Contacts of the helix formed by residues 93 - 119 (chain A) in PDB entry 1UK0
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 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 5.7 0.9 - - - +
56A GLN* 4.6 1.8 + - - +
59A VAL* 4.3 10.7 - - - +
90A LEU 4.3 2.6 + - - -
92A ASN* 1.4 89.8 + - - +
94A ALA* 1.3 79.3 + - - +
95A ASP* 3.1 16.1 + - - +
96A SER* 2.6 43.9 + - - +
97A VAL* 3.6 15.6 + - - +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 3.9 15.3 - - - +
93A ASN* 1.3 83.7 + - - +
95A ASP* 1.4 65.4 + - - +
97A VAL* 3.0 7.1 - - - +
98A GLN* 2.5 46.0 + - - +
226A THR* 5.2 4.9 - - + -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 3.1 12.4 + - - +
94A ALA* 1.4 74.1 + - - +
96A SER* 1.4 72.9 + - - +
97A VAL 2.5 3.3 + - - -
98A GLN* 2.6 25.2 + - - +
99A ALA* 3.2 8.9 + - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 3.7 21.7 - - - +
90A LEU 4.1 13.4 + - - -
91A LEU* 4.2 11.2 - - - -
93A ASN* 2.6 20.2 + - - +
95A ASP* 1.4 73.4 - - - +
97A VAL* 1.3 64.8 + - - +
99A ALA* 3.2 22.8 - - - +
100A LYS* 3.3 13.3 + - - +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.5 39.5 - - + +
55A VAL* 3.8 22.9 - - + -
56A GLN* 3.6 33.0 - - + +
90A LEU 5.4 0.4 + - - -
91A LEU* 4.5 10.9 - - + +
93A ASN* 3.6 12.3 + - - +
94A ALA 3.0 19.1 + - - +
95A ASP 2.5 8.3 + - - -
96A SER* 1.3 73.7 - - - +
98A GLN* 1.3 67.5 + - - +
100A LYS* 2.8 14.9 + - - +
101A VAL* 2.9 9.9 + - - +
224A PRO* 5.8 2.2 - - + -
227A GLY* 6.0 1.3 - - - -
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 3.9 5.2 + - - -
94A ALA* 2.5 52.5 + - - +
95A ASP* 2.6 27.6 + - - +
97A VAL* 1.3 74.1 - - - +
99A ALA* 1.4 52.7 + - - +
101A VAL* 2.5 38.4 + - + +
102A GLU* 3.1 13.3 + - - +
226A THR* 3.5 21.2 + - - +
227A GLY* 3.2 25.5 - - - +
228A TYR 6.3 0.6 - - - -
276A HIS* 5.7 3.0 - - - -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.6 5.9 - - - -
95A ASP 3.2 5.8 + - - +
96A SER* 3.2 20.6 - - - +
98A GLN* 1.4 75.9 - - - +
100A LYS* 1.3 73.7 + - + +
102A GLU* 3.5 24.6 + - - +
103A MET 3.7 5.4 + - - -
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.7 9.9 + - - +
29A GLU* 5.9 1.3 - - - -
52A LEU* 4.0 10.3 - - + -
75A PHE* 3.5 28.7 - - + -
76A TYR* 4.5 9.0 - - - +
81A HIS* 3.0 29.3 + - - -
83A PHE* 5.4 1.8 - - - -
89A PRO* 5.6 5.2 - - + -
91A LEU* 4.4 14.4 - - + -
96A SER* 3.4 17.7 - - - +
97A VAL 2.8 9.9 + - - +
99A ALA* 1.3 82.9 + - + +
101A VAL* 1.3 69.1 + - - +
103A MET* 2.9 40.2 + - - +
104A LEU* 3.4 26.5 + - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.0 13.5 - - + -
52A LEU* 4.1 6.2 - - + +
97A VAL 2.9 7.3 + - - +
98A GLN* 2.5 23.5 + - - +
100A LYS* 1.3 78.0 - - - +
102A GLU* 1.4 63.3 + - + +
104A LEU* 3.4 3.0 + - - +
105A ASP* 3.1 26.1 + - - +
224A PRO* 4.1 23.8 - - + -
227A GLY* 3.0 35.0 - - - +
228A TYR* 3.2 33.4 - - + +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.2 13.9 - - + +
98A GLN* 3.1 19.7 + - - +
99A ALA* 3.5 19.2 + - - +
101A VAL* 1.4 73.3 - - - +
103A MET* 1.3 70.0 + - - +
105A ASP* 2.9 16.0 + - + +
106A ASN* 2.5 29.4 + - - +
