Contacts of the helix formed by residues 112 - 135 (chain G) in PDB entry 4PKN
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 ASN 112 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO 5.1 1.0 + - - -
34A LYS* 3.2 45.4 - - + +
35A GLY 5.3 0.2 - - - +
36A ARG* 4.8 2.1 + - - +
110G GLY 3.8 1.4 + - - -
111G MET* 1.3 73.0 - - - +
113G PRO* 1.3 77.0 - - - +
114G MET* 3.5 11.9 + - - +
115G ASP* 3.1 35.3 + - + +
116G LEU* 3.1 21.6 + - - +
118G ARG* 4.8 2.6 - - - +
435G ASP* 3.5 19.8 + - - +
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Residues in contact with PRO 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.3 47.8 - - + +
13G ARG* 5.6 0.7 - - - +
107G VAL* 4.1 11.9 - - + -
111G MET 3.2 9.4 - - - +
112G ASN* 1.3 91.8 - - - +
114G MET* 1.3 58.0 + - - +
116G LEU* 2.8 31.8 + - + +
117G LYS* 3.0 11.8 + - - +
515G ILE* 3.5 24.7 - - + +
516G THR* 3.9 17.2 - - - +
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Residues in contact with MET 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 4.9 5.4 - - - +
35A GLY 4.4 17.0 - - - +
36A ARG* 5.9 2.9 - - + -
37A ASN* 4.4 12.1 - - - +
51A LYS* 5.7 3.1 - - + -
153A ASN* 3.7 26.0 - - - +
391A GLU* 4.9 8.3 - - - +
395A ARG* 4.8 16.8 - - - +
112G ASN* 3.3 11.4 + - - +
113G PRO* 1.3 79.4 - - - +
115G ASP* 1.3 58.8 + - - +
117G LYS* 3.7 22.6 + - + +
118G ARG* 3.3 48.1 + - + +
513G LEU* 6.0 1.1 - - + -
516G THR* 4.3 21.0 - - + +
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Residues in contact with ASP 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 4.6 7.3 - - - -
112G ASN* 3.1 31.3 + - - +
113G PRO 3.1 0.4 - - - -
114G MET* 1.3 78.3 - - - +
116G LEU* 1.3 64.3 + - - +
117G LYS 3.2 0.7 - - - -
118G ARG* 3.1 19.4 + - - +
119G GLY 3.0 18.5 + - - -
433G ASN* 3.5 21.5 + - - +
435G ASP* 3.8 16.1 - - + +
436G GLN* 3.0 37.0 + - + +
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G GLY* 4.0 4.5 - - - +
106G ALA* 3.9 17.9 - - + -
107G VAL* 3.7 31.6 - - + +
111G MET* 4.4 11.9 - - + -
112G ASN 3.1 15.4 + - - +
113G PRO* 2.8 9.0 + - + +
115G ASP* 1.3 73.1 - - - +
117G LYS* 1.3 66.4 + - - +
119G GLY 3.2 1.0 + - - -
120G ILE* 2.9 30.7 + - + +
435G ASP* 3.4 24.2 - - - +
438G VAL* 3.9 16.8 - - + -
439G GLY* 3.5 20.0 - - - +
442G VAL* 5.2 2.9 - - + -
515G ILE* 3.9 13.0 - - + -
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Residues in contact with LYS 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A GLU* 3.9 18.6 + - - -
391A GLU* 6.2 0.4 - - - -
395A ARG* 5.8 4.7 - - - +
113G PRO 3.0 10.8 + - - +
114G MET* 3.7 31.9 - - + +
116G LEU* 1.3 77.6 - - - +
118G ARG* 1.3 58.6 + - + +
120G ILE* 3.3 8.8 + - - +
121G ASP* 2.9 60.4 + - - +
509G SER* 4.1 8.3 + - - +
512G GLY* 3.7 27.3 - - - +
513G LEU* 4.0 36.2 - - + +
515G ILE* 4.4 1.2 - - - +
516G THR* 4.5 4.0 - - + -
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Residues in contact with ARG 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO 5.2 5.5 + - - -
153A ASN* 3.8 23.8 + - - +
154A SER* 4.3 14.5 + - - -
112G ASN* 4.8 2.0 - - - +
114G MET* 3.3 53.6 + - + +
115G ASP* 3.1 33.2 + - - +
117G LYS* 1.3 79.5 - - + +
119G GLY* 1.3 62.2 + - - +
121G ASP* 3.9 5.9 - - - +
122G LYS* 3.0 25.8 + - - +
432G GLN* 5.6 0.9 - - - -
436G GLN* 3.6 18.8 - - - +
