Contacts of the helix formed by residues 54 - 77 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ALA 3.5 5.7 - - - +
52A GLY 4.4 0.3 - - - -
53A ALA* 1.3 78.6 - - - +
55A LYS* 1.3 64.7 + - - +
56A GLU* 3.5 15.7 + - - +
57A LYS* 3.3 30.4 + - - +
58A LEU* 3.2 18.0 + - - +
97A TRP* 4.1 7.0 - - - -
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER* 1.3 73.1 - - - +
56A GLU* 1.3 82.0 + - - +
58A LEU* 3.3 3.2 + - + +
59A ILE* 3.0 41.1 + - + +
96A SER* 5.1 2.2 + - - -
97A TRP* 3.4 68.1 - - + +
100A GLU* 2.7 43.0 + - - +
101A VAL* 6.3 0.4 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 3.1 12.4 - - - +
55A LYS* 1.3 111.6 + - - +
57A LYS* 1.3 61.0 + - + +
59A ILE* 3.6 10.2 + - + +
60A LYS* 2.9 29.7 + - - +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU 4.3 6.0 + - - +
51A ALA* 3.6 20.8 - - - +
53A ALA* 3.9 25.5 - - + +
54A SER* 3.3 18.9 + - - +
56A GLU* 1.3 77.2 - - + +
58A LEU* 1.3 57.0 + - - +
60A LYS* 3.4 7.6 + - - +
61A GLU* 2.9 29.1 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.8 31.2 - - + -
51A ALA* 3.1 27.2 + - + +
52A GLY* 4.4 3.6 - - - +
54A SER 3.2 5.7 + - - +
55A LYS* 3.4 9.0 - - + +
56A GLU 3.3 0.2 - - - -
57A LYS* 1.3 74.1 - - - +
59A ILE* 1.3 65.7 + - + +
61A GLU* 3.2 3.5 + - - +
62A TYR* 3.1 42.6 + - + -
88A VAL* 4.0 14.1 - - + -
90A GLN* 4.3 4.9 - - + +
91A MET* 3.9 26.5 - - + -
97A TRP* 4.0 23.8 - - + -
101A VAL* 4.8 4.0 - - + -
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 3.0 38.2 + - + +
56A GLU* 3.8 9.9 - - + +
58A LEU* 1.3 74.6 - - + +
60A LYS* 1.3 59.2 + - - +
62A TYR* 3.4 3.7 + - - +
63A GLU* 2.9 37.2 + - - +
100A GLU* 3.8 33.2 - - + +
101A VAL* 4.0 27.8 - - + +
104A ALA* 3.9 23.1 - - + +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU 2.9 19.7 + - - +
57A LYS* 3.4 9.2 - - - +
58A LEU 3.1 0.2 - - - -
59A ILE* 1.3 74.2 - - - +
61A GLU* 1.3 65.6 + - - +
63A GLU* 3.1 25.4 + - + +
64A ARG* 3.0 46.6 + - - +
257D LYS* 3.9 25.7 + - - +
258D HIS* 3.2 44.0 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PRO* 3.6 22.8 - - + +
48A ARG* 2.7 66.1 + - - +
51A ALA* 3.7 15.1 - - + +
57A LYS 2.9 16.2 + - - +
58A LEU 3.2 5.6 + - - +
60A LYS* 1.3 74.7 - - - +
62A TYR* 1.3 59.0 + - - +
64A ARG* 3.0 15.9 + - - +
65A ILE* 2.9 34.4 + - + +
317A TYR* 3.6 15.0 - - + +
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Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.6 30.8 + + - -
47A PRO* 3.4 29.3 - - + +
58A LEU* 3.1 40.5 + - + +
59A ILE 3.8 3.8 - - - +
61A GLU* 1.3 74.1 - - + +
63A GLU* 1.3 57.7 + - + +
65A ILE* 3.3 9.5 + - + +
66A THR* 2.6 39.1 + - - -
85A THR* 3.5 26.4 - - + +
86A GLU 4.2 9.2 + - - -
88A VAL* 4.2 2.6 - - - +
91A MET* 3.5 33.1 - - + -
101A VAL* 3.4 28.9 - - + -
