Contacts of the helix formed by residues 111 - 136 (chain H) in PDB entry 3IYD
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 111 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 3.4 21.9 + - - +
109H ASN* 3.0 19.8 + - - +
110H PRO* 1.3 81.4 - - + +
112H ILE* 1.3 60.5 + - - +
114H MET* 3.1 26.4 + - - +
115H ARG* 3.6 22.6 + - - +
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Residues in contact with ILE 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H THR* 4.0 21.5 - - + +
13H TRP* 3.8 27.6 - - + -
14H PHE* 3.9 18.8 - - + -
69H PHE* 6.5 1.1 - - + -
102H PHE* 3.5 30.7 - - + -
105H LEU* 4.1 14.1 - - + +
106H ILE* 4.2 15.9 - - + -
109H ASN* 3.2 19.1 + - - +
110H PRO 3.1 0.8 - - - -
111H ASP* 1.3 78.8 - - - +
113H LEU* 1.3 64.3 + - - +
115H ARG* 3.5 15.7 + - + +
116H LEU* 3.8 6.6 + - + +
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Residues in contact with LEU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G PRO 5.8 1.1 - - - +
113G LEU* 4.7 23.1 - - + +
114G MET* 4.0 27.1 - - + +
117G SER* 5.2 0.7 - - - +
75H LEU* 4.8 10.5 - - + -
76H PHE* 4.3 13.7 - - + -
102H PHE* 4.9 2.0 - - + -
106H ILE* 3.8 41.7 - - + -
110H PRO* 3.0 11.0 + - + +
112H ILE* 1.3 79.1 - - - +
114H MET* 1.3 61.6 + - - +
115H ARG 3.1 5.9 + - - -
116H LEU* 3.5 12.1 + - + +
117H SER* 3.3 37.6 + - - +
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Residues in contact with MET 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G LEU* 3.8 17.0 - - + +
76G PHE* 3.5 54.2 - - + +
103G ARG* 4.9 13.5 - - + +
106G ILE* 5.4 5.4 - - + -
113G LEU* 4.5 19.3 - - + +
110H PRO 3.2 7.8 + - - +
111H ASP* 3.1 26.5 + - - +
113H LEU* 1.3 76.4 - - - +
115H ARG* 1.3 59.3 + - + +
118H ALA* 3.2 24.2 + - - +
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Residues in contact with ARG 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PRO* 5.7 6.9 - - - +
10H THR* 4.7 25.6 + - + -
11H LEU* 6.0 0.7 - - - +
69H PHE* 5.1 7.9 - - + -
111H ASP* 3.7 25.7 + - - +
112H ILE* 3.5 9.4 + - + +
113H LEU 3.1 0.4 - - - -
114H MET* 1.3 82.7 - - - +
116H LEU* 1.3 65.7 - - - +
118H ALA* 3.3 18.6 + - - +
119H GLN* 3.8 13.3 + - - +
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU* 4.4 10.1 - - + -
69H PHE* 3.4 47.1 - - + -
72H GLU* 3.7 35.2 - - + +
75H LEU* 3.6 31.0 - - + -
76H PHE* 5.3 3.1 - - + -
102H PHE* 4.7 7.6 - - + -
112H ILE* 3.8 8.1 + - + +
113H LEU* 3.5 14.0 + - + +
115H ARG* 1.3 75.2 - - - +
117H SER* 1.3 60.5 + - - +
118H ALA 3.0 8.5 + - - -
119H GLN* 3.4 13.2 + - + +
120H MET* 3.6 12.8 + - + +
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Residues in contact with SER 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G PHE* 3.1 42.8 - - - -
117G SER* 3.5 25.3 + - - -
120G MET* 4.2 3.9 - - - +
76H PHE* 3.6 15.9 - - - -
