Contacts of the helix formed by residues 108 - 139 (chain y) in PDB entry 3J45
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 GLU 108 (chain y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104y GLU* 3.2 29.9 + - + +
105y ILE* 3.3 13.5 + - - +
107y LYS* 1.4 74.4 - - + +
109y GLY* 1.3 68.3 + - - +
111y SER* 5.3 0.5 - - - -
112y GLY* 3.3 18.2 + - - -
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Residues in contact with GLY 109 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107y LYS 2.9 8.9 + - - -
108y GLU* 1.3 79.9 - - - +
110y GLU* 1.4 66.6 + - - +
111y SER* 3.4 1.3 - - - -
113y ARG* 3.4 33.0 + - - +
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Residues in contact with GLU 110 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109y GLY* 1.4 71.6 - - - -
111y SER* 1.3 57.3 + - - +
113y ARG* 3.2 37.6 + - - +
114y ARG* 3.0 65.8 + - - +
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Residues in contact with SER 111 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108y GLU 5.3 0.4 - - - -
109y GLY 5.3 0.2 - - - -
110y GLU* 1.3 72.6 - - - +
112y GLY* 1.3 59.3 + - - +
114y ARG* 3.5 20.8 + - - +
115y LYS* 2.9 35.3 + - - +
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Residues in contact with GLY 112 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105y ILE* 3.1 42.0 - - - +
108y GLU* 3.3 13.2 + - - -
110y GLU 3.3 0.6 - - - -
111y SER* 1.3 78.1 - - - +
113y ARG* 1.4 54.3 + - - +
115y LYS* 3.2 5.3 + - - -
116y ILE* 3.0 25.5 + - - +
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Residues in contact with ARG 113 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105y ILE 4.0 0.4 + - - -
106y LYS* 3.2 49.8 + - + +
107y LYS* 3.8 16.2 + - - +
109y GLY* 3.4 16.5 + - - +
110y GLU* 3.2 49.1 + - - +
112y GLY* 1.4 75.4 - - - +
114y ARG* 1.4 52.8 + - - +
116y ILE* 3.6 3.2 + - - +
117y SER* 3.2 26.2 + - - -
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Residues in contact with ARG 114 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G SER* 3.6 33.8 + - - +
34G PHE* 2.7 57.5 + - - +
36G ALA 5.8 0.2 - - - +
110y GLU* 3.0 46.9 + - - +
111y SER* 3.5 22.8 + - - +
113y ARG* 1.4 72.1 - - - +
115y LYS* 1.4 56.8 + - + +
117y SER* 3.2 8.9 + - - -
118y GLN* 2.9 37.0 + - - +
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Residues in contact with LYS 115 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G MET* 5.3 7.9 - - - +
105y ILE* 4.4 12.3 - - + -
111y SER* 2.9 23.4 + - - +
112y GLY* 3.2 5.8 + - - +
114y ARG* 1.4 68.7 - - + +
116y ILE* 1.4 59.5 + - - +
118y GLN* 2.3 49.1 + - - +
119y TYR* 3.0 62.2 + - + +
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Residues in contact with ILE 116 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92y ILE* 3.9 14.5 - - + +
93y GLN* 3.8 25.8 - - - +
96y THR* 4.1 11.9 - - + -
102y LEU* 3.9 40.4 - - + +
105y ILE* 4.1 8.1 - - + -
106y LYS* 4.0 29.2 - - + +
112y GLY 3.0 18.0 + - - +
113y ARG 3.9 5.6 - - - +
114y ARG 3.4 0.2 - - - -
115y LYS* 1.4 73.6 - - - +
117y SER* 1.3 61.9 + - - +
119y TYR* 3.2 18.5 + - + +
120y THR* 3.0 20.9 + - - +
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Residues in contact with SER 117 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G SER* 5.4 0.7 - - - -
