Contacts of the helix formed by residues 95 - 122 (chain F) in PDB entry 1QGH
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 MET 95 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 5.4 2.2 - - + -
34F MET* 3.6 47.1 - - + -
35F ARG 3.7 27.0 + - - +
36F GLY* 5.8 1.6 - - - -
38F ASN* 3.8 15.9 - - + +
39F PHE* 3.7 27.1 - - - +
42F LEU* 3.7 26.0 - - + -
94F THR* 1.3 75.7 - - + +
96F ASP* 1.3 58.4 + - - +
98F LEU* 3.3 6.9 + - - +
99F MET* 2.8 44.3 + - + +
149F PHE* 4.1 10.5 - - + -
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Residues in contact with ASP 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 2.8 40.6 + - - -
94F THR* 2.5 21.7 - - + +
95F MET* 1.3 69.4 - - - +
97F GLN* 1.3 64.1 + - + +
99F MET* 3.8 0.2 - - - +
100F GLU* 2.7 37.8 + - - +
149F PHE* 3.8 6.1 - - - -
150F LEU* 3.7 28.2 - - + +
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Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LYS* 4.0 15.2 - - - +
92F PRO 4.4 2.8 + - - +
93F LYS* 3.1 32.6 - - + +
94F THR* 3.0 46.5 + - + +
96F ASP* 1.3 81.7 - - + +
98F LEU* 1.3 62.1 + - - +
100F GLU* 3.3 14.9 + - - +
101F ASP* 3.1 19.8 + - - +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLN* 5.4 2.2 - - + +
30F ILE* 3.7 29.2 - - + +
33F TYR* 4.7 3.1 - - + -
34F MET* 3.9 36.3 - - + +
35F ARG 5.2 0.4 - - - +
89F TYR* 4.4 11.2 - - + +
93F LYS* 3.5 42.0 - - + +
94F THR 2.6 32.1 + - - +
95F MET* 3.5 6.7 - - - +
97F GLN* 1.3 70.7 - - - +
99F MET* 1.3 78.7 + - + +
101F ASP* 3.1 9.5 + - + +
102F LEU* 2.9 21.7 + - - +
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Residues in contact with MET 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ILE* 3.5 33.9 - - + -
34F MET* 4.7 0.9 - - + -
42F LEU* 4.2 17.5 - - + -
46F MET* 4.6 7.0 - - + -
95F MET* 2.8 29.5 + - + +
96F ASP 3.8 3.1 - - - +
98F LEU* 1.3 78.1 - - + +
100F GLU* 1.3 54.0 + - - +
102F LEU* 2.8 7.9 + - + +
103F VAL* 2.6 38.0 + - + +
146F PHE* 3.7 33.4 - - + -
149F PHE* 3.4 25.8 - - + -
150F LEU* 4.0 20.9 - - + -
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ASP* 2.7 25.2 + - - +
97F GLN* 3.6 15.8 - - - +
99F MET* 1.3 77.3 - - - +
101F ASP* 1.3 55.9 + - - +
103F VAL* 3.7 4.0 - - - +
104F GLY* 2.8 26.9 + - - -
150F LEU* 3.7 27.8 - - + +
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Residues in contact with ASP 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LYS* 3.2 40.6 + - - +
29F GLN* 4.7 4.0 + - - -
30F ILE* 5.2 4.1 - - + +
93F LYS* 4.5 16.3 + - - -
97F GLN 3.1 10.9 + - - +
98F LEU* 3.1 14.1 + - + +
100F GLU* 1.3 71.9 - - - +
102F LEU* 1.3 68.6 + - - +
104F GLY* 3.3 1.5 + - - -
105F THR* 3.1 22.7 + - - -
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F PHE* 3.4 34.5 - - + -
26F LYS* 5.2 1.3 - - - -
27F ILE* 4.8 3.4 - - + -
30F ILE* 4.0 18.8 - - + +
46F MET* 4.0 8.3 - - + -
49F LEU* 3.8 20.9 - - + -
98F LEU 2.9 12.5 + - - +
99F MET* 2.8 13.8 + - - +
101F ASP* 1.3 76.2 - - - +
103F VAL* 1.3 64.0 + - - +
105F THR* 3.1 4.4 + - - -
106F LEU* 2.9 26.4 + - + +
146F PHE* 3.8 41.7 - - + -
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Residues in contact with VAL 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F MET 2.6 21.3 + - - +
100F GLU* 3.7 7.0 - - - +
102F LEU* 1.3 75.5 - - - +
104F GLY* 1.3 64.6 + - - +
106F LEU* 3.2 10.0 + - + +
107F GLU* 2.8 33.4 + - + +
143F ILE* 4.9 7.6 - - + +
146F PHE* 3.4 35.7 - - + -
147F LYS* 3.8 32.1 - - + +
150F LEU* 4.4 13.9 - - + -
