Contacts of the helix formed by residues 88 - 116 (chain A) in PDB entry 1HS7
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR 5.9 0.2 - - - +
27A THR* 3.6 32.5 + - - +
84A LEU* 2.7 22.3 + - + +
85A ILE 3.3 1.0 - - - +
86A HIS 4.8 0.4 - - - -
87A GLN* 1.3 70.7 - - - +
89A GLY* 1.3 62.7 + - - +
90A LYS* 3.3 7.8 + - - +
91A LEU* 3.7 24.1 - - + +
92A SER* 2.8 33.1 + - - -
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS 5.6 1.3 - - - -
87A GLN 3.3 8.0 + - - -
88A ASN* 1.3 72.5 + - - +
90A LYS* 1.3 64.5 + - - +
92A SER* 3.2 17.8 - - - -
93A ALA* 3.3 7.1 + - - +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.3 9.0 + - - +
89A GLY* 1.3 74.5 - - - +
91A LEU* 1.3 59.3 + - + +
93A ALA* 2.9 18.1 + - - +
94A ASP* 2.7 25.8 + - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.5 35.0 - - + +
30A LEU* 3.4 28.0 - - + -
31A SER* 4.4 17.5 - - - +
34A ILE* 3.5 22.0 - - + -
85A ILE* 3.6 6.2 - - + +
88A ASN* 3.6 21.0 + - + +
89A GLY 3.5 0.2 - - - -
90A LYS* 1.3 80.9 - - + +
92A SER* 1.3 57.5 + - - +
94A ASP* 2.6 50.5 + - - +
95A PHE 3.4 4.2 + - - -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 2.9 32.0 + - - +
86A HIS* 4.6 7.1 + - - -
88A ASN 2.8 20.9 + - - -
89A GLY* 3.2 11.4 - - - -
91A LEU* 1.3 73.1 - - - +
93A ALA* 1.3 53.4 + - - +
95A PHE* 4.1 3.3 - - - -
96A LYS* 2.7 50.6 + - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY 3.3 5.5 + - - +
90A LYS* 2.9 12.3 + - - +
92A SER* 1.3 76.8 - - - +
94A ASP* 1.3 64.1 + - - +
96A LYS* 3.9 11.6 - - + +
97A ASN* 2.5 45.4 + - - +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 5.5 0.9 + - - -
34A ILE* 3.6 21.7 - - + +
90A LYS* 2.7 32.4 - - - +
91A LEU* 2.6 36.7 + - - +
93A ALA* 1.3 74.1 - - - +
95A PHE* 1.3 62.0 + - - +
97A ASN* 3.1 11.8 + - - +
98A LEU* 3.1 21.3 + - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 3.7 8.4 - - + +
37A PHE* 3.9 11.9 - + - -
76A ARG* 3.5 26.7 - - + -
79A ILE* 3.3 34.8 - - + -
80A GLU* 3.1 38.4 - - + -
85A ILE* 3.7 21.3 - - + -
91A LEU 3.4 2.4 + - - -
92A SER 4.1 0.2 - - - -
94A ASP* 1.3 78.1 - - - +
96A LYS* 1.3 77.6 + - + +
98A LEU* 2.8 13.6 + - - -
99A LYS* 2.7 70.7 + - + +
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 6.0 0.2 - - + -
92A SER* 2.7 42.1 + - - +
93A ALA* 3.2 11.6 + - - +
95A PHE* 1.3 94.1 - - + +
97A ASN* 1.3 53.6 + - - +
99A LYS* 3.0 17.1 - - - +
100A THR* 2.5 43.2 + - - +
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 2.5 44.2 + - - +
94A ASP* 3.5 7.0 + - - +
96A LYS* 1.3 73.6 - - - +
98A LEU* 1.3 64.2 + - + +
100A THR* 3.6 6.7 - - - +
101A LYS* 2.8 34.3 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 3.1 46.2 - - + +
37A PHE* 3.2 24.7 - - + -
38A ALA* 3.3 29.6 - - + -
41A SER* 3.3 13.4 + - - +
42A ARG* 5.3 4.3 - - - +
94A ASP 3.1 13.5 - - - +
95A PHE* 2.8 10.3 + - - +
97A ASN* 1.3 75.7 - - + +
99A LYS* 1.3 54.6 + - - +
100A THR 3.0 1.3 - - - -
101A LYS* 3.1 9.7 - - + +
