Contacts of the helix formed by residues 84 - 110 (chain D) in PDB entry 1ZMC
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 ASN 84 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLY* 2.8 19.8 + - - +
77C GLU* 3.0 40.4 + - + +
83D LEU* 1.3 74.0 - - - +
85D LEU* 1.3 63.4 + - - +
86D ASP* 3.3 13.6 + - - +
87D LYS* 3.1 33.1 + - - +
88D MET* 3.1 18.2 + - - +
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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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83D LEU* 3.6 19.6 + - + -
84D ASN* 1.3 73.8 - - - +
86D ASP* 1.3 64.3 + - - +
88D MET* 3.7 9.8 - - + +
89D MET* 3.0 44.8 + - + +
174D LEU 3.7 8.5 - - - +
175D LYS 3.3 35.9 - - - +
176D LYS* 3.7 16.2 - - - -
177D VAL* 3.9 6.1 - - + +
197D TRP* 4.0 24.0 - - + -
200D LEU* 4.3 13.7 - - + -
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Residues in contact with ASP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ASN* 3.2 10.0 + - - +
85D LEU* 1.3 77.4 - - - +
87D LYS* 1.3 59.3 + - - +
89D MET* 3.3 7.9 + - - +
90D GLU* 3.0 26.2 + - - +
175D LYS* 5.4 9.0 - - - +
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Residues in contact with LYS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA 3.5 19.7 - - - +
73C SER* 3.8 30.8 - - - +
75C GLY* 3.7 7.2 - - - +
77C GLU* 5.6 0.2 - - - +
84D ASN* 3.1 32.9 + - - +
86D ASP* 1.3 77.5 - - - +
88D MET* 1.3 65.6 + - - +
90D GLU* 3.0 44.9 + - - +
91D GLN 3.1 10.4 + - - -
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Residues in contact with MET 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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74C ARG* 3.0 33.9 - - - +
75C GLY* 3.7 1.2 - - - -
76C ILE* 4.1 12.6 - - + -
56D LEU* 4.4 13.0 - - + +
59D ASN* 3.6 42.1 + - + +
60D SER* 4.1 7.6 - - - -
63D TYR* 4.1 6.5 - - + -
83D LEU* 3.5 27.8 - - + -
84D ASN 3.1 10.8 + - - +
85D LEU* 3.7 14.8 - - + +
87D LYS* 1.3 78.6 - - - +
89D MET* 1.3 62.3 + - - +
90D GLU 3.3 0.3 + - - -
91D GLN* 3.4 11.1 + - - +
92D LYS* 3.4 10.4 + - - +
200D LEU* 4.2 19.1 - - + -
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Residues in contact with MET 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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56D LEU* 4.0 19.1 - - + -
85D LEU* 3.0 33.9 + - + +
86D ASP* 3.5 6.7 - - - +
87D LYS 3.2 0.2 - - - -
88D MET* 1.3 73.6 - - - +
90D GLU* 1.3 60.0 + - - +
92D LYS* 3.2 21.3 - - - +
93D SER* 3.0 31.7 + - - +
172D LEU 3.3 28.0 - - - +
173D SER* 4.4 4.7 - - - -
174D LEU 3.9 13.9 - - - +
197D TRP* 3.8 31.4 - - + -
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Residues in contact with GLU 90 (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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86D ASP 3.0 13.1 + - - +
87D LYS* 3.0 45.8 + - - +
89D MET* 1.3 76.8 - - - +
91D GLN* 1.3 67.7 + - - +
93D SER* 3.0 7.6 + - - +
94D THR* 2.8 36.2 + - - +
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Residues in contact with GLN 91 (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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73C SER* 3.6 26.2 + - - +
74C ARG* 4.0 18.8 - - + +
395C LYS 4.4 0.8 + - - -
396C THR 3.4 19.1 + - - +
398C ALA* 3.7 22.6 - - + +
55D ALA* 3.8 11.6 - - - +
59D ASN* 2.9 30.0 + - - +
87D LYS 3.1 4.0 + - - +
88D MET 3.6 9.2 - - - +
90D GLU* 1.3 78.0 - - - +
92D LYS* 1.3 63.1 + - - +
94D THR* 3.3 8.8 + - - +
95D ALA* 3.1 26.2 + - - +
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Residues in contact with LYS 92 (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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52D PRO* 3.8 39.9 - - + +
55D ALA* 4.1 9.5 - - + +
56D LEU* 3.9 26.7 - - + -
59D ASN* 5.3 0.2 - - - +
88D MET 3.4 6.6 + - - +
89D MET* 3.2 29.7 - - - +
91D GLN* 1.3 85.3 + - - +
93D SER* 1.3 74.8 + - - +
95D ALA* 3.2 5.1 + - - +
96D VAL* 3.0 28.1 + - + +
172D LEU* 3.0 27.0 + - + +
173D SER* 3.1 17.8 + - - -
