 - 144 (chain A) in PDB entry 2JXP
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 ALA 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU 3.0 10.0 + - - +
116A ALA* 2.8 13.5 + - - +
117A LYS 3.2 0.4 - - - -
118A ALA* 1.3 78.7 - - - +
120A GLU* 1.3 69.5 + - - +
121A GLU 3.4 1.1 - - - -
122A GLU* 2.9 7.2 + - - +
123A MET* 2.8 55.5 + - + +
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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
----------------------------------------------------------
107A LEU* 3.4 19.1 - - + -
108A PRO* 3.7 31.8 - - + +
110A LEU* 5.2 0.7 - - - +
116A ALA* 2.8 43.2 + - - +
117A LYS* 2.6 28.6 + - - +
119A ALA* 1.3 77.4 - - - +
121A GLU* 1.3 58.3 + - - +
122A GLU 2.9 2.3 + - - -
123A MET* 4.4 9.0 - - - +
124A LEU* 2.8 48.1 + - + +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 2.8 44.3 + - - -
63A LYS* 3.6 21.3 - - - +
79A LEU* 3.4 20.8 - - - +
107A LEU* 4.0 11.7 - - + +
117A LYS 4.3 15.8 + - - +
118A ALA 5.9 0.4 - - - -
119A ALA 3.4 1.2 - - - -
120A GLU* 1.3 76.8 - - - +
122A GLU* 1.3 55.3 + - - +
124A LEU* 5.3 0.7 - - - -
125A TYR* 3.2 29.3 - - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 4.6 12.0 + - - +
119A ALA* 2.9 9.4 + - - +
120A GLU 2.9 0.4 + - - -
121A GLU* 1.3 80.1 - - - +
123A MET* 1.3 60.8 + - + +
124A LEU 3.4 0.2 - - - -
125A TYR* 3.1 2.0 + - - +
126A LYS* 2.7 73.5 + - + +
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Residues in contact with MET 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 2.8 45.2 + - + +
120A GLU* 4.0 7.9 - - - +
122A GLU* 1.3 76.3 - - + +
124A LEU* 1.3 61.6 + - + +
126A LYS* 3.3 14.8 - - + +
127A ASP* 3.0 33.8 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.9 18.8 - - + -
105A ARG* 3.4 47.3 - - + +
106A ILE 3.2 33.7 - - - +
107A LEU* 3.9 13.9 - - + -
108A PRO* 4.6 0.2 - - + -
120A GLU* 2.8 31.8 + - + +
121A GLU* 5.3 0.2 - - - -
123A MET* 1.3 75.7 - - + +
125A TYR* 1.3 56.0 + - - +
127A ASP* 4.3 3.8 - - + +
128A MET* 3.0 31.0 + - - +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.3 59.4 + - + +
79A LEU* 5.5 0.4 - - - +
120A GLU 4.0 0.8 + - - -
121A GLU* 3.2 25.3 - - - +
122A GLU* 3.1 5.9 + - - +
124A LEU* 1.3 78.4 - - - +
126A LYS* 1.3 60.2 + - - +
128A MET* 3.3 11.6 + - + +
129A GLN* 2.8 59.0 + - + +
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Residues in contact with LYS 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 GLU* 2.7 54.5 + - + +
123A MET* 3.3 19.7 - - + +
125A TYR* 1.3 69.5 - - - +
127A ASP* 1.3 64.3 + - + +
129A GLN* 4.0 4.8 - - - +
130A LYS* 2.9 40.9 + - - +
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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
----------------------------------------------------------
105A ARG* 2.7 32.0 + - - +
123A MET 3.0 20.1 + - - +
124A LEU* 4.3 1.3 - - - +
126A LYS* 1.3 79.3 - - + +
128A MET* 1.3 57.6 + - - +
130A LYS* 3.8 5.9 - - - +
131A ASP* 2.9 31.5 + - - +
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Residues in contact with MET 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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61A ARG* 3.4 36.1 - - + +
79A LEU* 3.9 9.4 - - + +
81A TYR* 3.4 24.9 - - + -
103A LEU* 3.3 42.0 - - + +
105A ARG* 3.5 28.9 - - + +
124A LEU 3.0 27.2 + - - +
125A TYR* 3.6 13.2 - - + +
126A LYS 3.3 0.2 - - - -
127A ASP* 1.3 79.1 + - - +
129A GLN* 1.3 59.3 + - - +
131A ASP* 3.3 4.8 + - - -
132A ALA* 2.9 25.3 + - - +
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Residues in contact with GLN 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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26A THR* 4.8 12.6 + - - -
