Contacts of the helix formed by residues 54 - 77 (chain O) in PDB entry 2I2X
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 SER 54 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51O ALA 3.7 1.6 - - - +
52O GLY 3.3 2.0 + - - -
53O ALA* 1.3 80.3 - - - +
55O LYS* 1.3 64.6 + - - +
56O GLU* 3.6 15.7 + - - +
57O LYS* 3.3 29.7 + - - +
58O LEU* 3.1 23.4 + - - +
97O TRP* 4.0 12.5 - - - -
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Residues in contact with LYS 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O SER* 1.3 73.0 - - - +
56O GLU* 1.3 76.1 + - - +
58O LEU* 3.5 4.0 + - + +
59O ILE* 3.0 44.0 + - + +
96O SER* 5.1 2.6 + - - +
97O TRP* 3.5 72.0 - - + +
100O GLU* 3.4 37.8 + - - +
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Residues in contact with GLU 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O SER* 3.6 18.0 + - - +
55O LYS* 1.3 96.0 + - - +
57O LYS* 1.3 59.6 + - + +
59O ILE* 3.4 10.1 + - + +
60O LYS* 3.0 29.0 + - - +
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Residues in contact with LYS 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O GLU* 4.2 7.4 - - - +
51O ALA* 3.5 18.4 - - - +
53O ALA* 3.9 28.4 - - + +
54O SER* 3.3 20.0 + - - +
56O GLU* 1.3 78.1 - - - +
58O LEU* 1.3 57.5 + - - +
60O LYS* 3.4 8.6 - - - +
61O GLU* 3.0 26.3 + - - +
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Residues in contact with LEU 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O PRO* 4.0 29.2 - - + -
51O ALA 3.1 25.4 + - - +
52O GLY* 4.0 5.4 - - - -
54O SER 3.1 11.8 + - - +
55O LYS* 3.6 5.2 - - + +
57O LYS* 1.3 74.9 - - - +
59O ILE* 1.3 65.0 + - - +
61O GLU* 3.3 4.7 + - - +
62O TYR* 3.1 40.9 + - + -
88O VAL* 4.0 14.4 - - + -
90O GLN* 4.3 5.4 - - + +
91O MET* 3.9 26.2 - - + -
97O TRP* 4.0 24.2 - - + -
101O VAL* 5.0 3.8 - - + -
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Residues in contact with ILE 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O LYS* 3.0 33.5 + - + +
56O GLU* 3.7 9.9 - - + +
58O LEU* 1.3 74.5 - - - +
60O LYS* 1.3 65.5 + - - +
62O TYR* 3.2 4.9 + - - +
63O GLU* 2.9 33.5 + - - +
100O GLU* 3.7 33.9 - - + +
101O VAL* 4.1 27.8 - - + +
104O ALA* 3.8 24.6 - - + +
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Residues in contact with LYS 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N LYS* 3.4 41.4 + - - +
258N HIS* 3.2 39.8 + - - -
56O GLU 3.0 15.1 + - - +
57O LYS* 3.4 12.8 - - - +
59O ILE* 1.3 75.8 - - - +
61O GLU* 1.3 62.4 + - - +
63O GLU* 3.1 33.3 + - - +
64O ARG* 3.2 32.8 + - - +
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Residues in contact with GLU 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O PRO* 3.6 23.5 - - + +
48O ARG* 2.8 61.5 + - - +
51O ALA* 3.7 17.7 - - + +
57O LYS 3.0 14.0 + - - +
58O LEU* 3.4 9.2 - - - +
59O ILE 3.3 0.2 - - - -
60O LYS* 1.3 75.6 - - - +
62O TYR* 1.3 58.0 + - - +
64O ARG* 3.1 14.4 + - - +
65O ILE* 3.0 36.3 + - + +
317O TYR* 3.7 12.8 - - - -
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Residues in contact with TYR 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O TYR* 3.7 30.2 + + - -
47O PRO* 3.3 29.8 - - + +
58O LEU* 3.1 37.1 + - + -
59O ILE 3.8 5.8 - - - +
61O GLU* 1.3 81.2 - - + +
63O GLU* 1.3 54.0 + - - +
65O ILE* 3.4 10.3 + - + +
66O THR* 2.7 38.4 + - - -