104A ALA* 6.3 0.4 - - + -
105A GLN* 4.3 9.4 - - + -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 2.9 26.2 + - - +
60A LYS* 3.1 29.5 + - + +
62A TYR* 1.3 74.9 - - - +
64A ARG* 1.3 64.1 + - + +
66A THR* 4.4 0.7 - - - -
67A THR* 3.0 30.1 + - - -
104A ALA* 3.8 30.1 - - + +
105A GLN* 5.9 0.4 - - - -
108A ILE* 3.8 25.2 - - + +
258D HIS 6.0 1.6 - - - +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 4.3 10.4 - - - +
60A LYS* 3.0 38.4 + - - +
61A GLU* 3.0 16.0 + - - +
63A GLU* 1.3 76.5 - - + +
65A ILE* 1.3 57.9 + - - +
67A THR* 3.5 3.4 + - - -
68A ASP* 2.9 37.3 + - - +
317A TYR* 3.5 27.1 - - + +
216D GLN* 4.0 23.4 + - - +
217D ASP* 3.6 32.9 + - - -
257D LYS* 5.7 0.4 - - - +
258D HIS* 3.0 34.6 + - - +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.6 55.6 - - + -
47A PRO 4.7 5.4 - - - -
61A GLU* 2.9 27.4 + - + +
62A TYR* 3.6 22.4 - - + +
63A GLU 3.3 0.2 - - - -
64A ARG* 1.3 75.7 - - - +
66A THR* 1.3 64.8 + - - +
68A ASP* 3.2 3.1 + - - +
69A VAL* 3.0 31.7 + - + +
83A LEU* 5.1 0.2 - - + -
317A TYR* 3.6 43.7 - - + -
326A VAL* 3.8 10.5 - - + -
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TYR 2.6 22.4 + - - -
63A GLU 3.9 2.7 - - - -
65A ILE* 1.3 74.1 - - - +
67A THR* 1.3 65.3 + - - +
68A ASP 3.4 0.2 + - - -
69A VAL* 3.4 1.0 + - - +
70A MET* 3.0 31.1 + - + +
83A LEU* 3.8 22.6 - - + +
105A GLN* 3.2 47.4 + - - +
108A ILE* 3.8 20.2 - - + -
109A MET* 4.0 12.3 - - + -
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.0 18.2 + - - +
64A ARG* 3.9 4.7 - - - -
66A THR* 1.3 77.7 - - - +
68A ASP* 1.3 69.2 + - - +
70A MET 4.0 0.2 - - - -
71A GLU* 3.0 26.6 + - + +
108A ILE* 3.6 25.2 - - - +
112A TYR* 4.1 17.5 + - + +
258D HIS 5.6 5.3 + - - +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 2.9 22.9 + - - +
65A ILE 3.2 4.7 + - - +
67A THR* 1.3 81.8 - - - +
69A VAL* 1.3 56.3 + - - +
71A GLU* 3.9 1.9 - - - +
72A ARG 3.1 17.5 + - - -
317A TYR* 2.4 24.9 + - - -
324A THR* 3.1 30.3 + - + +
326A VAL* 3.8 2.2 - - + -
327A GLN* 3.0 38.4 + - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 3.8 18.4 - - + -
65A ILE* 3.0 21.7 + - + +
66A THR 3.7 3.8 - - - +
68A ASP* 1.3 73.7 - - - +
70A MET* 1.3 67.8 + - - +
72A ARG* 3.2 3.6 + - - +
73A MET* 3.0 26.2 + - + +
81A ILE* 3.6 32.5 - - + -
83A LEU* 4.2 16.4 - - + -
326A VAL* 3.8 27.8 - - + +
327A GLN* 4.8 1.1 - - - -
330A SER* 4.6 11.7 - - - +
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 3.0 32.1 + - + +
67A THR 4.1 0.2 - - - +
69A VAL* 1.3 76.7 - - - +
71A GLU* 1.3 65.2 + - - +
73A MET* 3.2 4.4 + - - +
74A VAL* 3.2 25.8 + - - +
81A ILE* 4.1 9.0 - - + -
83A LEU* 3.8 27.1 - - + -
108A ILE* 4.4 2.9 - - + -
109A MET* 4.3 11.7 - - + +
112A TYR* 3.5 41.3 - - + -