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Residues in contact with GLY 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F GLU 2.8 17.8 + - - -
101F ASP* 3.8 1.8 - - - -
102F LEU 3.2 0.2 - - - -
103F VAL* 1.3 78.1 - - - +
105F THR* 1.3 56.6 + - - +
107F GLU* 3.0 16.3 + - - +
108F LEU* 2.9 27.9 + - - +
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Residues in contact with THR 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F PHE* 3.4 37.7 - - + -
26F LYS* 3.6 18.6 - - - -
84F VAL* 3.9 28.0 - - + +
85F GLU 5.2 0.2 + - - -
101F ASP* 3.1 15.5 + - - -
102F LEU 3.1 7.2 + - - -
104F GLY* 1.3 76.0 - - - +
106F LEU* 1.3 64.6 + - - +
108F LEU* 3.2 8.6 + - + +
109F LEU* 3.0 24.8 + - + +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F PHE* 3.8 23.6 - - + -
49F LEU* 5.6 1.6 - - + -
53F PHE* 3.8 25.6 - - + -
102F LEU* 2.9 29.3 + - + +
103F VAL* 3.5 14.1 - - + +
104F GLY 3.1 0.2 - - - -
105F THR* 1.3 78.4 - - - +
107F GLU* 1.3 63.7 + - - +
109F LEU* 3.2 4.9 + - + +
110F ARG* 2.9 24.6 + - - +
139F ILE* 3.6 16.1 - - + +
142F HIS* 4.0 24.9 - - + -
143F ILE* 3.7 21.1 - - + +
146F PHE* 4.4 14.6 - - + -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F VAL* 2.8 26.7 + - + +
104F GLY* 3.4 14.9 - - - +
106F LEU* 1.3 74.8 - - - +
108F LEU* 1.3 64.6 + - - +
110F ARG* 3.2 26.1 + - - +
111F ASP* 2.9 32.2 + - - +
143F ILE* 3.9 18.2 - - + +
147F LYS* 3.4 27.2 + - - -
154F PRO 4.3 5.9 - - - +
155F LEU* 5.8 0.7 - - - -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN* 4.1 2.2 - - - +
83F SER* 3.7 30.7 - - - +
84F VAL* 4.0 22.9 - - + -
85F GLU* 5.3 0.9 - - + +
104F GLY 2.9 12.4 + - - +
105F THR* 3.5 11.0 - - - +
106F LEU 3.2 0.4 - - - -
107F GLU* 1.3 77.2 - - - +
109F LEU* 1.3 63.4 + - - +
111F ASP* 3.2 6.8 + - - +
112F GLU* 2.9 65.6 + - + +
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLN* 3.6 23.3 - - - +
19F ASN* 4.0 21.1 - - + +
20F LEU* 4.2 14.1 - - + -
23F PHE* 3.6 37.9 - - + -
53F PHE* 4.8 6.5 - - + -
84F VAL* 4.4 1.3 - - + -
105F THR* 3.0 25.0 + - + +
106F LEU* 3.7 8.3 - - + +
108F LEU* 1.3 76.8 - - + +
110F ARG* 1.3 57.3 + - - +
112F GLU* 3.3 1.5 + - - +
113F TYR* 2.7 50.6 + - + +
139F ILE* 4.2 13.7 - - + -
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Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU 2.9 13.0 + - - +
107F GLU* 3.3 32.9 + - - +
109F LEU* 1.3 76.8 - - - +
111F ASP* 1.3 93.2 + - - +
113F TYR* 3.1 6.7 + - - +
114F LYS* 2.9 24.0 + - + +
136F LYS* 4.2 21.6 - - + +
139F ILE* 4.0 14.6 - - + +
140F ASP* 3.2 26.4 + - - +
143F ILE* 3.7 19.8 - - + +
155F LEU* 3.7 27.1 - - - +
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Residues in contact with ASP 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F GLU* 2.9 23.9 + - - +
108F LEU* 3.7 5.3 + - - +
110F ARG* 1.3 106.1 + - - +
112F GLU* 1.3 63.9 + - + +
114F LYS* 3.1 17.9 + - - +
115F GLN* 3.0 27.2 + - - +
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 3.2 11.4 - - + -
15F HIS* 3.1 10.6 + - - -
16F GLN* 2.9 29.2 + - - +
19F ASN* 3.1 8.3 + - - -
83F SER* 2.5 27.8 + - - -
108F LEU* 2.9 38.8 + - + +
109F LEU* 3.9 3.8 - - - +
111F ASP* 1.3 77.9 - - + +
113F TYR* 1.3 64.6 + - - +
115F GLN* 3.0 14.8 + - + +
116F GLY 3.0 16.1 + - - -
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Residues in contact with TYR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 3.9 9.2 - + - -
16F GLN* 3.6 35.2 - - + +
20F LEU* 3.5 23.4 - - - +