113H LEU* 3.3 19.2 + - - +
116H LEU* 1.3 74.0 - - - +
118H ALA* 1.3 61.2 - - - +
119H GLN 3.4 0.7 - - - -
120H MET* 3.7 23.0 + - - +
121H ALA 4.2 0.5 + - - -
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Residues in contact with ALA 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G PHE* 3.6 25.0 - - + +
77G GLU* 5.5 6.5 - - + +
80G GLN* 5.7 1.9 + - - -
114H MET 3.2 21.7 + - - +
115H ARG* 3.3 13.7 + - - +
116H LEU 3.0 0.8 - - - -
117H SER* 1.3 79.1 - - - +
119H GLN* 1.3 61.8 + - + +
120H MET 3.7 0.3 + - - -
121H ALA* 3.9 13.5 + - - +
122H ARG* 4.6 2.9 + - - +
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Residues in contact with GLN 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 5.7 0.2 - - - -
67H GLY 3.1 24.9 + - - +
68H ASP* 3.6 13.2 + - - +
69H PHE* 3.3 34.3 - - + -
115H ARG 4.1 10.1 + - - +
116H LEU* 3.4 6.6 + - + +
117H SER 3.4 0.2 - - - -
118H ALA* 1.3 77.4 - - + +
120H MET* 1.3 59.7 + - - +
121H ALA 3.1 6.2 + - - -
122H ARG* 3.7 7.7 + - - +
123H ARG* 3.2 41.8 + - - +
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Residues in contact with MET 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G SER 4.9 0.4 - - - +
120G MET* 4.1 25.6 - - + +
121G ALA* 3.9 17.5 - - - +
124G LEU* 4.7 12.4 - - + +
72H GLU* 4.3 21.3 - - + +
73H LEU* 3.7 28.7 - - + -
76H PHE* 3.5 34.8 - - + -
116H LEU* 3.6 14.1 - - - +
117H SER* 3.9 20.0 - - - +
118H ALA 3.3 1.0 - - - -
119H GLN* 1.3 78.1 - - + +
121H ALA* 1.3 61.0 + - - +
123H ARG* 4.2 13.8 - - - +
124H LEU* 3.9 16.6 + - - +
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LEU* 3.7 44.9 - - + +
76G PHE* 4.5 7.4 - - + -
80G GLN* 5.0 6.5 - - - +
120G MET* 4.3 5.8 - - + -
117H SER 4.2 1.2 + - - -
118H ALA 3.9 11.4 + - - +
119H GLN 3.1 0.6 - - - -
120H MET* 1.3 78.6 - - - +
122H ARG* 1.3 64.5 + - - +
123H ARG 3.3 0.2 - - - -
124H LEU* 3.3 9.9 + - - +
125H GLN* 3.3 25.1 + - - +
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Residues in contact with ARG 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G GLU* 4.1 21.2 + - - +
80G GLN* 4.1 21.3 - - - +
118H ALA 4.6 2.8 + - - +
119H GLN* 3.7 11.0 + - - +
121H ALA* 1.3 74.4 - - - +
123H ARG* 1.3 62.4 + - + +
124H LEU 3.1 6.0 + - - -
125H GLN* 3.0 34.9 + - - +
126H VAL* 3.4 32.6 + - + +
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Residues in contact with ARG 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 3.3 24.8 - - + +
62H SER* 5.3 5.4 + - - +
64H LEU* 3.5 15.7 - - + +
68H ASP* 3.3 34.6 + - - +
69H PHE* 3.4 19.4 + - - +
72H GLU* 2.9 32.3 + - - -
119H GLN* 3.2 35.1 + - - +
120H MET* 4.4 9.5 - - - +
121H ALA 3.3 0.8 - - - -
122H ARG* 1.3 77.4 - - + +
124H LEU* 1.3 57.2 + - - +
126H VAL* 3.9 9.7 - - - +
127H THR* 3.0 22.2 + - - -
680H CMP 3.6 33.1 + - + +
