Contacts of the helix formed by residues 54 - 76 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ALA 3.7 4.3 - - - +
53E ALA* 1.3 86.2 - - - +
55E LYS* 1.3 63.1 + - - +
56E GLU* 3.7 16.8 + - - +
57E LYS* 3.3 35.4 + - - +
58E LEU* 3.5 16.3 + - - +
97E TRP* 4.5 1.3 - - - -
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Residues in contact with LYS 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ALA 3.7 0.4 + - - -
54E SER* 1.3 71.9 - - - +
56E GLU* 1.3 80.9 + - - +
58E LEU* 3.4 5.0 - - + +
59E ILE* 3.1 41.7 + - + +
96E SER* 5.6 0.9 + - - +
97E TRP* 3.4 70.4 - - + +
100E GLU* 3.1 38.4 + - + +
101E VAL* 6.5 0.4 - - + -
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Residues in contact with GLU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER* 3.2 17.6 - - - +
55E LYS* 1.3 99.3 + - - +
57E LYS* 1.3 55.9 + - + +
59E ILE* 3.0 16.6 + - + +
60E LYS* 2.8 35.3 + - - +
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E GLU* 4.4 7.2 - - + +
51E ALA* 3.5 18.1 - - - +
53E ALA* 4.4 19.8 - - + +
54E SER* 3.3 24.8 + - - +
55E LYS 3.5 0.2 - - - -
56E GLU* 1.3 77.0 - - + +
58E LEU* 1.3 56.4 + - - +
60E LYS* 3.7 6.8 + - - +
61E GLU* 3.2 27.0 + - - +
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Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PRO* 4.1 24.9 - - + -
51E ALA 3.1 29.8 + - - +
52E GLY* 3.8 9.9 - - - -
54E SER 3.5 4.8 + - - +
55E LYS* 3.4 10.1 - - + +
56E GLU 3.1 0.2 - - - -
57E LYS* 1.3 73.2 - - - +
59E ILE* 1.3 66.5 + - - +
61E GLU* 3.2 5.6 + - - +
62E TYR* 3.0 39.4 + - + -
88E VAL* 4.4 7.9 - - + -
90E GLN* 4.3 7.4 - - + +
91E MET* 3.7 23.1 - - + -
97E TRP* 3.7 31.6 - - + -
101E VAL* 4.9 5.6 - - + -
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Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E LYS* 3.1 45.9 + - + +
56E GLU* 3.0 15.0 + - + +
58E LEU* 1.3 78.6 - - - +
60E LYS* 1.3 57.6 + - - +
62E TYR* 3.1 9.5 + - - +
63E GLU* 3.0 44.2 + - - +
97E TRP 5.3 0.2 - - - +
100E GLU* 4.1 15.9 - - + +
101E VAL* 4.6 24.4 - - + +
104E ALA* 4.1 13.5 - - + +
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Residues in contact with LYS 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLU 2.8 17.5 + - - +
57E LYS* 4.0 7.9 - - - +
59E ILE* 1.3 69.9 - - + +
61E GLU* 1.3 61.5 + - - +
63E GLU* 3.1 28.2 + - + +
64E ARG* 2.9 47.6 + - - +
257H LYS* 3.2 27.9 + - - +
258H HIS* 2.7 37.4 + - - -
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E PRO* 3.5 26.0 - - + -
48E ARG* 2.9 61.9 + - - +
51E ALA* 3.6 14.6 - - + +
57E LYS 3.2 12.9 + - - +
58E LEU* 3.3 9.9 - - - +
60E LYS* 1.3 78.2 - - - +
62E TYR* 1.3 56.9 + - + +
64E ARG* 3.4 10.5 + - - +
65E ILE* 3.1 36.2 + - + +
317E TYR* 3.6 13.8 - - - -
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Residues in contact with TYR 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E TYR* 4.0 22.8 + + - -
47E PRO* 3.4 29.7 - - + +
58E LEU* 3.0 39.4 + - + -
59E ILE* 3.1 7.1 + - - +
61E GLU* 1.3 73.9 - - + +
63E GLU* 1.3 56.7 + - - +
65E ILE* 3.4 18.0 + - + +
66E THR* 2.7 38.0 + - - -
