Contacts of the helix formed by residues 118 - 143 (chain H) in PDB entry 1JI4
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 118 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H THR* 4.0 7.3 - - - +
57H ARG* 2.9 25.7 + - - -
61H LEU* 3.8 17.7 - - - +
113H ALA* 2.8 20.4 + - + +
116H GLU* 3.3 11.6 - - + +
117H GLY* 1.3 73.1 - - - +
119H LYS* 1.3 63.8 + - - +
120H VAL* 3.7 1.7 + - - +
121H THR* 2.6 29.7 + - - -
122H VAL* 3.1 23.1 + - - +
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Residues in contact with LYS 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H GLY* 3.0 16.4 + - - +
118H ASP* 1.3 70.7 + - - +
120H VAL* 1.3 66.0 + - + +
122H VAL* 3.3 8.1 + - - +
123H THR* 3.2 27.2 + - - +
107K LYS* 5.0 9.0 - - + +
110K SER* 3.2 28.5 + - - +
111K ASN* 3.0 31.7 - - - +
114K GLU* 3.2 23.8 + - - -
122K VAL* 5.3 0.8 - - - +
126K ASP* 4.1 23.1 + - - +
129K LEU* 4.9 11.4 - - + -
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Residues in contact with VAL 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ARG* 3.1 37.9 - - - +
60H GLN* 5.2 1.3 - - - +
118H ASP* 3.4 1.5 - - - +
119H LYS* 1.3 75.2 - - + +
121H THR* 1.3 64.8 + - - +
123H THR* 3.3 9.6 + - - -
124H TYR* 3.1 21.6 + - + +
126K ASP 4.7 4.0 - - - +
129K LEU* 4.1 19.3 - - + -
130K ALA* 4.2 26.0 - - + +
133K GLN* 3.2 32.5 - - - +
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Residues in contact with THR 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H THR* 3.8 10.1 - - + -
7H LEU* 4.4 8.3 - - + -
57H ARG* 2.9 24.9 + - + +
61H LEU* 4.0 2.1 - - - +
109H LEU* 3.5 35.0 - - + -
113H ALA* 4.0 4.5 - - + -
118H ASP* 2.6 35.1 + - - -
120H VAL* 1.3 76.3 - - - +
122H VAL* 1.3 59.2 + - - +
124H TYR* 3.3 7.5 + - + +
125H ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 5.2 0.7 - - - +
110H SER* 3.7 15.3 - - - +
113H ALA* 3.6 6.7 - - + -
114H GLU* 3.4 44.9 - - + +
118H ASP 3.1 16.8 + - - +
119H LYS* 3.5 10.5 - - - +
120H VAL 3.2 0.2 - - - -
121H THR* 1.3 79.4 - - - +
123H THR* 1.3 61.0 + - + +
125H ALA* 3.2 6.0 + - - +
126H ASP* 2.9 42.8 + - - +
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Residues in contact with THR 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 6.5 0.2 - - - -
119H LYS 3.2 16.5 + - - +
120H VAL* 3.3 11.5 + - - +
121H THR 3.4 0.2 - - - -
122H VAL* 1.3 76.3 - - + +
124H TYR* 1.3 68.5 + - - +
126H ASP* 3.4 6.6 + - - +
127H ASP* 3.0 37.8 + - - +
126K ASP* 4.1 29.8 + - + +
127K ASP* 5.1 8.8 + - - +
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Residues in contact with TYR 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LEU* 5.4 2.9 - - + -
50H MET* 3.6 28.1 + - - +
53H ASP* 3.7 34.3 + - + +
54H LEU* 3.8 25.4 - - + +
57H ARG* 5.8 9.6 - - + -
106H PHE* 3.9 6.1 - + - -
109H LEU* 4.6 7.0 - - + -
120H VAL* 3.1 11.0 + - + +
121H THR* 3.5 13.0 - - + +
122H VAL 3.2 0.2 - - - -
123H THR* 1.3 83.0 + - - +
125H ALA* 1.3 65.4 + - - +
127H ASP* 3.2 9.1 + - + +
128H GLN* 3.1 57.0 + - + +
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Residues in contact with ALA 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H PHE* 3.7 29.4 - - + +
109H LEU* 3.5 21.5 - - + -
110H SER* 3.8 14.1 - - - +
121H THR 2.9 17.0 + - - +
122H VAL 3.5 5.2 - - - +
124H TYR* 1.3 77.5 - - - +
126H ASP* 1.3 56.3 + - - +
128H GLN* 3.3 3.8 + - - +
129H LEU* 3.0 31.9 + - - +
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Residues in contact with ASP 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 3.9 26.9 - - + +
120A VAL* 4.6 5.4 - - - +
