Contacts of the helix formed by residues 65 - 89 (chain D) in PDB entry 2IT0
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 THR 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D GLY* 2.9 31.8 + - - +
53D LEU 2.9 21.8 + - - -
54D LEU* 3.8 8.7 - - - +
55D ARG* 4.2 21.5 - - - +
64D LEU* 1.3 75.5 - - - +
66D GLU* 1.3 60.4 + - - +
67D LYS* 3.6 2.8 + - - -
68D GLY 2.9 11.6 + - - -
69D ARG* 2.9 26.9 + - - +
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D THR* 1.3 75.8 - - - +
67D LYS* 1.3 66.3 + - - +
69D ARG* 3.3 8.5 + - - +
70D ALA* 3.1 22.6 + - + +
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ASP* 3.3 22.4 + - - +
52D GLY 4.1 8.3 - - - +
53D LEU* 4.0 20.0 - - + +
65D THR* 3.9 6.7 - - - +
66D GLU* 1.3 81.9 - - - +
68D GLY* 1.3 61.9 + - - +
70D ALA* 3.2 8.9 + - - +
71D LEU* 3.1 37.4 + - + +
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.6 15.2 - - - +
53D LEU* 3.4 34.0 - - - +
64D LEU* 4.0 6.8 - - - +
65D THR* 2.9 10.7 + - - -
67D LYS* 1.3 74.3 - - - +
69D ARG* 1.3 64.1 + - - +
71D LEU* 3.7 1.7 + - - +
72D ALA* 3.2 22.7 + - - +
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TYR* 3.5 23.2 + - + -
19D GLU* 2.8 42.1 + - - -
64D LEU* 3.9 28.0 + - + +
65D THR 2.9 19.9 + - - +
66D GLU* 3.6 9.6 - - - +
68D GLY* 1.3 72.7 - - - +
70D ALA* 1.3 72.0 + - - +
72D ALA* 3.1 3.1 + - - +
73D ILE* 3.0 40.4 + - + +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLU* 3.1 10.9 + - + +
67D LYS* 3.5 10.8 - - - +
69D ARG* 1.3 81.6 - - - +
71D LEU* 1.3 69.6 + - + +
73D ILE* 2.9 19.9 + - - +
74D ALA* 3.1 12.6 + - - +
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 6.3 0.2 - - + -
9D GLU* 6.3 0.7 - - + -
12D LEU* 4.2 17.5 - - + -
53D LEU* 4.0 26.9 - - + -
67D LYS* 3.1 24.5 + - + +
68D GLY 4.0 5.2 - - - +
69D ARG 3.3 0.2 - - - -
70D ALA* 1.3 82.4 - - + +
72D ALA* 1.3 62.9 + - - +
74D ALA* 3.2 10.9 + - + +
75D VAL* 3.1 27.4 + - + +
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.9 36.5 - - + +
13D ARG* 5.1 1.9 - - - +
16D TYR* 4.1 20.4 - - + -
64D LEU* 4.2 5.2 - - + -
68D GLY 3.2 15.2 + - - +
69D ARG 3.1 5.4 + - - +
71D LEU* 1.3 75.3 - - - +
73D ILE* 1.3 68.0 + - - +
75D VAL* 2.9 16.5 + - - +
76D MET* 2.9 14.9 + - - +
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Residues in contact with ILE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D TYR* 3.9 26.5 - - + +
69D ARG* 3.0 35.3 + - + +
70D ALA* 2.9 12.4 + - - +
72D ALA* 1.3 76.3 - - - +
74D ALA* 1.3 53.3 + - - +
76D MET* 3.1 7.8 + - - +
77D ARG* 2.8 35.3 + - - +
133D PRO* 3.9 6.5 - - + +
134D GLY* 3.3 39.0 - - - +
137D GLU* 4.0 16.4 - - + +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ALA 3.1 8.7 + - - +
71D LEU* 3.5 14.4 - - + +
73D ILE* 1.3 80.9 - - - +
75D VAL* 1.3 59.9 + - + +
77D ARG* 3.5 30.4 + - - +
78D LYS* 3.1 42.0 + - - +
110D GLU* 5.6 2.7 - - - +
113D GLU* 4.0 0.3 - - - +