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Residues in contact with LEU 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 4.9 6.7 - - - +
73G LEU* 4.0 27.8 - - + -
83G SER* 5.4 0.3 - - - -
120G MET* 5.3 7.2 - - + +
123G ARG* 3.9 26.7 - - + +
124G LEU* 3.9 16.2 - - + +
127G THR* 3.7 29.4 - - + +
679G CMP 5.0 15.9 - - + +
120H MET 3.9 10.7 + - - +
121H ALA 3.3 10.0 + - - +
122H ARG 3.1 0.6 - - - -
123H ARG* 1.3 79.1 - - - +
125H GLN* 1.3 59.0 + - - +
126H VAL 3.4 0.4 - - - -
127H THR* 3.9 2.4 - - - -
128H SER* 3.0 42.4 + - - +
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Residues in contact with GLN 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LEU* 3.6 29.9 - - + +
80G GLN* 3.6 27.0 + - - +
81G GLU 4.3 10.4 + - - +
83G SER* 3.8 20.2 - - - -
679G CMP 3.9 5.1 + - - -
121H ALA 3.3 17.2 + - - +
122H ARG* 3.0 37.3 + - - +
124H LEU* 1.3 75.6 - - - +
126H VAL* 1.3 60.0 + - + +
127H THR 3.1 6.1 + - - -
128H SER* 5.0 0.4 - - - -
129H GLU* 3.4 35.8 + - - +
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Residues in contact with VAL 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H SER* 5.0 10.1 - - - +
122H ARG* 3.4 34.8 - - + +
123H ARG* 3.9 15.0 - - - +
125H GLN* 1.3 77.6 - - + +
127H THR* 1.3 61.8 + - - +
129H GLU* 4.6 1.6 - - - -
130H LYS* 3.5 18.4 - - - +
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Residues in contact with THR 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 5.5 1.1 - - + -
127G THR* 3.7 29.2 - - + +
128G SER* 4.1 20.1 + - - +
131G VAL* 4.1 10.0 - - + +
61H LEU* 5.2 7.3 + - + +
62H SER* 5.2 2.9 - - - -
123H ARG 3.0 22.4 + - - -
124H LEU* 3.6 5.3 + - - -
125H GLN 3.1 0.2 - - - -
126H VAL* 1.3 83.6 + - - +
128H SER* 1.3 64.0 + - - +
129H GLU 3.3 1.6 - - - -
130H LYS* 3.4 10.8 + - + +
131H VAL* 3.3 18.4 + - - +
680H CMP 4.9 5.2 + - - -
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Residues in contact with SER 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 3.5 21.9 - - - +
61G LEU* 4.8 7.7 - - - +
83G SER* 5.2 2.9 - - - -
84G ALA* 4.8 8.1 - - - -
127G THR* 3.5 19.7 - - - +
679G CMP 3.5 31.1 + - - -
124H LEU* 3.0 22.7 + - - +
125H GLN* 4.6 3.1 - - - -
127H THR* 1.3 79.1 - - - +
129H GLU* 1.3 63.0 + - - +
130H LYS 3.2 0.9 + - - -
131H VAL* 3.8 10.2 + - - +
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLN* 3.7 17.3 + - - +
51G ILE* 4.6 8.5 - - + +
82G ARG 4.1 2.6 - - - +
83G SER* 2.8 44.4 - - - +
84G ALA* 5.6 0.4 - - + -
125H GLN* 3.4 22.4 + - - +
126H VAL* 5.2 1.3 - - - -
127H THR 3.3 0.2 - - - -
128H SER* 1.3 77.1 - - - +
130H LYS* 1.3 60.2 + - - +
131H VAL 3.5 0.4 - - - -
132H GLY* 4.3 4.1 + - - -
133H ASN* 3.8 20.3 + - - +
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Residues in contact with LYS 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G VAL* 5.6 4.9 - - + -