123A THR* 4.0 28.3 + - + +
110H SER* 2.6 30.2 + - - -
122H VAL* 2.9 29.5 + - - +
123H THR* 3.9 7.0 - - - +
125H ALA* 1.3 76.3 - - - +
127H ASP* 1.3 63.2 + - - +
129H LEU* 3.4 9.4 - - - +
130H ALA* 3.1 21.1 + - - +
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Residues in contact with ASP 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 5.0 9.7 + - - +
123H THR* 3.0 33.0 + - - +
124H TYR* 3.2 7.9 + - + +
126H ASP* 1.3 76.3 - - - +
128H GLN* 1.3 76.5 + - - +
130H ALA* 3.3 9.5 + - - +
131H LYS* 3.3 27.2 + - - +
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Residues in contact with GLN 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H MET* 4.7 11.6 - - - +
53H ASP* 5.7 0.4 + - - -
106H PHE* 3.6 36.8 - - + -
124H TYR* 3.1 50.3 + - + +
125H ALA 3.7 6.1 - - - +
127H ASP* 1.3 82.4 - - - +
129H LEU* 1.3 60.4 + - - +
131H LYS* 3.2 30.6 + - - +
132H LEU* 2.9 35.4 + - + +
707H MPD 4.6 8.7 + - + +
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Residues in contact with LEU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 4.7 10.5 - - + -
120A VAL* 4.0 11.4 - - + -
103H GLU* 3.5 42.4 - - + +
106H PHE* 3.6 30.5 - - + +
107H LYS* 4.1 15.0 - - + -
110H SER* 4.6 2.2 - - - -
125H ALA 3.0 17.5 + - - +
126H ASP* 3.4 24.9 - - - +
127H ASP 3.2 0.2 - - - -
128H GLN* 1.3 77.0 - - - +
130H ALA* 1.3 56.8 + - - +
132H LEU* 3.3 3.6 + - + +
133H GLN* 2.9 46.5 + - - +
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Residues in contact with ALA 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 5.0 2.4 + - - -
120A VAL* 4.0 26.3 - - + +
123A THR* 5.4 4.3 - - - +
126H ASP 3.1 10.5 + - - +
127H ASP* 3.4 12.6 - - - +
128H GLN 3.2 0.2 - - - -
129H LEU* 1.3 80.9 - - - +
131H LYS* 1.3 61.2 + - + +
133H GLN* 3.5 2.3 + - - +
134H LYS* 3.2 23.0 + - - +
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Residues in contact with LYS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLU* 3.7 20.0 + - - +
127H ASP* 3.3 13.9 + - - +
128H GLN* 3.2 34.9 + - - +
130H ALA* 1.3 76.7 - - + +
132H LEU* 1.3 62.8 + - - +
134H LYS* 3.4 6.2 + - - +
135H SER* 3.1 27.4 + - - -
707H MPD 3.9 35.7 - - + +
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Residues in contact with LEU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H TYR* 4.0 32.3 - - + +
102H LEU* 4.0 11.0 - - + -
103H GLU* 3.9 23.8 - - + +
106H PHE* 3.6 34.1 - - + -
128H GLN* 2.9 21.6 + - + +
129H LEU* 3.7 5.8 - - - +
131H LYS* 1.3 77.2 - - - +
133H GLN* 1.3 57.4 + - + +
135H SER* 3.3 4.8 + - - -
136H ILE* 2.9 41.1 + - + +
707H MPD 3.4 29.6 - - + -
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Residues in contact with GLN 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.9 42.6 + - - +
60A GLN* 4.0 8.1 - - + +
61A LEU* 5.3 0.3 - - - +
118A ASP* 5.7 0.2 + - - -
120A VAL* 3.2 22.3 - - - +
103H GLU* 3.1 31.1 + - + +
107H LYS* 4.0 16.8 - - - +
129H LEU* 2.9 22.4 + - - +
130H ALA* 4.0 4.0 - - - +
131H LYS 3.3 0.2 - - - -
132H LEU* 1.3 76.9 - - - +
134H LYS* 1.3 61.4 + - - +
136H ILE* 3.9 6.5 - - + +
137H TRP* 3.3 21.3 + - - +
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Residues in contact with LYS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 5.3 5.1 + - - -
56A GLU* 4.0 17.4 + - - -
60A GLN* 3.8 22.8 - - - +
37D HIS* 5.8 0.2 - - - -
808D UNX 3.7 19.5 - - - -
130H ALA 3.2 16.6 + - - +
131H LYS* 3.8 6.1 - - - +
132H LEU 3.3 0.2 - - - -
133H GLN* 1.3 77.2 - - - +
135H SER* 1.3 62.2 + - - +
137H TRP* 3.3 16.9 + - + +
138H MET* 3.2 41.3 + - + +