36G ALA 4.1 2.8 + - - -
37G GLY* 3.3 27.7 - - - -
38G ALA* 3.5 8.4 + - - +
85y TYR* 5.4 0.9 + - - -
113y ARG 3.2 16.0 + - - -
114y ARG* 3.2 11.9 + - - -
116y ILE* 1.3 79.4 - - - +
118y GLN* 1.3 57.7 + - - +
120y THR* 3.6 9.0 - - - -
121y ARG* 3.1 44.9 + - - +
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Residues in contact with GLN 118 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G MET* 2.8 51.9 + - + +
31G GLY* 4.2 6.1 - - - -
33G SER* 4.0 8.2 + - - +
34G PHE* 6.4 0.2 - - - -
114y ARG* 2.9 25.1 + - - +
115y LYS* 2.3 64.2 + - - +
117y SER* 1.3 69.1 - - - +
119y TYR* 1.4 61.3 - - + +
120y THR 3.2 0.7 - - - -
121y ARG* 3.3 12.1 + - - +
122y TYR* 3.0 27.2 + - - +
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Residues in contact with TYR 119 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92y ILE* 5.1 12.8 - - + +
102y LEU* 4.1 27.6 - - + -
105y ILE* 4.9 16.5 - - + +
115y LYS* 3.0 53.2 + - + +
116y ILE* 3.2 17.0 + - + +
118y GLN* 1.4 75.0 - - + +
120y THR* 1.4 56.5 + - - +
122y TYR* 3.9 10.1 - + - +
123y GLY* 2.9 22.8 + - - -
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Residues in contact with THR 120 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ALA* 5.6 1.6 - - + -
85y TYR* 4.0 21.1 - - + +
88y ALA* 4.3 8.8 - - + +
89y SER* 4.0 30.4 - - - +
92y ILE* 3.8 25.3 - - - +
116y ILE* 3.0 14.8 + - - +
117y SER* 3.6 14.4 - - - -
119y TYR* 1.4 71.8 - - - +
121y ARG* 1.4 62.0 - - - +
123y GLY* 3.2 2.9 + - - -
124y THR* 2.9 31.4 + - - -
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Residues in contact with ARG 121 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASP* 2.4 61.8 + - - +
30G MET* 3.4 11.5 + - + +
32G ALA 4.9 0.7 - - - -
33G SER* 3.3 22.4 - - - -
36G ALA 4.6 2.4 + - - -
38G ALA 4.3 6.3 - - - +
85y TYR* 4.1 11.2 + - + +
117y SER* 3.1 32.6 + - - +
118y GLN* 3.3 13.3 + - - +
120y THR* 1.4 79.1 - - - +
122y TYR* 1.4 59.9 + - - +
124y THR* 3.3 11.6 + - - -
125y LEU* 3.4 15.7 + - - +
172y MET* 3.8 21.8 - - - +
176y GLU* 2.6 45.6 + - - +
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Residues in contact with TYR 122 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G MET* 4.5 20.7 - - + +
118y GLN 3.0 16.2 + - - +
119y TYR* 4.2 9.4 - + + +
121y ARG* 1.4 69.5 - - - +
123y GLY* 1.3 63.7 + - - +
125y LEU* 2.6 65.2 - - + +
126y VAL* 3.2 17.2 + - + +
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Residues in contact with GLY 123 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88y ALA* 5.1 3.4 - - - -
92y ILE* 6.1 3.1 - - - -
119y TYR 2.9 17.6 + - - -
120y THR* 3.2 8.0 + - - -
122y TYR* 1.3 76.9 - - - +
124y THR* 1.4 54.9 + - - +
126y VAL* 3.1 23.3 + - - +
127y LEU* 3.2 20.2 + - - +
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Residues in contact with THR 124 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84y PRO* 4.2 11.6 - - + +
85y TYR* 3.5 38.9 - - + +
88y ALA* 3.4 19.3 - - - +
120y THR 2.9 22.4 + - - -
121y ARG 3.6 7.0 - - - -
122y TYR 3.3 0.6 - - - -
123y GLY* 1.4 72.6 - - - +
125y LEU* 1.4 57.7 + - - +
127y LEU* 3.6 7.9 + - - +
128y ALA* 3.2 23.2 + - - +
168y THR* 4.5 10.9 - - + +
172y MET* 4.1 18.8 - - + -