85E THR* 3.7 20.4 - - + +
86E GLU 4.2 7.4 + - - -
88E VAL* 4.5 1.6 - - - +
91E MET* 3.5 33.5 - - - -
101E VAL* 3.5 33.0 - - + +
104E ALA* 5.8 0.7 - - + -
105E GLN* 4.3 12.5 - - + +
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Residues in contact with GLU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE* 3.0 26.2 + - - +
60E LYS* 3.4 38.4 + - + +
62E TYR* 1.3 76.9 - - - +
64E ARG* 1.3 55.0 + - - +
66E THR* 3.5 1.1 + - - -
67E THR* 2.7 38.5 + - - +
104E ALA* 3.9 24.3 - - + +
108E ILE* 3.7 26.8 - - + +
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ARG* 4.4 8.1 - - - +
60E LYS* 2.9 34.7 + - + +
61E GLU* 3.6 23.6 - - - +
62E TYR 3.3 0.2 - - - -
63E GLU* 1.3 76.2 - - - +
65E ILE* 1.3 62.8 + - - +
67E THR* 3.9 4.0 - - - -
68E ASP* 3.0 30.8 + - - +
317E TYR* 3.6 23.1 + - + +
215H ASN* 5.1 1.6 - - - +
216H GLN* 3.1 27.7 - - - +
217H ASP* 3.2 32.5 + - - -
257H LYS 5.3 0.2 - - - -
258H HIS* 2.9 35.1 + - - +
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Residues in contact with ILE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E TYR* 3.8 47.6 - - + -
46E ALA 4.8 0.2 - - - +
47E PRO* 4.7 5.4 - - + -
61E GLU* 3.1 25.2 + - + +
62E TYR* 3.6 27.4 - - + +
64E ARG* 1.3 76.1 - - - +
66E THR* 1.3 58.6 + - - +
68E ASP* 3.1 5.0 + - - +
69E VAL* 2.9 31.9 + - + +
83E LEU* 5.2 0.7 - - + -
105E GLN* 5.4 0.2 - - - +
317E TYR* 3.6 43.5 - - + -
326E VAL* 4.1 10.3 - - + +
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Residues in contact with THR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E TYR 2.7 21.8 + - - -
63E GLU* 3.9 4.7 - - - -
65E ILE* 1.3 72.1 - - - +
67E THR* 1.3 66.7 + - - +
69E VAL* 3.5 1.0 + - - +
70E MET* 3.1 33.0 + - + +
83E LEU* 4.0 17.7 - - + +
105E GLN* 3.2 52.0 + - - +
108E ILE* 4.1 11.9 - - + -
109E MET* 3.8 19.1 - - + -
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Residues in contact with THR 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLU 2.7 23.6 + - - -
64E ARG* 3.9 5.5 - - - -
66E THR* 1.3 75.4 - - - +
68E ASP* 1.3 63.8 + - - +
70E MET* 3.9 0.9 - - - +
71E GLU* 2.8 37.8 + - + +
108E ILE* 3.8 22.3 - - + +
112E TYR* 3.9 19.7 + - + +
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ARG* 3.0 17.5 + - - +
65E ILE 3.1 4.7 + - - +
67E THR* 1.3 82.0 - - - +
69E VAL* 1.3 62.3 + - - +
71E GLU* 3.7 1.1 - - - +
72E ARG* 3.1 17.3 + - - +
317E TYR* 2.6 34.8 + - - -
324E THR* 3.3 16.0 + - + -
326E VAL* 4.0 2.0 - - + -
327E GLN* 3.3 42.2 + - + +
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Residues in contact with VAL 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ILE* 3.8 33.2 - - + -
65E ILE* 2.9 27.5 + - + +
66E THR 3.9 0.4 - - - +
68E ASP* 1.3 71.9 - - - +
70E MET* 1.3 64.7 + - - +
72E ARG* 3.1 13.4 + - - +
73E MET* 3.2 18.8 + - + +
81E ILE* 3.9 22.0 - - + -
83E LEU* 3.9 21.8 - - + -
326E VAL* 3.8 26.7 - - + +
327E GLN* 5.0 0.9 - - - -
330E SER* 4.5 9.0 - - - +
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Residues in contact with MET 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E THR* 3.1 26.9 + - + +