227A GLY 6.0 0.4 - - - -
246A TYR* 5.5 6.8 - - - -
501A FRM 5.9 4.9 - - - -
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Residues in contact with MET 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.1 44.0 - - + -
30A ILE* 3.3 29.4 - - + -
75A PHE* 3.9 15.5 - - + -
79A ILE* 4.6 4.3 - - + -
81A HIS* 3.8 12.1 - - - -
99A ALA 3.7 6.0 + - - +
100A LYS* 2.9 38.4 + - - +
101A VAL 3.4 1.2 - - - -
102A GLU* 1.3 83.7 - - - +
104A LEU* 1.4 81.7 + - + +
106A ASN* 3.3 3.5 + - - +
107A LEU* 2.8 36.8 + - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.6 19.8 - - + +
48A ALA* 3.7 20.4 - - + +
49A TYR* 3.3 35.9 - - + -
52A LEU* 3.5 31.6 - - + -
75A PHE* 4.2 2.9 - - + -
79A ILE* 3.8 20.2 - - + -
100A LYS 3.4 3.6 + - - +
101A VAL 3.8 2.2 - - - +
102A GLU 3.2 0.6 - - - -
103A MET* 1.4 81.0 - - + +
105A ASP* 1.4 60.2 - - - +
107A LEU* 3.4 23.6 + - + +
108A LEU* 2.8 33.3 + - - +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 2.7 25.5 + - - -
101A VAL* 3.1 16.5 + - - +
102A GLU* 2.9 14.7 + - - +
104A LEU* 1.4 68.9 - - - +
106A ASN* 1.3 60.0 + - - +
108A LEU* 2.9 26.7 + - - +
109A ASP* 3.4 4.7 + - - +
219A ALA* 4.1 3.4 - - - +
228A TYR* 3.4 36.8 + - - -
501A FRM 3.1 61.3 - - + +
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Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.9 0.2 - - + -
28A TYR* 3.4 31.4 + - + -
102A GLU* 2.5 34.2 + - - +
103A MET 3.3 4.9 - - - +
105A ASP* 1.3 73.7 - - - +
107A LEU* 1.3 67.9 + - - +
108A LEU 2.7 2.7 + - - -
109A ASP* 3.0 2.9 + - - -
110A ILE* 2.9 33.8 + - + +
204A ARG* 3.7 16.4 + - - +
206A THR* 5.2 0.7 - - - +
207A ASN* 3.4 31.0 + - - +
501A FRM 4.0 7.3 - - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET* 4.0 22.7 - - + -
28A TYR* 5.9 1.6 - - + -
30A ILE* 3.8 25.6 - - + -
35A MET* 4.6 8.5 - - + -
40A LEU* 3.6 36.6 - - + +
45A ILE* 3.6 16.2 - - + +
79A ILE* 4.7 3.4 - - + -
103A MET* 2.8 25.4 + - + +
104A LEU* 3.4 33.9 - - + +
106A ASN* 1.3 69.5 - - - +
108A LEU* 1.3 60.0 + - - +
110A ILE* 4.4 5.2 - - + -
111A GLU* 2.8 31.4 + - - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 5.0 11.7 - - + +
45A ILE* 3.5 34.3 - - + -
46A GLN* 5.4 2.0 - - + +
49A TYR* 3.2 32.1 - - + +
104A LEU 2.8 17.0 + - - +
105A ASP 2.9 9.6 + - - +
106A ASN 2.7 3.4 + - - -
107A LEU* 1.3 77.4 - - - +
109A ASP* 1.3 63.1 + - - +
111A GLU* 3.5 2.6 - - + +
112A VAL* 2.9 25.2 + - + +
217A ARG* 5.1 0.4 - - - +
220A PRO* 4.1 11.0 - - + -
501A FRM 3.5 31.4 - - + -
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP 3.4 3.8 + - - +
106A ASN 3.0 5.0 + - - +
108A LEU* 1.3 74.0 - - - +
110A ILE* 1.4 54.8 + - - +
112A VAL* 2.8 6.7 + - - +
113A ALA* 2.7 32.2 + - - +
206A THR 3.7 4.4 - - - +
207A ASN* 3.0 53.5 - - - +
210A GLY* 4.0 6.0 + - - -
211A ILE* 3.3 15.6 - - - +
217A ARG* 2.7 39.4 + - - -
501A FRM 3.7 16.8 - - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 4.1 20.2 - - + +
24A ALA* 3.8 28.5 - - + -
25A MET* 3.9 23.3 - - + -
37A LEU* 4.4 4.7 - - + -
40A LEU* 3.8 17.5 - - + -
106A ASN* 2.9 25.7 + - + +