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Residues in contact with LEU 125 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G LYS* 3.6 54.2 + - + +
30G MET* 5.3 4.3 - - - -
121y ARG 3.4 6.6 + - - +
122y TYR* 2.6 65.7 - - + +
124y THR* 1.4 79.5 - - - +
126y VAL* 1.3 87.7 + - + +
128y ALA* 3.4 7.6 + - - +
129y ILE* 3.1 32.4 + - + +
165y VAL* 5.9 0.4 - - + -
168y THR* 5.6 2.2 - - - -
172y MET* 5.5 3.3 - - + -
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Residues in contact with VAL 126 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122y TYR* 3.8 22.9 - - + +
123y GLY* 3.1 13.0 + - - +
125y LEU* 1.3 98.1 - - + +
127y LEU* 1.4 65.3 + - + +
129y ILE* 3.3 8.0 + - + +
130y PHE* 3.2 22.3 + - + +
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Residues in contact with LEU 127 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84y PRO* 3.9 24.7 - - + +
87y SER* 5.1 0.9 - - - -
88y ALA* 4.2 18.4 - - + +
123y GLY 3.2 12.6 + - - +
124y THR* 3.6 8.3 - - - +
126y VAL* 1.4 80.5 - - + +
128y ALA* 1.4 56.2 + - - +
130y PHE* 3.6 16.8 + - + +
131y GLN* 3.1 32.8 + - - +
286y PHE* 3.9 33.9 - - + -
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Residues in contact with ALA 128 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80y LEU* 3.4 20.8 - - + +
84y PRO* 5.6 0.9 - - + -
124y THR 3.2 12.1 + - - +
125y LEU* 3.6 10.8 - - - +
126y VAL 3.3 0.2 - - - -
127y LEU* 1.4 78.0 - - - +
129y ILE* 1.4 58.0 + - - +
131y GLN* 3.2 5.3 + - - +
132y SER* 2.8 32.7 + - - -
165y VAL* 4.5 11.9 - - + -
168y THR* 4.0 23.8 - - + -
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Residues in contact with ILE 129 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 5.3 0.4 - - + -
26G LYS* 3.9 18.4 - - - +
125y LEU* 3.1 22.2 + - + +
126y VAL* 3.3 8.9 + - + +
128y ALA* 1.4 75.4 - - - +
130y PHE* 1.3 54.5 + - - +
132y SER* 3.3 1.9 + - - -
133y ILE* 3.0 40.6 + - + +
161y VAL* 4.9 7.9 - - + -
165y VAL* 3.6 27.8 - - + -
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Residues in contact with PHE 130 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126y VAL* 3.2 13.3 + - + +
127y LEU* 3.7 20.2 - - + +
129y ILE* 1.3 70.2 - - - +
131y GLN* 1.3 64.6 - - - +
133y ILE* 3.7 8.7 + - + +
134y GLY* 3.2 19.2 + - - -
290y ILE* 3.7 40.8 - - + -
294y PHE* 4.3 17.8 - + - -
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Residues in contact with GLN 131 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64y PHE* 4.2 13.1 - - - -
80y LEU* 3.5 36.5 + - + +
84y PRO* 3.6 16.3 - - - +
127y LEU 3.1 20.8 + - - +
128y ALA* 3.5 7.1 - - - +
130y PHE* 1.3 76.4 - - - +
132y SER* 1.4 60.0 + - - +
134y GLY* 3.2 1.8 + - - +
135y ILE* 2.9 32.3 + - - +
286y PHE* 3.5 33.0 - - - -
290y ILE* 3.4 28.6 - - + +
293y TRP* 3.7 17.8 - - + -
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Residues in contact with SER 132 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80y LEU* 3.6 12.6 - - - +
128y ALA 2.8 17.7 + - - -
129y ILE 3.3 5.1 + - - -
131y GLN* 1.4 70.8 - - - +
133y ILE* 1.4 60.6 + - - +
135y ILE* 3.4 10.4 - - - +
136y ALA* 3.1 31.7 + - - +
160y ALA* 5.8 0.2 - - - +
161y VAL* 3.8 30.8 - - - +
164y LEU* 3.9 14.5 - - - +
165y VAL* 3.7 11.4 - - - +