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Residues in contact with GLY 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G ASP 3.0 12.0 + - - -
116G LEU 3.2 2.4 + - - -
118G ARG* 1.3 76.5 - - - +
120G ILE* 1.3 64.1 + - - +
122G LYS* 3.3 4.5 + - - +
123G ALA* 3.0 20.1 + - - +
436G GLN* 3.3 31.1 - - - +
440G ILE* 3.3 20.1 - - - +
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Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ILE* 3.7 31.6 - - + -
116G LEU* 2.9 21.7 + - + +
117G LYS* 3.6 4.0 - - - +
119G GLY* 1.3 76.1 - - - +
121G ASP* 1.3 67.9 + - - +
123G ALA* 3.1 4.2 + - - +
124G VAL* 2.9 22.5 + - - +
439G GLY* 3.4 22.1 - - - +
442G VAL* 4.3 12.3 - - + -
443G ALA* 4.3 14.8 - - + -
508G ALA* 4.2 26.7 - - + +
512G GLY* 4.7 7.4 - - - -
515G ILE* 4.0 22.9 - - + -
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Residues in contact with ASP 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU* 4.8 4.4 - - - +
117G LYS* 2.9 61.9 + - - +
118G ARG* 3.9 6.2 - - - +
120G ILE* 1.3 76.6 - - - +
122G LYS* 1.3 53.2 + - - +
124G VAL* 3.5 7.2 + - - +
125G THR* 2.6 39.1 + - - +
508G ALA* 4.0 16.8 - - - +
509G SER* 5.1 1.6 - - - -
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Residues in contact with LYS 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ARG 3.0 18.3 + - - +
119G GLY* 3.6 6.3 - - - +
121G ASP* 1.3 75.4 - - - +
123G ALA* 1.3 65.7 + - - +
125G THR* 3.3 7.7 + - - -
126G ALA* 3.0 23.4 + - + +
429G LEU* 4.0 21.1 - - + +
430G ARG 2.9 28.6 + - - +
431G GLY* 4.0 10.6 - - - -
432G GLN* 6.3 0.4 - - - +
436G GLN* 5.8 1.8 - - - +
440G ILE* 4.6 9.4 - - + -
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Residues in contact with ALA 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G GLY 3.0 17.1 + - - +
120G ILE 3.6 3.8 - - - +
122G LYS* 1.3 75.5 - - - +
124G VAL* 1.3 57.8 + - - +
126G ALA* 3.3 1.4 + - - +
127G ALA* 2.9 28.4 + - - +
426G LEU* 3.5 6.8 - - - +
429G LEU* 4.0 12.8 - - - +
440G ILE* 3.7 24.9 - - + +
443G ALA* 3.9 19.5 - - + -
444G LEU* 4.3 9.9 - - + -
447G MET* 6.1 0.9 - - - -
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ILE* 5.5 0.7 - - + -
120G ILE* 2.9 21.6 + - + +
121G ASP* 3.7 6.7 - - - +
123G ALA* 1.3 73.2 - - - +
125G THR* 1.3 69.9 + - - +
127G ALA* 2.9 14.8 + - - +
128G VAL* 3.0 19.1 + - + +
443G ALA* 4.7 9.0 - - + -
447G MET* 5.8 1.6 - - + -
504G LEU* 3.5 33.2 - - + -
505G GLN* 4.4 14.1 - - + +
508G ALA* 3.3 34.3 - - + -
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Residues in contact with THR 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ASP* 2.6 26.0 + - - +
122G LYS* 3.6 8.3 - - - -
124G VAL* 1.3 78.4 - - - +
126G ALA* 1.3 61.8 - - - +
128G VAL* 3.6 13.5 + - - +
129G GLU* 3.7 18.6 + - + +
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Residues in contact with ALA 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LYS* 3.0 13.4 + - + +
123G ALA 3.6 8.5 - - - +
125G THR* 1.3 77.0 - - - +
127G ALA* 1.3 63.9 + - - +
129G GLU* 3.0 12.7 + - - +
130G GLU* 3.0 22.2 + - - +
426G LEU* 4.0 18.8 - - + -
429G LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G ALA 2.9 16.3 + - - +
124G VAL* 2.9 9.5 + - - +
126G ALA* 1.3 76.4 - - - +
128G VAL* 1.3 58.0 + - - +
130G GLU* 3.3 3.4 + - - +
131G LEU* 2.9 33.9 + - + +
419G LEU* 5.9 0.4 - - + -