85O THR* 3.6 26.3 - - + +
86O GLU 3.9 8.8 + - - -
88O VAL* 4.6 1.7 + - - +
91O MET* 3.6 32.9 - - + -
101O VAL* 3.6 28.3 - - + -
104O ALA* 6.3 0.9 - - + -
105O GLN* 4.4 9.9 - - + -
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Residues in contact with GLU 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258N HIS* 6.1 0.2 - - - +
59O ILE* 2.9 24.1 + - - +
60O LYS* 3.3 37.4 + - + +
62O TYR* 1.3 76.9 - - - +
64O ARG* 1.3 57.8 + - + +
66O THR* 3.4 1.4 + - - -
67O THR* 2.8 35.9 + - - +
104O ALA* 3.8 26.6 - - + +
108O ILE* 3.4 24.6 - - + +
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Residues in contact with ARG 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216N GLN* 3.8 15.9 + - - +
217N ASP* 3.5 25.6 + - - -
257N LYS* 4.7 6.3 - - - +
258N HIS* 3.3 47.2 + - + +
48O ARG* 4.4 12.3 - - - +
60O LYS* 3.4 33.7 - - - +
61O GLU* 3.1 14.2 + - - +
63O GLU* 1.3 73.6 - - + +
65O ILE* 1.3 60.5 + - - +
67O THR* 4.6 4.3 - - - -
68O ASP* 2.8 37.9 + - - +
317O TYR* 3.5 27.4 - - + +
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Residues in contact with ILE 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O TYR* 3.5 60.6 - - + -
47O PRO 4.7 5.8 - - - -
61O GLU* 3.0 25.6 + - + +
62O TYR* 3.5 24.2 - - + +
64O ARG* 1.3 78.3 - - - +
66O THR* 1.3 62.8 + - - +
68O ASP* 3.4 2.1 + - - +
69O VAL* 3.1 24.2 + - + +
317O TYR* 3.7 43.7 - - + -
326O VAL* 3.9 7.4 - - + +
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Residues in contact with THR 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62O TYR 2.7 22.7 + - - -
63O GLU 3.8 3.1 - - - -
65O ILE* 1.3 71.7 - - - +
67O THR* 1.3 62.5 + - - +
69O VAL* 3.4 1.7 + - - +
70O MET* 3.0 30.7 + - + +
83O LEU* 3.8 22.8 - - + +
105O GLN* 3.3 47.0 + - - +
108O ILE* 4.0 17.0 - - + -
109O MET* 3.8 15.3 - - + -
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Residues in contact with THR 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O GLU* 2.8 23.8 + - - +
64O ARG* 3.9 5.2 - - - -
66O THR* 1.3 74.7 - - - +
68O ASP* 1.3 68.8 + - - +
70O MET* 4.0 1.3 - - - -
71O GLU* 3.0 29.6 + - + +
108O ILE* 3.3 24.2 - - - +
112O TYR* 3.9 20.0 + - + +
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Residues in contact with ASP 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O ARG* 2.8 22.7 + - - +
65O ILE 3.7 3.8 - - - +
67O THR* 1.3 76.5 - - - +
69O VAL* 1.3 56.9 + - - +
71O GLU* 3.6 2.7 + - - +
72O ARG 3.0 22.2 + - - -
317O TYR* 2.6 24.2 + - - -
324O THR* 3.0 28.2 + - + +
326O VAL* 4.1 1.3 - - + -
327O GLN* 3.2 37.4 + - + +
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Residues in contact with VAL 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ILE* 3.9 16.8 - - + -
65O ILE* 3.1 21.3 + - + +
66O THR 3.8 2.9 - - - +
68O ASP* 1.3 72.6 - - - +
70O MET* 1.3 69.5 + - - +
72O ARG* 3.1 7.3 + - - +
73O MET* 3.0 25.7 + - + +
81O ILE* 3.6 33.4 - - + -
83O LEU* 4.1 15.7 - - + -
326O VAL* 3.5 34.1 - - + +
327O GLN* 5.1 0.2 - - - -
330O SER* 4.6 6.5 - - - +
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Residues in contact with MET 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O THR* 3.0 31.5 + - + +
67O THR 4.1 0.2 - - - +
69O VAL* 1.3 76.4 - - - +
71O GLU* 1.3 62.7 + - - +
73O MET* 3.3 4.5 + - - +
74O VAL* 3.2 27.9 + - - +
81O ILE* 3.7 25.6 - - + -