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Residues in contact with ILE 133 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129y ILE* 3.0 29.4 + - + +
130y PHE* 3.9 9.2 - - + +
132y SER* 1.4 74.3 - - - +
134y GLY* 1.3 64.7 + - - +
136y ALA* 4.0 1.2 - - - +
137y THR* 3.1 36.1 + - - +
157y TYR* 5.9 5.4 - - + -
158y PHE* 6.5 0.4 - - - -
161y VAL* 4.2 21.3 - - + -
294y PHE* 5.3 6.2 - - + -
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Residues in contact with GLY 134 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130y PHE 3.2 6.8 + - - -
131y GLN* 3.2 6.8 + - - -
133y ILE* 1.3 75.4 - - - +
135y ILE* 1.4 63.6 + - - +
137y THR* 4.8 0.2 - - - -
138y GLY* 3.2 21.0 + - - -
293y TRP* 4.6 10.0 - - - +
294y PHE* 3.3 45.4 - - - -
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Residues in contact with ILE 135 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44y ILE* 6.2 2.9 - - + -
49y LEU* 5.5 7.0 - - + -
57y ARG* 5.3 2.0 + - - +
72y LEU* 3.9 18.8 - - + -
79y ALA* 5.9 1.6 - - + -
80y LEU* 5.0 5.6 - - + -
131y GLN 2.9 15.4 + - - +
132y SER* 3.4 17.3 - - - +
134y GLY* 1.4 75.2 - - - +
136y ALA* 1.3 69.3 + - + +
138y GLY* 3.5 0.3 + - - -
139y LEU* 3.3 50.4 + - + +
164y LEU* 4.2 17.3 - - + -
293y TRP* 3.7 49.5 - - + +
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Residues in contact with ALA 136 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44y ILE* 5.9 3.6 - - - -
132y SER 3.1 17.4 + - - +
133y ILE* 4.0 4.5 - - - +
135y ILE* 1.3 83.4 - - + +
137y THR* 1.4 59.5 + - - +
139y LEU* 4.1 7.3 + - - +
140y PRO* 3.5 10.7 - - - +
146y GLN* 5.9 0.2 - - - +
156y PHE* 4.8 5.4 - - + -
157y TYR* 3.1 48.7 - - + +
160y ALA* 4.5 10.8 - - + -
161y VAL* 4.6 1.3 - - + -
164y LEU* 6.4 0.4 - - + -
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Residues in contact with THR 137 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133y ILE* 3.1 23.4 + - - +
134y GLY 4.8 0.4 - - - -
136y ALA* 1.4 73.9 - - - +
138y GLY* 1.3 63.1 + - - +
139y LEU 3.5 0.4 - - - -
140y PRO* 3.7 1.1 - - - +
141y ASN* 3.0 48.8 + - - +
157y TYR* 3.7 32.0 - - + +
294y PHE* 6.2 2.9 - - - -
298y THR* 4.9 1.7 + - - +
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Residues in contact with GLY 138 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57y ARG* 4.2 7.0 - - - -
134y GLY 3.2 18.7 + - - -
135y ILE* 3.9 1.3 - - - -
136y ALA 3.5 0.6 - - - -
137y THR* 1.3 76.7 - - - +
139y LEU* 1.3 65.1 + - - +
140y PRO 3.7 0.2 - - - -
141y ASN* 4.1 2.4 + - - +
143y PRO* 3.7 8.3 - - - +
293y TRP 4.2 8.7 - - - -
294y PHE* 5.8 2.4 - - - -
297y GLY* 3.5 31.0 - - - -
298y THR 4.9 3.1 - - - -
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Residues in contact with LEU 139 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44y ILE* 3.9 28.0 - - + -
49y LEU* 3.9 23.3 - - + -
52y LEU* 3.7 21.0 - - + +
53y LEU* 5.0 0.9 - - + -
57y ARG* 3.6 31.4 - - - +
135y ILE* 3.3 31.6 + - + +
136y ALA* 4.8 3.8 - - - +
138y GLY* 1.3 75.9 - - - +
140y PRO* 1.4 60.6 - - + +
143y PRO* 3.3 23.0 - - - +
144y GLY* 3.6 9.4 + - - +
146y GLN* 3.7 19.7 - - + +
156y PHE* 6.5 0.4 - - + -
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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).
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