27A ILE* 4.8 10.8 - - - +
30A ASP* 5.4 11.1 + - - +
61A ARG* 4.4 0.5 - - - +
81A TYR* 2.9 45.4 + - - -
125A TYR* 2.8 54.3 + - + +
126A LYS* 4.0 5.6 - - - +
128A MET* 1.3 72.0 - - - +
130A LYS* 1.3 62.9 + - - +
132A ALA* 3.4 4.8 + - - +
133A VAL* 3.1 25.9 + - - +
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Residues in contact with LYS 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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30A ASP* 5.8 2.6 + - - -
126A LYS* 2.9 26.1 + - - +
127A ASP* 3.8 5.6 - - - +
129A GLN* 1.3 73.2 - - - +
131A ASP* 1.3 66.1 + - - +
133A VAL* 3.0 9.7 - - + +
134A GLN* 3.0 46.5 + - + +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.3 23.2 - - + +
105A ARG* 6.2 0.2 - - - +
127A ASP* 2.9 24.6 + - - +
128A MET* 3.5 8.1 - - - +
129A GLN 3.3 0.2 - - - -
130A LYS* 1.3 75.7 - - - +
132A ALA* 1.3 50.7 + - - +
134A GLN* 3.0 8.9 + - - +
135A GLN* 2.7 65.6 + - - +
138A ARG* 5.7 2.4 + - - -
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Residues in contact with ALA 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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27A ILE* 5.3 4.9 - - + -
81A TYR* 3.6 22.7 - - + +
83A VAL* 4.3 10.1 - - + -
101A ILE* 3.5 5.6 - - + +
103A LEU* 3.6 18.1 - - + +
128A MET 2.9 19.8 + - - +
129A GLN* 3.4 4.5 + - - +
131A ASP* 1.3 72.0 - - - +
133A VAL* 1.3 57.6 + - - +
135A GLN* 3.2 9.5 + - - +
136A ILE* 3.0 34.1 + - - +
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Residues in contact with VAL 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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27A ILE* 4.7 11.4 - - + +
30A ASP* 4.0 13.9 - - + +
31A LEU* 3.6 45.5 - - + +
34A VAL* 3.8 24.0 - - + -
129A GLN 3.1 11.5 + - - +
130A LYS* 3.0 26.2 - - + +
132A ALA* 1.3 78.4 - - - +
134A GLN* 1.3 60.3 + - + +
136A ILE* 3.6 9.8 + - - +
137A LEU* 3.0 26.7 + - - +
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Residues in contact with GLN 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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34A VAL* 3.3 30.9 - - - +
38A HIS* 3.7 24.5 + - - -
130A LYS* 3.0 39.9 + - + +
131A ASP* 3.0 8.8 + - - +
133A VAL* 1.3 74.6 - - - +
135A GLN* 1.3 61.3 + - + +
137A LEU* 3.4 24.1 - - - +
138A ARG* 2.9 44.1 + - - +
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Residues in contact with GLN 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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101A ILE* 3.9 21.5 - - + +
103A LEU* 5.0 3.6 - - - +
131A ASP* 2.7 58.3 + - - +
132A ALA* 3.3 9.9 - - - +
134A GLN* 1.3 71.3 - - - +
136A ILE* 1.3 55.0 + - - +
138A ARG* 3.0 30.5 + - - +
139A GLN* 2.8 45.7 + - + +
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Residues in contact with ILE 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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27A ILE* 3.7 30.5 - - + -
31A LEU* 4.3 20.9 - - + -
54A ILE* 4.6 11.7 - - + -
56A ILE* 5.9 2.5 - - + -
83A VAL* 4.4 7.2 - - + -
85A ALA* 5.2 9.0 - - + -
98A LEU* 4.4 14.4 - - + -
101A ILE* 3.5 17.7 - - + -
132A ALA 3.0 14.8 + - - +
133A VAL* 3.8 9.0 - - - +
135A GLN* 1.3 73.6 - - - +
137A LEU* 1.3 58.7 + - - +
139A GLN* 3.1 12.4 + - - +
140A VAL* 2.8 48.2 + - + +
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Residues in contact with LEU 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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10A SER* 4.6 8.1 - - - +
