Contacts of the helix formed by residues 65 - 89 (chain A) in PDB entry 2ISZ
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY* 2.9 32.3 + - - +
53A LEU 3.2 16.1 + - - -
54A LEU* 3.8 15.0 - - - +
55A ARG* 4.5 5.6 - - + +
63A GLU 3.6 0.6 + - - -
64A LEU* 1.3 77.9 - - - +
66A GLU* 1.3 65.6 + - - +
67A LYS* 3.3 3.1 + - - -
68A GLY 3.1 14.4 + - - -
69A ARG* 3.1 21.0 + - - +
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Residues in contact with GLU 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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64A LEU 5.1 0.9 - - - +
65A THR* 1.3 80.4 - - - +
67A LYS* 1.3 60.7 + - - +
69A ARG* 3.4 15.3 + - - +
70A ALA* 3.0 30.7 + - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP 2.9 28.0 + - - -
52A GLY* 3.1 20.5 + - - +
53A LEU* 3.8 16.6 - - + -
65A THR* 3.3 2.2 + - - +
66A GLU* 1.3 79.6 - - - +
68A GLY* 1.3 60.5 + - - +
70A ALA* 3.6 5.2 + - - +
71A LEU* 3.2 23.9 + - + +
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Residues in contact with GLY 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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12A LEU* 4.0 9.9 - - - +
53A LEU* 3.2 33.8 + - - +
64A LEU* 4.0 6.9 - - - +
65A THR* 3.1 9.9 + - - -
67A LYS* 1.3 75.0 - - - +
69A ARG* 1.3 60.1 + - - +
71A LEU* 3.6 1.9 + - - +
72A ALA* 3.0 29.3 + - - +
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Residues in contact with ARG 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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16A TYR* 4.3 14.3 - - + -
19A GLU* 3.1 40.2 + - - -
64A LEU* 3.8 32.8 + - + +
65A THR 3.1 20.1 + - - +
66A GLU* 4.0 14.1 + - - +
67A LYS 3.4 0.2 - - - -
68A GLY* 1.3 76.5 - - - +
70A ALA* 1.3 64.0 + - - +
72A ALA* 3.8 0.5 - - - +
73A ILE* 3.0 42.6 + - + +
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Residues in contact with ALA 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 GLU 3.0 17.7 + - - +
67A LYS* 3.9 6.7 - - - +
68A GLY 3.4 0.2 - - - -
69A ARG* 1.3 76.7 - - - +
71A LEU* 1.3 57.1 + - - +
73A ILE* 3.8 9.1 + - - +
74A ALA* 3.2 25.1 + - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 4.9 5.6 - - + -
9A GLU* 4.2 18.8 - - + +
12A LEU* 3.2 28.3 - - + -
53A LEU* 4.3 13.2 - - + -
67A LYS* 3.2 18.5 + - + +
68A GLY* 3.9 1.1 - - - +
69A ARG 3.2 0.2 - - - -
70A ALA* 1.3 76.7 - - - +
72A ALA* 1.3 63.5 - - - +
74A ALA* 3.1 9.9 + - + +
75A VAL* 3.0 36.9 + - + +
78A LYS* 6.4 0.9 - - - -
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Residues in contact with ALA 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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12A LEU* 3.8 36.7 - - + +
13A ARG* 4.5 3.3 - - - +
16A TYR* 4.2 12.1 - - + -
64A LEU* 4.0 13.7 - - + -
68A GLY 3.0 19.3 + - - +
69A ARG 3.8 3.4 - - - +
71A LEU* 1.3 75.5 - - - +
73A ILE* 1.3 58.0 + - - +
75A VAL* 3.2 7.1 + - - +
76A MET* 2.9 29.7 + - - +
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Residues in contact with ILE 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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16A TYR* 3.6 29.6 - - + +
69A ARG* 3.0 38.9 + - + +
70A ALA* 3.9 7.9 - - - +
72A ALA* 1.3 73.4 - - - +
74A ALA* 1.3 68.0 + - - +
76A MET* 3.3 7.6 + - - +
77A ARG* 2.9 27.7 + - - +
133A PRO* 4.0 6.5 - - + +
134A GLY* 3.8 31.4 - - - +
137A GLU* 4.7 15.9 - - + +
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Residues in contact with ALA 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 ALA 3.2 12.5 + - - +
71A LEU* 3.1 18.5 + - + +
73A ILE* 1.3 80.1 - - - +
75A VAL* 1.3 56.2 + - - +
77A ARG* 3.3 29.8 + - - +
78A LYS* 3.1 44.0 + - - +
110A GLU* 4.6 5.2 - - - +
113A GLU* 4.3 0.5 - - - +