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Residues in contact with SER 93 (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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89D MET* 3.0 13.5 + - - +
90D GLU* 3.0 10.9 + - - -
92D LYS* 1.3 89.8 + - - +
94D THR* 1.3 57.9 + - - +
96D VAL* 3.5 6.8 + - - +
97D LYS* 2.9 30.5 + - - +
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Residues in contact with THR 94 (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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90D GLU* 2.8 31.2 + - - +
91D GLN* 3.3 13.9 - - - +
93D SER* 1.3 74.9 - - - +
95D ALA* 1.3 66.9 + - - +
97D LYS* 3.3 6.3 + - - +
98D ALA* 3.0 25.3 + - + +
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Residues in contact with ALA 95 (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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395C LYS* 3.9 27.3 - - + +
396C THR* 4.0 17.0 - - - +
51D ILE* 4.9 4.3 - - + -
55D ALA* 5.2 2.9 - - + -
91D GLN* 3.1 16.5 + - - +
92D LYS* 3.6 9.4 - - - +
94D THR* 1.3 78.1 - - - +
96D VAL* 1.3 64.9 + - - +
98D ALA* 3.2 7.4 + - - +
99D LEU* 3.0 29.7 + - + +
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Residues in contact with VAL 96 (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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46D LEU* 3.5 37.6 - - + +
47D ASN* 4.3 14.6 - - - +
51D ILE* 4.1 7.6 - - + -
52D PRO* 3.9 26.7 - - + -
92D LYS* 3.0 23.3 + - + +
93D SER* 3.7 7.6 - - - +
95D ALA* 1.3 78.0 - - - +
97D LYS* 1.3 57.8 + - - +
99D LEU 3.4 0.3 + - - -
100D THR* 2.9 43.0 + - + +
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Residues in contact with LYS 97 (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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93D SER 2.9 17.9 + - - +
94D THR* 3.8 6.7 - - - +
95D ALA 3.2 0.4 - - - -
96D VAL* 1.3 75.7 - - - +
98D ALA* 1.3 66.3 + - - +
100D THR* 2.7 23.3 + - - +
101D GLY* 2.9 9.5 + - - -
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Residues in contact with ALA 98 (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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395C LYS* 3.5 32.5 - - - +
94D THR* 3.0 19.5 + - + +
95D ALA 3.6 3.4 - - - +
97D LYS* 1.3 79.6 - - - +
99D LEU* 1.3 58.2 + - - +
101D GLY* 3.3 2.6 + - - -
102D GLY* 2.9 23.7 + - - -
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Residues in contact with LEU 99 (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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389C ALA 5.6 1.8 - - - +
390C ALA* 5.1 10.1 - - - +
391C ASN 5.0 0.9 - - - +
392C SER* 4.2 25.4 - - - +
395C LYS* 4.0 33.4 - - + -
396C THR* 4.4 6.1 - - - +
46D LEU* 3.7 18.4 - - + -
51D ILE* 3.9 30.7 - - + -
95D ALA 3.0 14.6 + - - +
98D ALA* 1.3 74.4 - - - +
100D THR* 1.3 59.5 + - - +
102D GLY* 2.8 17.8 + - - +
103D ILE* 3.1 17.0 + - - +
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Residues in contact with THR 100 (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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40D THR* 3.1 37.7 + - + +
41D LEU* 4.3 7.0 + - - +
46D LEU* 3.4 23.1 - - + -
47D ASN* 3.6 8.3 - - - +
96D VAL* 2.9 29.9 + - + +
97D LYS* 2.7 27.1 + - - +
99D LEU* 1.3 73.9 - - - +
101D GLY* 1.3 64.5 + - - +
102D GLY 3.2 0.5 + - - -
103D ILE* 3.3 13.1 + - - +
104D ALA* 3.3 11.1 + - - +
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Residues in contact with GLY 101 (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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97D LYS 2.9 9.0 + - - -
98D ALA 3.6 4.7 - - - -
100D THR* 1.3 83.3 + - - +
102D GLY* 1.3 60.5 + - - +
103D ILE 3.4 0.2 - - - -
104D ALA* 3.4 10.0 + - - +
105D HIS* 3.1 22.5 + - - +
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Residues in contact with GLY 102 (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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98D ALA 2.9 10.7 + - - -