126H VAL 3.5 21.4 + - - +
127H THR* 3.4 9.1 + - - +
128H SER 3.2 1.0 - - - -
129H GLU* 1.3 77.8 - - - +
131H VAL* 1.3 66.1 + - + +
132H GLY 3.2 2.0 - - - -
133H ASN* 3.2 21.5 + - + +
134H LEU* 3.2 36.7 + - + +
142H ARG* 4.1 9.9 + - - +
145H GLN* 5.1 5.3 - - - +
146H THR* 3.8 20.6 + - - +
149H ASN* 4.9 13.9 - - - +
175H ILE* 3.3 36.7 + - + +
176H VAL* 4.8 1.0 - - - +
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Residues in contact with VAL 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G MET* 4.7 10.9 - - + +
61G LEU* 3.6 32.8 - - + -
127G THR* 4.7 7.0 - - + +
130G LYS* 4.7 7.9 - - + +
131G VAL* 3.6 24.5 - - + +
134G LEU* 3.7 24.9 - - + -
127H THR 3.3 16.6 - - - +
128H SER* 4.1 6.1 - - - +
129H GLU 3.5 0.4 - - - -
130H LYS* 1.3 77.8 - - - +
132H GLY* 1.3 61.3 + - - +
134H LEU* 3.0 27.2 + - - +
135H ALA* 3.9 4.3 + - - +
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Residues in contact with GLY 132 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 3.5 29.9 - - - +
53G ASP* 6.5 0.2 - - - -
59G MET* 5.4 4.0 - - - -
129H GLU 4.3 1.5 + - - -
130H LYS 3.2 1.0 - - - -
131H VAL* 1.3 78.8 - - - +
133H ASN* 1.3 66.2 + - - +
134H LEU 3.3 0.9 + - - -
135H ALA* 3.6 3.3 + - - +
136H PHE* 3.1 36.6 + - - +
137H LEU* 4.5 0.5 - - - +
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Residues in contact with ASN 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H GLU 3.8 16.7 + - - +
130H LYS* 3.2 24.2 + - + +
132H GLY* 1.3 79.6 - - - +
134H LEU* 1.3 59.7 + - + +
135H ALA 3.3 3.9 + - - -
137H LEU* 3.4 42.9 + - + +
142H ARG* 3.2 24.5 - - + +
145H GLN* 5.1 9.2 - - + +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G VAL* 3.8 28.9 - - + +
134G LEU* 4.1 26.2 - - + +
130H LYS* 3.2 32.1 - - + +
131H VAL* 3.0 12.8 + - - +
133H ASN* 1.3 79.1 - - - +
135H ALA* 1.3 59.3 + - - +
137H LEU 5.3 0.2 - - - -
142H ARG* 3.6 22.8 + - + +
175H ILE 3.3 25.6 - - - +
176H VAL* 3.2 32.8 - - - +
177H GLY* 4.6 4.7 - - - +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G MET* 5.1 8.7 - - + -
134G LEU* 5.1 6.7 - - + -
177G GLY* 5.0 22.9 - - - +
131H VAL 4.2 5.4 - - - +
132H GLY* 3.6 3.8 + - - +
133H ASN 3.3 1.2 + - - -
134H LEU* 1.3 78.8 - - - +
136H PHE* 1.3 86.4 + - + +
137H LEU 4.5 2.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 5.7 1.8 - - + -
52G LYS 5.7 0.7 - - - -
53G ASP* 3.0 39.5 - - + +
54G GLU* 4.7 8.1 - - - +
55G GLU* 4.9 1.8 - - - +
57G LYS* 3.4 52.5 - - + -
58G GLU 4.5 5.4 - - - -
59G MET* 4.6 14.6 - - + -
132H GLY* 3.1 26.9 + - - -
135H ALA* 1.3 95.3 - - + +
137H LEU* 1.3 74.7 + - + +
138H ASP* 3.5 2.4 + - - +
----------------------------------------------------------
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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