118A ILE* 3.7 39.7 - - + -
120A CYS* 4.1 17.5 - - - -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR* 3.0 22.1 + - + +
68A ASP* 3.9 5.8 - - - +
70A MET* 1.3 78.6 - - - +
72A ARG* 1.3 63.9 + - - +
74A VAL* 3.2 6.5 + - - +
75A GLN* 3.0 55.0 + - + +
112A TYR* 2.8 34.9 + - - +
116A TYR* 4.7 5.4 + - - -
327A GLN* 4.8 6.1 - - - +
234C LEU* 5.1 1.6 - - - +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP 3.1 19.1 + - - +
69A VAL 3.2 4.2 + - - +
71A GLU* 1.3 77.1 - - - +
73A MET* 1.3 64.8 + - + +
75A GLN* 3.1 8.9 + - - +
76A VAL* 3.1 26.5 + - + +
78A PHE* 5.8 0.7 - - + -
322A GLY 3.2 27.5 + - - -
323A GLY* 4.6 0.8 - - - -
327A GLN* 3.6 63.2 + - + +
328A CYS* 4.1 7.3 - - - +
330A SER* 4.6 5.6 - - - +
331A GLU* 3.0 34.4 + - + +
292C THR* 4.3 4.2 + - - -
296C SER* 3.7 25.9 + - - +
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Residues in contact with MET 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO* 3.8 1.8 - - + -
69A VAL* 3.0 21.5 + - + +
70A MET* 3.2 4.0 + - - +
72A ARG* 1.3 78.6 - - - +
74A VAL* 1.3 58.5 + - - +
76A VAL* 3.4 0.9 + - - -
77A GLY 3.1 7.1 + - - -
78A PHE* 2.9 63.3 + - + +
80A ALA 3.2 27.4 - - - +
81A ILE* 3.5 33.0 - - + -
118A ILE* 3.6 18.8 - - + -
330A SER* 4.4 19.7 - - - +
331A GLU* 5.2 0.4 - - - -
334A ALA* 3.7 17.7 - - + -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MET 3.2 13.2 + - - +
71A GLU* 3.3 17.0 - - - +
73A MET* 1.3 74.4 - - - +
75A GLN* 1.3 64.2 + - - +
76A VAL 3.3 0.5 + - - -
77A GLY* 3.4 2.3 + - - -
112A TYR* 4.1 13.0 - - + -
116A TYR* 3.8 40.2 - - + +
118A ILE* 4.2 20.0 - - + -
233C LEU* 4.1 4.9 - - - +
234C LEU* 3.5 26.1 - - + +
16D TYR* 3.3 35.9 - - + +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.0 47.8 + - + +
72A ARG* 3.1 12.1 + - - +
74A VAL* 1.3 78.7 - - - +
76A VAL* 1.3 63.2 + - + +
232C GLY* 3.2 20.8 - - - -
233C LEU* 3.0 29.1 + - - +
234C LEU* 3.0 44.5 + - + +
235C ASN* 3.5 17.9 + - - +
298C VAL* 5.2 1.0 - - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG* 3.1 22.9 + - + +
75A GLN* 1.3 82.0 - - + +
77A GLY* 1.3 59.0 + - - +
78A PHE* 3.4 31.4 - - + -
331A GLU* 3.5 9.9 - - - +
335A TYR* 3.5 27.1 - - + +
233C LEU* 3.7 5.2 - - - -
296C SER* 3.4 24.9 - - - +
297C ASP 3.6 9.0 - - - +
298C VAL* 4.6 4.7 - - + +
363C ARG* 3.1 26.6 + - - +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET 3.1 2.6 + - - -
74A VAL 3.4 3.8 + - - -
75A GLN 3.4 0.2 - - - -
76A VAL* 1.3 80.9 - - - +
78A PHE* 1.3 64.5 + - - +
79A PRO 3.5 0.7 - - - -
233C LEU* 3.5 9.5 - - - +
363C ARG* 4.0 5.4 - - - -
13D LEU* 3.5 7.7 - - - +
14D THR 3.0 44.4 + - - -
16D TYR* 3.7 8.7 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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