102A TYR* 2.6 37.6 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.0 20.6 - - + -
76A ARG* 3.3 38.8 - - - +
80A GLU* 5.1 0.4 - - - +
95A PHE* 2.7 63.2 + - + +
96A LYS* 3.0 29.4 - - + +
98A LEU* 1.3 70.8 - - - +
100A THR* 1.3 72.6 + - - +
102A TYR* 3.5 2.5 - - - +
103A GLN* 2.9 45.8 + - - +
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Residues in contact with THR 100 (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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96A LYS* 2.5 25.5 + - - +
97A ASN* 3.6 7.9 - - - +
99A LYS* 1.3 91.8 + - - +
101A LYS* 1.3 67.5 - - - +
103A GLN* 3.1 22.7 + - - +
104A SER* 3.4 11.0 + - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.3 24.7 - - - +
42A ARG* 3.0 37.0 - - - +
45A GLU* 3.5 17.1 + - - -
97A ASN* 2.8 21.5 + - + +
98A LEU* 3.1 20.9 - - + +
100A THR* 1.3 76.1 - - + +
102A TYR* 1.3 66.0 + - - +
104A SER* 3.1 19.7 + - - -
105A LEU* 3.2 22.9 + - - +
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 17.3 - + + -
41A SER* 4.0 9.0 - - - +
44A LEU* 3.6 24.0 - - + -
69A ILE* 2.7 55.5 + - + +
72A CYS* 4.0 14.1 - - + -
73A THR* 4.1 15.4 - - - -
76A ARG* 4.2 18.2 - - - -
98A LEU 2.6 23.1 + - - +
99A LYS* 3.5 11.9 - - - +
101A LYS* 1.3 75.5 - - - +
103A GLN* 1.3 59.1 + - - +
105A LEU* 3.1 18.4 + - + +
106A GLN* 2.9 45.1 + - - +
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Residues in contact with GLN 103 (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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76A ARG* 4.2 19.9 + - - +
99A LYS* 2.9 38.7 + - - +
100A THR* 3.1 10.6 + - - +
102A TYR* 1.3 77.1 - - + +
104A SER* 1.3 55.8 + - - +
106A GLN* 3.2 24.7 + - - +
107A GLN* 2.7 42.9 + - + +
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Residues in contact with SER 104 (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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100A THR* 3.4 13.3 + - - +
101A LYS* 3.1 12.0 + - - -
103A GLN* 1.3 77.9 - - - +
105A LEU* 1.3 60.6 + - - +
107A GLN* 3.4 7.8 + - - +
108A SER* 2.8 32.3 + - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 2.8 33.2 - - - +
44A LEU* 3.4 27.6 - - + -
45A GLU* 3.0 33.2 - - + +
48A CYS* 3.5 5.3 - - + +
101A LYS* 3.2 16.6 - - - +
102A TYR* 3.3 21.1 - - - +
104A SER* 1.3 77.0 - - - +
106A GLN* 1.3 66.8 + - - +
108A SER* 3.3 4.5 + - - -
109A TYR* 2.9 27.9 + - - +
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.6 11.2 - - + +
69A ILE* 4.4 12.0 - - + +
76A ARG* 5.7 0.2 - - - +
102A TYR* 2.9 55.8 + - + +
103A GLN* 3.2 39.4 + - - +
105A LEU* 1.3 75.0 - - - +
107A GLN* 1.3 54.1 + - + +
109A TYR* 3.9 4.4 - - - -
110A ASN* 2.6 56.0 + - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 2.7 32.6 + - - +
104A SER* 3.6 6.1 - - - +
106A GLN* 1.3 80.4 - - + +
108A SER* 1.3 61.5 + - - +
110A ASN* 3.8 7.5 + - - +
111A GLN* 2.6 36.9 + - - +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A CYS* 6.0 1.1 - - - -
104A SER 2.8 21.7 + - - -
105A LEU* 3.9 5.2 - - - -