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Residues in contact with VAL 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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9A GLU* 3.7 39.3 - - + +
12A LEU* 5.9 0.4 - - + -
13A ARG* 3.5 17.9 - - + -
71A LEU* 3.0 24.7 + - + +
72A ALA* 3.2 7.8 + - - +
74A ALA* 1.3 74.4 - - + +
76A MET* 1.3 59.7 + - - +
78A LYS* 3.4 10.8 + - + +
79A HIS* 2.9 26.7 + - - +
105A GLU* 3.4 37.8 - - + +
106A HIS* 4.2 8.1 - - + -
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Residues in contact with MET 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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13A ARG* 3.5 23.0 - - - +
16A TYR* 3.7 28.0 - - + -
17A ASP* 3.0 29.2 - - - +
20A GLU* 4.0 2.0 - - - +
72A ALA 2.9 15.2 + - - +
73A ILE 3.3 4.7 + - - +
75A VAL* 1.3 76.8 - - - +
77A ARG* 1.3 61.8 + - - +
79A HIS* 3.4 9.4 + - - +
80A ARG* 3.1 66.6 + - - +
133A PRO* 3.6 24.0 - - + -
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Residues in contact with ARG 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 ILE* 2.9 19.6 + - - +
74A ALA* 3.4 22.3 - - - +
75A VAL 3.2 0.2 - - - -
76A MET* 1.3 73.6 - - - +
78A LYS* 1.3 59.4 + - - +
79A HIS 3.4 0.2 + - - -
80A ARG* 3.4 1.9 + - - -
81A LEU* 2.9 38.1 + - + +
110A GLU* 2.7 33.1 + - - +
113A GLU* 2.5 34.7 + - - +
132A ILE* 3.8 18.8 - - + +
133A PRO* 3.1 19.0 - - - +
134A GLY* 2.9 34.9 + - - -
135A LEU* 4.3 2.5 - - + +
137A GLU* 4.3 7.5 - - - +
138A LEU* 3.4 28.8 - - - +
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Residues in contact with LYS 78 (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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9A GLU* 6.6 0.2 - - - -
71A LEU* 6.4 0.7 - - - -
74A ALA* 3.1 27.1 + - - +
75A VAL* 3.8 7.9 - - - +
77A ARG* 1.3 73.7 - - - +
79A HIS* 1.3 60.0 + - - +
81A LEU* 3.7 1.5 - - - -
82A ALA* 2.8 33.1 + - - +
105A GLU* 3.2 31.6 - - - +
106A HIS 5.7 0.7 - - - -
108A MET* 3.2 44.3 + - + +
110A GLU* 3.7 18.8 + - - +
113A GLU* 2.3 44.6 + - + +
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Residues in contact with HIS 79 (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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13A ARG* 4.0 8.3 + - - +
75A VAL 2.9 13.1 + - - +
76A MET* 3.5 15.9 - - - +
77A ARG 3.2 0.2 - - - -
78A LYS* 1.3 78.3 - - - +
80A ARG* 1.3 63.9 + - + +
82A ALA* 3.4 5.2 - - - +
83A GLU* 2.7 40.1 + - - +
98A HIS* 3.2 31.4 - + - -
101A ALA* 3.6 15.0 + - + +
102A CYS* 3.6 8.9 + - - -
105A GLU* 3.1 33.5 + - - +
1001A NI 2.0 43.9 - - + +
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Residues in contact with ARG 80 (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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16A TYR* 5.5 0.6 - - - -
17A ASP* 5.1 0.2 + - - -
20A GLU* 2.7 42.2 + - - -
76A MET* 3.1 48.6 + - - +
77A ARG 4.2 0.9 - - - +
79A HIS* 1.3 77.1 - - + +
81A LEU* 1.3 61.4 + - - +
83A GLU* 3.4 14.9 + - - +
84A ARG* 3.1 29.8 + - - +
126A SER* 3.6 17.1 - - - -
130A ASN* 3.4 35.8 + - - +
131A PRO 2.6 38.6 + - - -
132A ILE* 3.9 18.3 - - + +
133A PRO* 4.3 2.2 - - - +
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Residues in contact with LEU 81 (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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77A ARG* 2.9 22.6 + - + +
78A LYS* 3.9 4.3 - - - +
80A ARG* 1.3 73.2 - - - +
82A ALA* 1.3 60.4 + - - +
84A ARG* 3.3 4.3 + - - +
85A LEU* 3.0 27.2 + - - +
108A MET* 4.7 1.1 - - + -
113A GLU* 3.6 49.6 - - + +
116A LEU* 4.2 16.3 - - + +
117A VAL* 4.3 18.4 - - + +
120A LEU* 4.1 13.1 - - + +
123A PRO* 4.0 27.6 - - + +
132A ILE* 4.2 13.2 - - + -
135A LEU* 5.1 1.8 - - + -
138A LEU* 4.5 1.6 - - + -