83O LEU* 4.1 16.2 - - - -
108O ILE* 4.6 2.0 - - + -
109O MET* 4.4 13.5 - - + +
112O TYR* 3.6 40.2 - - + -
118O ILE* 3.7 31.9 - - + -
120O CYS* 4.1 18.4 - - - -
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Residues in contact with GLU 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M LEU* 4.6 3.6 - - - +
67O THR* 3.0 20.9 + - + +
68O ASP* 3.7 5.8 - - - +
70O MET* 1.3 74.2 - - - +
72O ARG* 1.3 65.5 + - - +
74O VAL* 3.4 6.8 - - - +
75O GLN* 3.0 58.2 + - + +
112O TYR* 2.7 36.9 + - - +
116O TYR* 5.1 2.6 + - - -
327O GLN* 4.9 6.5 - - - +
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Residues in contact with ARG 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M THR* 4.6 3.2 + - - -
296M SER* 3.7 27.4 + - - +
68O ASP 3.0 18.7 + - - +
69O VAL 3.1 4.5 + - - +
71O GLU* 1.3 75.4 - - - +
73O MET* 1.3 65.9 + - - +
75O GLN* 3.1 16.1 + - - +
76O VAL* 3.2 18.8 + - + +
78O PHE* 5.8 0.7 - - + -
322O GLY 2.8 29.1 + - - -
323O GLY* 4.7 0.6 - - - -
327O GLN* 3.5 68.7 + - + +
328O CYS* 4.4 5.5 - - - +
330O SER* 4.4 6.7 - - - +
331O GLU* 3.1 28.2 + - + +
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Residues in contact with MET 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O PRO* 3.9 2.0 - - + -
69O VAL* 3.0 19.6 + - + +
70O MET* 3.6 5.2 - - - +
72O ARG* 1.3 77.1 - - - +
74O VAL* 1.3 62.5 + - - +
76O VAL 3.5 0.2 + - - -
77O GLY 3.1 4.0 + - - -
78O PHE* 3.0 64.1 + - + +
80O ALA 3.2 26.2 - - - +
81O ILE* 3.7 33.4 - - + -
118O ILE* 3.6 18.4 - - + -
330O SER* 4.3 21.5 - - - +
331O GLU 5.2 0.2 - - - -
334O ALA* 3.6 18.8 - - + -
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Residues in contact with VAL 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M LEU* 3.9 7.8 - - - +
234M LEU* 3.7 24.7 - - + +
16N TYR* 3.2 37.6 - - + +
70O MET 3.2 11.8 + - - +
71O GLU* 3.4 18.4 - - - +
73O MET* 1.3 77.7 - - - +
75O GLN* 1.3 64.2 + - - +
76O VAL 3.4 0.3 + - - -
77O GLY 3.5 2.3 + - - -
112O TYR* 4.2 5.6 - - + -
116O TYR* 3.8 41.5 - - + -
118O ILE* 4.2 17.0 - - + -
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Residues in contact with GLN 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M GLY* 3.1 30.7 - - - -
233M LEU* 2.7 32.8 + - - +
234M LEU* 3.1 34.7 + - + +
235M ASN* 3.4 17.2 + - - +
298M VAL* 5.1 1.4 - - - +
71O GLU* 3.0 51.2 + - + +
72O ARG* 3.1 12.6 + - - +
74O VAL* 1.3 77.9 - - - +
76O VAL* 1.3 62.7 + - + +
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Residues in contact with VAL 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232M GLY* 6.1 0.7 - - - -
233M LEU* 3.7 5.2 - - - -
296M SER* 3.5 12.1 - - - +
297M ASP 3.7 9.2 - - - +
298M VAL* 4.7 6.1 - - + -
363M ARG* 2.8 32.8 + - - +
72O ARG* 3.2 19.0 + - - +
75O GLN* 1.3 80.8 - - + +
77O GLY* 1.3 59.4 + - - +
78O PHE* 3.4 31.4 - - + -
331O GLU* 3.5 22.7 - - - +
335O TYR* 3.4 27.6 - - + +
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Residues in contact with GLY 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M LEU* 3.4 11.1 - - - +
363M ARG* 3.7 3.6 - - - -
13N LEU* 3.4 13.0 - - - +
14N THR 3.0 44.3 + - - -
16N TYR* 3.7 8.3 - - - -
73O MET 3.1 4.0 + - - -
74O VAL 3.5 1.6 + - - -
76O VAL* 1.3 80.4 - - - +
78O PHE* 1.3 63.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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