12A LEU* 5.3 2.1 - - + +
31A LEU* 5.1 3.1 - - + +
34A VAL* 3.6 13.9 - - + -
35A ILE* 4.0 28.5 - - + -
38A HIS* 3.6 22.9 - - + +
39A THR* 3.4 29.4 - - + -
133A VAL 3.0 18.1 + - - +
134A GLN* 3.4 27.8 - - - +
136A ILE* 1.3 77.9 - - - +
138A ARG* 1.3 57.7 + - - +
140A VAL* 3.8 6.1 - - + +
141A SER* 2.9 32.3 + - - +
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Residues in contact with ARG 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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131A ASP* 5.7 2.4 + - - -
134A GLN* 2.9 30.8 + - - +
135A GLN* 3.0 29.6 + - - +
137A LEU* 1.3 76.7 - - - +
139A GLN* 1.3 59.0 + - + +
141A SER* 3.1 8.6 + - - +
142A ALA* 3.0 28.9 + - + +
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Residues in contact with GLN 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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98A LEU* 3.4 38.3 - - + +
99A GLN* 3.0 39.1 + - - +
100A GLU 4.5 1.4 + - - -
101A ILE* 4.3 19.8 - - - +
135A GLN* 2.8 26.0 + - + +
136A ILE* 3.1 14.1 + - - +
138A ARG* 1.3 72.3 - - + +
140A VAL* 1.3 54.8 + - - +
142A ALA* 3.1 6.3 + - - +
143A PHE* 2.8 44.3 + - + -
150A HIS* 4.6 4.4 + - - +
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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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12A LEU* 3.9 7.0 - - + -
14A PHE* 3.5 37.4 - - + -
54A ILE* 4.1 29.8 - - + -
87A LEU* 3.8 27.1 - - + -
98A LEU* 5.2 3.1 - - + -
136A ILE* 2.8 38.5 + - + +
137A LEU* 3.8 6.5 - - + +
139A GLN* 1.3 72.5 - - + +
141A SER* 1.3 61.8 + - - +
143A PHE* 3.3 12.1 + - - +
144A THR 3.7 7.8 + - - -
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Residues in contact with SER 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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10A SER 4.4 16.0 + - - -
11A GLU 4.7 5.1 - - - +
12A LEU* 4.0 24.7 - - - +
39A THR* 5.6 0.4 - - - -
137A LEU* 2.9 19.9 + - - +
138A ARG* 3.1 16.1 + - - +
140A VAL* 1.3 77.5 - - - +
142A ALA* 1.3 56.0 + - - +
143A PHE 3.5 0.2 - - - -
144A THR* 3.0 22.2 - - - +
145A SER* 4.3 3.5 + - - -
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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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138A ARG* 3.0 21.8 + - + +
139A GLN* 3.1 7.4 + - - +
141A SER* 1.3 75.8 - - - +
143A PHE* 1.3 59.0 + - - +
144A THR 3.2 2.0 - - - -
145A SER* 2.9 12.6 + - - -
146A ALA 2.8 23.6 + - - -
147A GLY* 3.3 12.7 + - - +
149A GLU* 4.2 7.7 - - - +
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Residues in contact with PHE 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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14A PHE* 6.1 1.1 - - + -
87A LEU* 3.7 26.0 - - + -
96A ALA* 3.7 29.2 - - + -
97A SER 5.1 3.4 - - - -
98A LEU* 3.5 35.0 - - + -
99A GLN* 5.6 1.3 - - + -
139A GLN* 2.8 32.0 + - + +
140A VAL 3.3 7.7 + - - +
142A ALA* 1.3 73.6 - - - +
144A THR* 1.3 60.4 + - - +
145A SER 3.2 1.2 + - - -
146A ALA* 3.5 24.9 + - - +
147A GLY* 3.7 27.6 - - - -
148A LEU* 4.2 6.1 - - + -
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Residues in contact with THR 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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12A LEU* 4.7 2.0 - - + -
13A PRO* 3.1 36.1 - - + +
14A PHE* 4.0 22.4 - - - -
140A VAL 3.7 3.4 + - - -
141A SER* 3.0 31.2 - - - +
143A PHE* 1.3 77.8 - - - +
145A SER* 1.3 64.8 + - - +
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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