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Residues in contact with ALA 82 (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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78A LYS 2.8 19.9 + - - +
79A HIS* 3.4 5.6 - - - +
81A LEU* 1.3 72.7 - - - +
83A GLU* 1.3 67.3 + - - +
85A LEU* 3.3 6.9 + - - +
86A LEU* 2.9 31.7 + - + +
101A ALA* 4.1 9.2 - - + +
104A TRP* 4.1 24.7 - - + -
108A MET* 3.8 19.7 - - - -
116A LEU* 5.2 0.9 - - - -
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Residues in contact with GLU 83 (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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79A HIS* 2.9 22.2 + - - +
80A ARG* 3.6 7.8 + - - +
81A LEU 3.3 0.2 - - - -
82A ALA* 1.3 76.2 - - - +
84A ARG* 1.3 61.2 + - - +
86A LEU* 3.2 7.8 + - - +
87A VAL* 3.0 28.6 + - - +
97A VAL* 4.4 12.8 - - + +
98A HIS* 3.7 5.0 - - - +
101A ALA* 3.6 15.0 - - + -
126A SER* 3.4 23.9 + - - -
127A PRO* 3.6 16.6 - - + -
128A PHE* 3.8 12.9 - - - -
130A ASN* 5.5 0.5 - - - +
1001A NI 2.0 47.3 - - - +
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Residues in contact with ARG 84 (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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80A ARG 3.1 12.4 + - - +
81A LEU* 3.6 9.9 - - - +
82A ALA 3.2 0.2 - - - -
83A GLU* 1.3 72.8 - - - +
85A LEU* 1.3 65.7 + - - +
87A VAL* 4.5 0.7 - - - +
88A ASP* 2.8 66.7 + - - +
120A LEU* 3.9 14.6 - - + -
123A PRO* 3.6 25.9 - - + +
125A THR* 2.9 49.2 + - - +
126A SER 3.5 5.5 + - - -
127A PRO* 3.5 30.7 - - + +
132A ILE* 5.1 1.3 - - + -
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Residues in contact with LEU 85 (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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81A LEU 3.0 13.1 + - - +
82A ALA* 3.6 8.1 - - - +
84A ARG* 1.3 74.1 - - - +
86A LEU* 1.3 58.9 + - - +
89A VAL* 2.9 52.3 + - + +
90A ILE* 3.0 22.1 + - + -
104A TRP* 3.7 30.7 - - + -
108A MET* 6.5 0.2 - - - -
116A LEU* 4.1 32.5 - - + -
119A VAL* 6.4 1.1 - - + -
120A LEU* 4.0 9.3 - - + +
85B LEU* 4.6 8.3 - - + -
89B VAL* 5.6 2.7 - - + -
90B ILE* 4.5 18.4 - - + -
104B TRP* 4.6 3.8 - - + -
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Residues in contact with LEU 86 (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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82A ALA* 2.9 27.1 + - + +
83A GLU* 3.5 5.6 - - - +
84A ARG 3.1 0.4 - - - -
85A LEU* 1.3 77.8 - - - +
87A VAL* 1.3 56.7 + - - +
90A ILE* 3.6 22.9 - - + +
91A GLY 2.9 7.3 + - - -
92A LEU* 2.8 40.2 + - + -
97A VAL* 4.0 18.2 - - + +
100A GLU* 3.6 29.4 - - + -
101A ALA* 4.1 6.7 - - + +
104A TRP* 4.2 16.8 - - + -
112B VAL* 3.8 28.9 - - + -
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Residues in contact with VAL 87 (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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83A GLU 3.0 17.0 + - - +
84A ARG* 4.1 0.9 - - - +
86A LEU* 1.3 77.2 - - - +
88A ASP* 1.3 75.7 + - - +
89A VAL 3.4 0.2 - - - -
91A GLY* 3.5 18.1 + - - +
92A LEU 4.6 4.5 - - - +
94A TRP* 3.9 37.5 - - + +
97A VAL* 3.7 27.1 - - + -
127A PRO* 3.7 24.2 - - + -
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Residues in contact with ASP 88 (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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84A ARG* 2.8 57.6 + - - +
87A VAL* 1.3 86.3 - - - +
89A VAL* 1.3 67.4 + - + +
120A LEU* 4.5 13.2 - - + +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 2.9 29.4 + - + +
88A ASP* 1.3 81.9 - - + +
90A ILE* 1.3 67.7 + - + +
91A GLY 3.4 0.4 + - - -
119A VAL* 5.6 4.3 - - + -
120A LEU* 3.7 28.5 - - + -
85B LEU* 5.2 2.2 - - + -
89B VAL* 4.4 18.8 - - + -
119B VAL* 3.8 29.0 - - + +
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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