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Residues in contact with SER 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H TYR* 3.5 26.5 - - - -
131H LYS 3.1 15.5 + - - -
132H LEU 3.8 2.5 - - - -
134H LYS* 1.3 75.3 - - - +
136H ILE* 1.3 60.0 + - - +
138H MET* 3.2 19.6 + - - +
139H LEU* 2.8 36.2 + - - +
707H MPD 2.6 24.1 + - - +
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H LEU* 4.1 9.0 - - + -
99H TYR* 3.9 39.5 - - + +
100H LYS* 4.0 14.4 - - + +
103H GLU* 3.6 30.7 - - + +
132H LEU* 2.9 27.3 + - + +
133H GLN* 3.9 7.0 - - + +
134H LYS 3.3 0.2 - - - -
135H SER* 1.3 76.2 - - - +
137H TRP* 1.3 63.4 + - - +
139H LEU* 3.6 6.8 - - - +
140H GLN* 2.9 48.0 + - - +
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Residues in contact with TRP 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 3.7 43.7 - - + -
59A VAL* 3.4 30.8 - - + +
60A GLN* 3.7 31.6 - - + -
26D TRP* 3.7 26.9 + - - -
29D LYS* 5.0 5.2 - - - +
33D PHE* 4.1 15.3 - + - -
37D HIS* 3.8 15.0 - + - -
133H GLN 3.3 10.8 + - - +
134H LYS* 3.4 26.9 - - + +
135H SER 3.2 0.6 - - - -
136H ILE* 1.3 80.8 - - - +
138H MET* 1.3 67.3 + - + +
140H GLN* 3.2 11.6 + - - +
141H ALA* 2.8 39.5 + - + +
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Residues in contact with MET 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 3.6 38.8 - - + -
34D PHE* 6.6 0.4 - - - -
37D HIS* 4.8 11.7 - - - -
134H LYS* 3.2 38.0 + - + +
135H SER* 3.2 20.6 + - - +
137H TRP* 1.3 94.0 - - + +
139H LEU* 1.3 63.3 - - + +
141H ALA* 3.4 2.1 + - - +
142H HIS* 3.0 24.8 + - - +
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Residues in contact with LEU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ILE* 6.2 2.9 - - + -
92H PHE* 3.7 48.9 - - + +
95H ILE* 4.1 12.3 - - + -
96H LEU* 3.9 19.3 - - + +
99H TYR* 3.6 33.9 - - + -
135H SER* 2.8 28.0 + - - +
136H ILE* 3.6 5.8 - - - +
138H MET* 1.3 72.1 - - + +
140H GLN* 1.3 63.3 + - - +
142H HIS* 3.3 8.4 + - + +
143H LEU* 3.1 28.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H LEU* 3.9 19.7 - - + -
100H LYS* 3.0 32.4 + - - -
136H ILE* 2.9 29.3 + - - +
137H TRP* 3.6 10.2 - - - +
139H LEU* 1.3 75.8 - - - +
141H ALA* 1.3 65.1 + - - +
143H LEU* 3.3 8.1 + - - +
144H ALA* 3.2 22.4 + - - +
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Residues in contact with ALA 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL 3.6 9.2 - - - +
29D LYS* 3.2 23.9 - - - +
30D GLY 2.8 29.1 + - - -
33D PHE* 3.5 31.4 - - + -
137H TRP* 2.8 23.7 + - + +
138H MET 3.7 1.1 - - - +
140H GLN* 1.3 75.6 - - - +
142H HIS* 1.3 54.8 + - - +
144H ALA* 3.2 8.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLY* 2.9 31.5 + - - +
31D THR* 3.1 53.3 + - + +
33D PHE* 4.0 12.5 + - + +
34D PHE* 5.1 4.0 + - - +
32H ASP* 4.6 3.6 - - - -
88H SER* 3.8 5.4 + - - -
89H LYS* 5.6 0.6 + - - -
92H PHE* 3.1 48.0 - + - -
138H MET 3.0 14.4 + - - +
139H LEU* 3.3 13.2 - - + +
140H GLN 3.2 0.2 - - - -
141H ALA* 1.3 78.0 - - - +
143H LEU* 1.3 69.1 + - + +
144H ALA* 3.2 2.5 + - - +
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Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D THR* 5.8 2.0 - - + -
89H LYS* 3.9 36.8 - - + +
92H PHE* 4.0 31.6 - - + +
93H LYS* 4.2 17.5 - - + -
96H LEU* 4.0 21.5 - - + -
139H LEU 3.1 19.8 + - - +
140H GLN* 3.3 6.4 + - - +
142H HIS* 1.3 84.4 - - + +
144H ALA* 1.3 58.5 + - - +
----------------------------------------------------------
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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