422G VAL* 3.7 13.4 - - + +
426G LEU* 3.8 9.6 - - + +
447G MET* 3.5 31.6 - - + -
504G LEU* 4.4 4.0 - - + -
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Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G VAL* 3.0 22.3 + - + +
125G THR* 3.8 9.6 - - - +
126G ALA 3.2 0.2 - - - -
127G ALA* 1.3 76.5 - - - +
129G GLU* 1.3 62.2 + - - +
131G LEU* 3.3 9.6 + - + +
132G LYS* 2.9 45.5 + - - +
501G ARG* 3.6 27.6 - - + +
504G LEU* 4.9 4.7 - - + -
505G GLN* 3.5 37.7 - - + +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G THR* 3.7 16.4 - - + +
126G ALA* 3.0 10.5 + - - +
128G VAL* 1.3 85.7 - - - +
130G GLU* 1.3 66.2 + - + +
132G LYS* 3.1 22.9 + - - +
133G ALA* 2.9 20.8 + - - +
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G ALA 3.0 14.9 + - - +
127G ALA 3.3 4.2 + - - +
129G GLU* 1.3 76.5 - - + +
131G LEU* 1.3 57.4 + - - +
133G ALA* 3.1 13.1 - - - +
134G LEU* 3.0 32.7 + - + +
422G VAL* 3.7 26.0 - - + -
425G LYS* 3.2 39.5 + - + +
426G LEU* 4.1 21.4 - - + +
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Residues in contact with LEU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ALA 2.9 16.8 + - - +
128G VAL* 3.4 11.7 - - + +
129G GLU 3.1 0.2 - - - -
130G GLU* 1.3 72.5 - - - +
132G LYS* 1.3 62.9 + - - +
133G ALA 2.9 4.6 + - - -
134G LEU* 3.0 5.4 + - + +
135G SER* 3.0 22.3 + - - -
412G VAL* 4.4 15.4 - - + +
418G ALA* 4.3 16.2 - - + -
419G LEU* 4.2 11.0 - - + -
422G VAL* 3.9 20.6 - - + -
497G THR* 4.2 11.8 - - + +
500G THR* 3.6 32.3 - - + -
501G ARG* 3.7 27.8 - - + +
504G LEU* 5.5 2.5 - - + -
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Residues in contact with LYS 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G VAL* 2.9 33.9 + - + +
129G GLU* 3.1 26.0 + - - +
131G LEU* 1.3 75.9 - - + +
133G ALA* 1.3 60.5 + - - +
135G SER* 3.7 18.3 + - - +
409G GLU* 4.0 22.3 + - + +
497G THR* 4.9 6.3 - - + +
501G ARG* 4.4 13.3 - - + +
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Residues in contact with ALA 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G GLU 2.9 12.6 + - - +
130G GLU* 3.1 24.2 - - - +
131G LEU 2.9 0.2 - - - -
132G LYS* 1.3 78.3 - - - +
134G LEU* 1.3 66.7 + - + +
135G SER 3.2 5.9 + - - +
425G LYS* 5.3 2.2 - - - +
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G GLU* 3.0 25.6 + - - +
131G LEU* 3.0 6.7 + - + +
133G ALA* 1.3 76.5 - - - +
135G SER* 1.3 63.5 + - - +
136G VAL* 3.3 8.3 + - - +
411G VAL 4.2 3.3 - - - +
412G VAL* 3.7 29.3 - - + +
413G ALA* 5.5 1.6 - - + +
418G ALA* 4.7 7.4 - - - +
421G ARG* 4.5 26.0 - - + -
422G VAL* 4.8 8.3 - - + -
425G LYS* 3.3 34.3 - - + +
474G GLY* 5.7 2.0 - - - +
475G ASN* 5.1 9.0 - - - +
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Residues in contact with SER 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU 3.0 14.1 + - - -
132G LYS* 3.8 13.2 - - - +
133G ALA 3.1 7.8 - - - +
134G LEU* 1.3 77.9 - - - +
136G VAL* 1.3 61.7 + - - +
137G PRO* 4.5 2.6 - - - +
409G GLU 3.1 18.4 + - - -
410G GLY* 3.6 6.1 - - - -
411G VAL 3.4 8.3 - - - -
412G VAL* 4.7 0.9 - - - +
497G THR* 3.1 28.6 + - - -
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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) + - + + + + + -
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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