99D LEU* 2.8 11.8 + - - -
101D GLY* 1.3 76.0 - - - +
103D ILE* 1.3 59.4 + - - +
105D HIS* 3.1 9.9 + - - +
106D LEU* 2.9 39.9 + - - +
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Residues in contact with ILE 103 (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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19D TYR* 3.6 55.6 - - + -
41D LEU* 3.7 24.5 - - + +
42D GLY* 3.6 30.7 - - - +
46D LEU* 3.7 16.4 - - + -
99D LEU 3.1 9.7 + - - +
100D THR 3.3 6.0 + - - +
102D GLY* 1.3 75.9 - - - +
104D ALA* 1.3 57.1 + - - +
106D LEU* 3.2 10.3 + - + +
107D PHE* 2.9 35.6 + - + +
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Residues in contact with ALA 104 (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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41D LEU* 3.7 17.2 - - + +
100D THR 3.3 10.6 + - - +
101D GLY* 3.6 13.2 - - - +
102D GLY 3.1 0.4 - - - -
103D ILE* 1.3 79.5 - - - +
105D HIS* 1.3 61.8 + - - +
107D PHE* 3.5 4.2 + - - +
108D LYS* 3.3 25.9 + - - +
114D HIS* 6.1 0.7 - - - +
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Residues in contact with HIS 105 (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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474C PHE* 6.0 5.6 - + - -
101D GLY 3.1 13.0 + - - +
102D GLY* 3.1 12.5 + - - +
104D ALA* 1.3 78.1 - - - +
106D LEU* 1.3 65.6 + - + +
108D LYS* 3.2 9.7 + - - +
109D GLN* 3.0 53.4 + - + +
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Residues in contact with LEU 106 (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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472C ILE 3.8 8.5 - - - +
473C ASN* 3.6 53.8 - - + +
474C PHE* 3.8 10.1 - - + +
19D TYR* 4.7 2.5 - - + -
23D ILE* 4.2 17.3 - - + -
102D GLY* 2.9 24.9 + - - +
103D ILE* 3.7 9.2 - - + +
105D HIS* 1.3 82.3 - - + +
107D PHE* 1.3 66.4 + - - +
109D GLN* 3.3 21.8 + - - +
110D ASN* 3.0 32.5 + - - +
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Residues in contact with PHE 107 (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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14D SER* 4.9 0.4 - - - -
19D TYR* 3.6 47.6 - + + -
22D ALA* 3.9 7.6 - - + -
23D ILE* 3.9 13.5 - - + -
34D CYS* 3.6 33.2 - - + -
41D LEU* 3.9 28.3 - - + -
103D ILE* 2.9 22.5 + - + +
104D ALA* 3.8 6.5 - - - +
105D HIS 3.3 0.2 - - - -
106D LEU* 1.3 76.2 - - - +
108D LYS* 1.3 61.6 + - + +
110D ASN 3.3 0.3 + - - -
111D LYS 3.1 3.3 + - - -
112D VAL* 2.7 56.2 + - + +
114D HIS* 4.3 16.4 - - + -
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Residues in contact with LYS 108 (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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104D ALA 3.3 13.4 + - - +
105D HIS* 3.2 13.6 + - - +
106D LEU 3.2 0.2 - - - -
107D PHE* 1.3 80.5 - - + +
109D GLN* 1.3 61.7 + - - +
111D LYS* 3.3 13.1 + - - +
112D VAL 5.0 2.7 - - - +
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Residues in contact with GLN 109 (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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474C PHE* 3.1 32.8 + - - +
27D GLN* 6.0 0.8 - - - +
105D HIS* 3.0 45.2 + - + +
106D LEU* 3.3 16.5 + - - +
108D LYS* 1.3 77.2 - - - +
110D ASN* 1.3 68.1 + - - +
111D LYS* 3.7 2.8 + - - +
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Residues in contact with ASN 110 (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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470C LYS* 4.9 6.6 + - - +
472C ILE 4.8 3.0 + - - -
23D ILE* 3.6 25.9 - - + +
26D ALA* 3.2 23.7 - - + +
27D GLN* 3.2 28.7 + - - +
106D LEU* 3.0 31.8 + - - +
108D LYS 3.2 0.2 - - - -
109D GLN* 1.3 94.3 + - - +
111D LYS* 1.3 70.6 + - - +
112D VAL* 3.2 15.7 - - + -
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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
------------------------------------------------------------
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