107A LEU* 4.0 5.4 - - + +
109A ASP* 1.4 69.2 - - - +
111A GLU* 1.4 60.3 + - - +
113A ALA* 2.9 21.3 - - - +
114A TYR* 3.0 9.5 + - - +
206A THR* 3.6 31.9 - - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.6 41.7 - - + +
41A SER* 5.0 0.3 - - - -
42A LYS* 3.9 34.2 - - + +
43A ARG* 5.6 0.9 + - - -
45A ILE* 4.3 10.8 - - + -
107A LEU 2.8 23.6 + - - +
108A LEU* 3.5 4.0 - - + +
110A ILE* 1.4 69.8 - - - +
112A VAL* 1.3 73.9 + - + +
113A ALA 3.1 0.2 + - - -
114A TYR* 5.1 2.5 - - - -
115A SER* 2.7 67.5 + - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 2.9 27.1 + - + +
109A ASP* 2.8 12.7 + - - +
111A GLU* 1.3 91.7 - - + +
113A ALA* 1.4 50.5 + - - +
115A SER* 4.9 0.4 - - - -
116A LEU* 2.6 55.4 + - + +
210A GLY* 4.5 6.1 - - - -
213A SER* 4.4 4.7 - - - +
214A GLN* 4.4 21.3 - - + +
217A ARG* 4.1 16.4 - - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE 5.2 0.9 - - - +
16A PHE* 3.6 8.8 - - + -
21A MET* 4.3 16.2 - - + -
109A ASP 2.7 15.2 + - - +
110A ILE* 2.9 13.2 - - - +
112A VAL* 1.4 69.4 - - - +
114A TYR* 1.3 59.9 + - - +
116A LEU* 3.1 18.2 - - - +
117A LEU* 3.2 11.1 + - - +
206A THR 3.7 10.5 - - - +
209A ALA* 3.5 30.2 - - + +
210A GLY 4.7 0.6 - - - +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.1 23.6 - - + -
21A MET* 3.5 23.3 - - - -
22A LYS* 6.0 0.3 + - - -
37A LEU* 2.6 45.9 + - + +
38A GLY* 4.0 9.6 + - - -
40A LEU* 6.1 2.5 - - + -
110A ILE 3.0 9.8 + - - +
111A GLU* 4.3 2.0 - - - +
113A ALA* 1.3 74.2 - - - +
115A SER* 1.3 72.9 + - - +
116A LEU 3.0 1.1 - - - -
117A LEU* 2.8 37.4 - - + +
118A ARG* 3.3 48.5 + - + +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 5.7 2.3 - - - -
111A GLU* 2.7 50.4 + - - +
112A VAL* 4.7 0.4 - - - -
114A TYR* 1.3 79.7 - - - +
116A LEU* 1.3 66.2 + - - +
118A ARG* 3.7 15.2 + - - +
119A GLY 4.5 0.7 + - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.9 14.8 - - + -
112A VAL* 2.6 36.3 + - + +
113A ALA* 3.1 11.9 - - - +
114A TYR 3.0 0.2 - - - -
115A SER* 1.3 79.1 - - - +
117A LEU* 1.4 62.0 - - - +
119A GLY* 3.2 8.3 + - - -
135A LYS* 2.8 70.6 + - + +
136A LEU* 6.1 0.4 - - + -
209A ALA 5.0 3.8 - - - +
213A SER* 3.7 29.8 - - - +
214A GLN* 6.0 0.9 - - - +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.4 36.3 - - + +
18A VAL* 3.5 31.2 - - + -
21A MET* 3.8 19.5 - - + -
113A ALA 3.2 3.2 + - - +
114A TYR* 2.8 26.5 - - + +
116A LEU* 1.4 74.2 - - - +
118A ARG* 1.3 53.2 + - + +
119A GLY* 2.6 20.4 + - - -
120A GLY 4.1 0.3 + - - -
132A ASN* 4.3 19.1 - - - +
135A LYS* 3.2 14.8 + - - +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 4.7 10.5 - - - -
114A TYR* 3.3 53.4 + - + +
115A SER* 4.2 10.3 - - - +
116A LEU 3.2 2.6 + - - -
117A LEU* 1.3 69.8 - - + +
119A GLY* 1.3 65.3 + - - +
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER 4.5 0.8 + - - -
116A LEU 3.2 9.6 + - - -
117A LEU 2.6 11.0 + - - -
118A ARG* 1.3 75.8 - - - +
120A GLY* 1.3 52.1 + - - -
121A SER 2.6 19.5 + - - -
135A LYS* 4.5 2.9 - - - -
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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