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLU* 3.6 52.0 - - + +
12D LEU* 5.6 0.4 - - + -
13D ARG* 4.4 7.9 - - + -
71D LEU* 3.1 17.7 + - + +
72D ALA* 2.9 12.7 + - - +
74D ALA* 1.3 71.2 - - + +
76D MET* 1.3 59.3 + - - +
78D LYS* 3.8 9.8 - - - +
79D HIS* 3.0 27.0 + - - +
105D GLU* 3.7 34.5 - - + +
106D HIS* 4.1 6.1 - - + -
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Residues in contact with MET 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 4.4 15.2 - - + +
16D TYR* 3.0 39.9 - - + -
17D ASP* 3.7 20.2 - - - +
20D GLU* 3.7 9.4 - - - +
72D ALA 2.9 10.7 + - - +
73D ILE* 3.4 9.4 - - - +
75D VAL* 1.3 77.0 - - - +
77D ARG* 1.3 65.5 + - - +
79D HIS* 3.3 8.8 + - - +
80D ARG* 3.1 67.9 + - - +
133D PRO* 3.4 23.1 - - + -
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Residues in contact with ARG 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE* 2.8 17.0 + - - +
74D ALA* 3.6 30.5 - - - +
76D MET* 1.3 78.2 - - - +
78D LYS* 1.3 56.1 + - - +
80D ARG* 4.1 0.2 - - - -
81D LEU* 3.0 39.9 + - + +
110D GLU* 4.1 20.4 + - - +
113D GLU* 2.8 29.2 + - - +
132D ILE* 4.1 15.3 - - + +
133D PRO* 3.2 21.7 - - - +
134D GLY* 2.9 41.4 + - - -
135D LEU* 4.0 4.0 - - + +
137D GLU* 4.4 9.3 - - - +
138D LEU* 3.4 28.1 - - - +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLU* 6.0 2.0 - - - -
74D ALA* 3.1 31.6 + - - +
75D VAL* 3.8 8.3 - - + +
77D ARG* 1.3 73.4 - - - +
79D HIS* 1.3 57.0 + - - +
81D LEU* 3.3 0.4 + - - -
82D ALA* 2.8 37.0 + - - +
105D GLU* 3.3 28.5 - - - +
106D HIS 5.9 0.2 - - - -
108D MET* 3.0 47.7 + - + +
110D GLU* 4.0 16.8 - - - +
113D GLU* 3.1 35.2 + - + -
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Residues in contact with HIS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 4.0 14.0 + - - -
75D VAL 3.0 12.5 + - - +
76D MET* 3.3 9.8 + - - +
78D LYS* 1.3 75.2 - - - +
80D ARG* 1.3 73.6 + - + +
82D ALA* 4.4 0.7 - - - -
83D GLU* 2.6 36.3 + - - +
98D HIS* 3.1 24.6 - + - -
101D ALA* 3.4 22.2 + - + +
102D CYS 3.9 2.0 + - - -
105D GLU* 3.2 33.3 + - - +
1001D NI 2.0 46.2 - - + +
2001D ACT 3.1 2.6 + - - -
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASP* 4.6 3.4 + - - -
20D GLU* 3.0 40.8 + - - -
76D MET* 3.1 51.4 + - - +
77D ARG 4.3 0.4 - - - +
79D HIS* 1.3 81.2 - - + +
81D LEU* 1.3 62.0 + - - +
82D ALA 3.2 0.9 - - - -
83D GLU* 3.1 12.3 + - - +
84D ARG* 2.9 31.2 + - - +
126D SER* 3.6 20.5 - - - -
130D ASN* 3.5 20.8 - - - +
131D PRO* 2.7 36.9 + - - +
132D ILE* 3.6 22.4 - - + +
133D PRO* 4.5 1.6 - - - +
2001D ACT 3.8 17.0 + - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ARG* 3.0 29.9 + - + +
78D LYS* 3.9 3.1 - - - +
80D ARG* 1.3 72.7 - - - +
82D ALA* 1.3 65.4 + - - +
84D ARG* 3.3 4.3 + - + +
85D LEU* 3.0 24.4 + - - +
108D MET* 4.9 1.6 - - + -
113D GLU* 3.8 44.9 - - + +
116D LEU* 3.9 18.0 - - + +
117D VAL* 4.6 13.0 - - + +
120D LEU* 3.9 7.6 - - + +
123D PRO* 3.8 30.1 - - + -