107A GLN* 1.3 73.1 - - - +
109A TYR* 1.3 58.1 + - - +
111A GLN* 2.8 29.9 + - - +
112A ARG* 3.5 30.3 + - - +
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Residues in contact with TYR 109 (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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44A LEU* 4.4 0.9 - - + -
48A CYS* 3.1 50.2 - - + +
51A ILE* 3.3 32.5 - - + -
61A ARG* 3.9 5.2 + - - +
64A ILE* 2.9 39.1 - - + +
65A GLU* 3.3 10.1 - - - +
69A ILE* 3.9 11.4 - - + -
105A LEU 2.9 5.1 + - - +
106A GLN* 3.9 11.0 - - - -
108A SER* 1.3 75.8 - - - +
110A ASN* 1.3 66.7 + - - +
111A GLN 3.1 1.6 - - - -
112A ARG* 3.0 5.8 + - - +
113A LYS* 2.7 72.3 + - + -
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Residues in contact with ASN 110 (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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65A GLU* 3.7 9.8 + - - +
69A ILE* 5.7 0.4 - - - +
106A GLN* 2.6 45.3 + - - +
107A GLN* 3.4 10.0 + - - +
109A TYR* 1.3 78.8 - - - +
111A GLN* 1.3 60.9 + - - +
113A LYS* 2.7 47.2 + - - +
114A SER* 3.2 9.5 + - - -
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLN* 2.6 24.7 + - - +
108A SER* 2.8 38.2 + - - +
110A ASN* 1.3 73.4 - - - +
112A ARG* 1.3 58.4 + - + +
114A SER* 2.6 28.2 + - - -
115A LEU* 2.7 35.4 - - + +
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A CYS* 3.5 17.6 + - - +
49A THR* 3.0 39.0 + - - +
51A ILE* 3.9 20.7 + - + -
53A SER* 5.3 2.2 - - - -
108A SER* 3.6 28.9 + - - +
109A TYR* 3.0 9.1 + - - +
111A GLN* 1.3 82.7 - - + +
113A LYS* 1.3 54.5 + - - +
115A LEU* 3.0 13.8 + - + +
116A PHE* 2.6 62.5 + - + +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.7 7.8 - - + +
61A ARG* 3.3 44.3 + - - +
65A GLU* 3.0 35.6 + - - +
109A TYR* 2.7 48.8 + - + +
110A ASN* 2.7 33.2 + - + +
112A ARG* 1.3 73.1 - - - +
114A SER* 1.3 64.0 + - - +
116A PHE 3.9 10.9 - - - -
117A PRO* 4.1 4.7 - - - +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN 3.2 10.8 + - - -
111A GLN* 2.6 20.6 + - - -
113A LYS* 1.3 79.2 - - - +
115A LEU* 1.3 63.4 + - - -
117A PRO* 4.0 9.4 - - - +
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Residues in contact with LEU 115 (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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111A GLN* 2.7 39.3 - - + +
112A ARG* 3.4 26.0 - - + +
114A SER* 1.3 82.1 - - - +
116A PHE* 1.3 72.0 + - + +
117A PRO* 2.8 16.2 - - - +
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Residues in contact with PHE 116 (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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52A GLY* 3.3 43.9 - - - -
56A ASP* 4.8 2.9 - - - +
61A ARG* 4.4 6.6 + - - -
112A ARG* 2.6 56.9 + - + +
113A LYS* 3.9 8.2 - - - +
115A LEU* 1.3 87.8 - - + +
117A PRO* 1.3 64.4 - - - +
118A LEU* 3.7 4.7 + - - +
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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