56F GLN* 2.8 19.6 + - - -
60F VAL* 4.8 1.0 - - + +
109F LEU* 2.7 38.1 + - + +
110F ARG* 3.6 5.8 - - - +
112F GLU* 1.3 73.6 - - - +
114F LYS* 1.3 52.1 + - - +
116F GLY* 2.8 3.1 + - - -
117F ILE* 2.5 51.9 + - + +
132F LEU* 3.9 19.2 - - + +
135F PHE* 3.3 42.5 - + + -
136F LYS* 4.2 6.7 - - + -
139F ILE* 3.8 17.3 - - + -
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLY* 3.7 14.5 + - - -
126D ASP* 2.6 33.1 + - - +
110F ARG* 2.9 13.5 + - + +
111F ASP* 3.2 16.2 - - - +
112F GLU 3.1 0.2 - - - -
113F TYR* 1.3 75.9 - - - +
115F GLN* 1.3 62.7 + - - +
117F ILE* 3.0 13.7 + - + +
118F GLU* 2.8 57.0 + - - +
136F LYS* 4.6 14.3 - - + +
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Residues in contact with GLN 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 4.8 4.0 - - + -
111F ASP* 3.0 24.7 + - - +
112F GLU* 3.4 17.7 - - + +
114F LYS* 1.3 81.5 - - - +
116F GLY* 1.3 57.5 + - - +
118F GLU* 3.2 27.6 + - - +
119F LEU* 2.8 32.2 + - + +
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Residues in contact with GLY 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 3.4 36.7 - - - -
112F GLU 3.0 6.3 + - - -
113F TYR 2.8 9.8 + - - -
115F GLN* 1.3 74.7 - - - +
117F ILE* 1.3 64.4 + - - +
119F LEU* 3.6 5.3 - - - +
120F THR* 2.9 31.8 + - - -
132F LEU* 4.0 4.5 - - - -
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 3.7 31.4 - - + +
113F TYR 2.5 34.7 + - - +
114F LYS* 3.2 11.4 - - + +
115F GLN 3.0 0.2 - - - -
116F GLY* 1.3 79.3 - - - +
118F GLU* 1.3 64.5 + - - +
120F THR* 4.7 0.4 - - - -
121F ASP* 3.2 8.0 + - + +
129F ASN* 3.2 35.7 + - - +
132F LEU* 3.7 41.1 - - + +
133F ILE* 3.8 14.4 - - + +
136F LYS* 4.2 21.5 - - + -
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Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LYS* 2.8 46.7 + - - +
115F GLN* 3.2 31.6 - - - +
117F ILE* 1.3 71.2 - - - +
119F LEU* 1.3 66.1 + - - +
121F ASP* 3.1 10.1 + - - +
122F LYS* 2.9 31.6 + - + +
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Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 4.3 23.1 - - + +
8F ASP 4.0 20.9 - - - +
9F THR* 4.1 12.3 - - - +
12F PHE* 4.4 14.6 - - + -
115F GLN* 2.8 19.0 + - + +
116F GLY* 3.6 7.2 - - - +
118F GLU* 1.3 80.9 - - - +
120F THR* 1.3 54.3 + - - +
122F LYS* 3.2 6.8 + - + +
123F GLU* 2.7 57.7 + - - +
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Residues in contact with THR 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F THR* 4.1 12.3 + - - +
12F PHE* 5.7 1.2 - - - -
116F GLY* 2.9 22.2 + - - -
117F ILE 3.8 2.9 - - - -
119F LEU* 1.3 76.8 - - - +
121F ASP* 1.3 59.9 + - - +
123F GLU* 3.5 6.8 + - - -
124F GLY 3.0 6.2 + - - -
125F ASP* 2.6 66.6 + - + +
128F THR* 3.7 8.6 - - - +
129F ASN* 2.8 31.8 - - + +
132F LEU* 3.9 11.0 - - - +
----------------------------------------------------------
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Residues in contact with ASP 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ILE* 3.2 10.8 + - + +
118F GLU* 3.1 14.0 + - - +
120F THR* 1.3 75.9 - - - +
122F LYS* 1.3 81.7 + - - +
124F GLY* 2.8 16.7 + - - -
129F ASN* 3.9 14.7 - - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F GLU* 2.9 17.2 + - + +
119F LEU* 3.5 9.9 - - + +
121F ASP* 1.3 95.1 + - - +
123F GLU* 1.3 63.1 + - - +
124F GLY* 3.1 3.8 + - - -
----------------------------------------------------------
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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