132D ILE* 4.1 17.9 - - + -
135D LEU* 4.9 3.4 - - + -
138D LEU* 4.8 1.6 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LYS 2.8 19.7 + - - +
79D HIS* 3.6 6.7 - - - +
81D LEU* 1.3 76.9 - - - +
83D GLU* 1.3 55.0 + - - +
85D LEU* 3.4 6.4 + - - +
86D LEU* 2.9 37.3 + - + +
101D ALA* 3.8 13.5 - - + -
104D TRP* 4.2 24.0 - - + -
105D GLU 5.1 0.4 - - - +
108D MET* 4.1 15.3 - - - -
116D LEU* 4.9 2.0 - - - -
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D HIS* 2.6 24.5 + - - +
80D ARG* 3.1 11.0 + - - +
82D ALA* 1.3 73.2 - - - +
84D ARG* 1.3 67.8 + - - +
86D LEU* 3.2 2.9 + - - +
87D VAL* 3.1 27.0 + - - +
97D VAL* 3.5 24.2 - - + +
98D HIS* 3.0 6.2 + - - -
101D ALA* 3.5 10.1 - - + -
126D SER* 3.5 10.4 - - - -
127D PRO* 3.6 12.1 - - + -
128D PHE* 3.3 17.2 - - - -
1001D NI 1.9 39.9 - - - +
2001D ACT 3.1 14.9 - - - +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG 2.9 15.5 + - - +
81D LEU* 3.5 6.3 - - - +
83D GLU* 1.3 75.0 - - - +
85D LEU* 1.3 59.2 + - - +
87D VAL* 3.2 1.4 + - - +
88D ASP* 2.8 73.5 + - - +
120D LEU* 3.4 20.2 - - + -
123D PRO* 3.4 28.2 - - + +
125D THR* 2.8 48.5 + - - +
126D SER 3.5 13.3 + - - -
127D PRO* 3.4 26.1 - - + +
132D ILE* 4.3 4.3 - - + -
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 4.8 7.0 - - + -
89C VAL* 5.1 3.1 - - + -
90C ILE* 4.3 21.8 - - + -
104C TRP* 5.0 2.7 - - + -
81D LEU 3.0 17.2 + - - +
82D ALA* 3.7 5.2 - - - +
84D ARG* 1.3 75.4 - - - +
86D LEU* 1.3 58.0 + - - +
89D VAL* 3.2 31.4 + - + +
90D ILE* 3.0 36.6 + - + +
104D TRP* 4.0 28.5 - - + -
116D LEU* 4.1 29.8 - - + -
119D VAL* 6.1 2.2 - - + -
120D LEU* 3.8 13.6 - - + +
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C VAL* 4.3 11.7 - - + -
82D ALA* 2.9 27.6 + - + +
83D GLU 3.2 4.7 + - - +
85D LEU* 1.3 76.5 - - + +
87D VAL* 1.3 59.8 + - - +
90D ILE* 3.7 26.8 - - + -
91D GLY 3.0 7.8 + - - -
92D LEU* 3.0 34.1 + - + +
97D VAL* 3.5 35.9 - - + +
100D GLU* 3.6 20.9 - - + -
101D ALA* 4.0 10.8 - - + +
104D TRP* 3.7 26.5 - - + -
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLU 3.1 15.2 + - - +
84D ARG* 3.9 1.8 - - - +
86D LEU* 1.3 76.6 - - - +
88D ASP* 1.3 75.9 + - - +
89D VAL 3.3 0.7 + - - -
91D GLY* 3.5 17.7 + - - -
92D LEU 4.8 7.9 - - - +
94D TRP* 3.9 27.6 - - + -
97D VAL* 3.9 25.8 - - + -
127D PRO* 3.5 23.6 - - + -
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ARG* 2.8 61.2 + - - +
87D VAL* 1.3 82.4 - - - +
89D VAL* 1.3 62.0 + - + +
120D LEU* 4.4 20.3 - - + +
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Residues in contact with VAL 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 5.3 1.6 - - + -
89C VAL* 3.9 28.0 - - + -
115C ARG* 5.1 0.5 + - - -
119C VAL* 3.8 23.3 - - + +
85D LEU* 3.2 23.4 + - + +
88D ASP* 1.3 82.9 - - + +
90D ILE* 1.3 73.1 + - + +
91D GLY* 3.2 3.1 + - - -
119D VAL* 5.2 7.2 - - + +
120D LEU* 4.0 25.1 - - + -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il