69E VAL* 1.3 75.8 - - - +
71E GLU* 1.3 62.9 + - - +
73E MET* 3.3 6.0 + - - +
74E VAL* 3.2 27.4 + - - +
81E ILE* 3.9 29.2 - - + -
83E LEU* 4.0 17.7 - - - -
109E MET* 4.5 10.5 - - - +
112E TYR* 3.5 50.7 - - + -
118E ILE* 3.8 24.0 - - + -
120E CYS* 4.3 13.5 - - - -
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Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E THR* 2.8 26.8 + - + +
68E ASP* 3.7 7.0 - - - +
70E MET* 1.3 73.9 - - - +
72E ARG* 1.3 61.6 + - - +
74E VAL* 3.4 7.6 - - - +
75E GLN* 3.1 55.0 + - + +
112E TYR* 2.6 34.6 + - - +
116E TYR* 5.1 3.6 + - - -
327E GLN* 4.6 7.6 - - - +
234G LEU* 4.9 3.5 - - - +
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Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ASP 3.1 12.8 + - - +
69E VAL 3.1 5.6 + - - +
71E GLU* 1.3 80.2 - - - +
73E MET* 1.3 63.5 + - - +
75E GLN* 3.3 6.5 + - - +
76E VAL* 3.2 27.5 + - + +
78E PHE* 4.5 0.8 - - + -
322E GLY 2.6 30.5 + - - -
323E GLY* 4.9 0.4 - - - -
327E GLN* 3.1 72.7 + - + +
328E CYS* 4.7 1.4 - - - +
330E SER* 4.7 5.2 - - - +
331E GLU* 2.8 31.4 + - + +
292G THR* 4.7 6.1 + - - -
295G HIS 4.7 0.2 - - - -
296G SER* 3.6 25.5 - - - +
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Residues in contact with MET 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PRO* 4.0 3.1 - - + -
69E VAL* 3.2 15.9 + - + +
70E MET* 3.7 4.5 - - - +
71E GLU 3.3 0.2 - - - -
72E ARG* 1.3 79.4 - - - +
74E VAL* 1.3 58.2 + - - +
76E VAL 3.8 0.3 - - - -
77E GLY 3.1 8.7 + - - -
78E PHE* 3.0 47.3 + - + -
80E ALA 3.3 25.8 - - - +
81E ILE* 3.4 30.3 - - + -
118E ILE* 3.6 19.3 - - + -
330E SER* 4.1 24.7 - - - +
331E GLU* 5.1 0.7 - - - -
334E ALA* 3.5 27.1 - - + -
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Residues in contact with VAL 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E MET 3.2 12.7 + - - +
71E GLU* 3.4 19.7 - - - +
73E MET* 1.3 76.1 - - - +
75E GLN* 1.3 61.9 + - + +
77E GLY* 3.5 2.9 + - - -
112E TYR* 4.3 8.1 - - + -
116E TYR* 3.9 40.4 - - + +
118E ILE* 4.1 19.5 - - + -
233G LEU* 4.2 5.5 - - - +
234G LEU* 3.6 28.5 - - + +
16H TYR* 3.4 33.6 - - + +
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLU* 3.1 49.6 + - + +
72E ARG* 3.7 11.4 - - - +
73E MET 3.2 0.6 - - - -
74E VAL* 1.3 79.8 - - - +
76E VAL* 1.3 61.8 + - + +
77E GLY 3.3 0.9 - - - -
232G GLY* 3.1 24.6 + - - -
233G LEU* 2.8 32.2 + - - +
234G LEU* 3.0 45.5 + - + +
235G ASN* 3.8 13.9 + - - +
296G SER* 6.0 0.4 - - - +
298G VAL* 5.5 0.9 - - - +
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ARG* 3.2 19.2 + - - +
75E GLN* 1.3 81.4 - - + +
77E GLY* 1.3 56.3 + - - +
78E PHE* 3.4 29.1 + - + -
331E GLU* 3.6 12.6 - - - +
335E TYR* 3.1 29.6 - - + +
233G LEU* 3.7 5.6 - - - -
296G SER* 3.5 24.2 - - - +
297G ASP 3.6 8.1 - - - +
298G VAL* 4.6 5.4 - - + -
363G ARG* 3.2 28.4 + - - +
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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) + - + + + + + -
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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