Contacts of the helix formed by residues 93 - 117 (chain F) in PDB entry 1Q0K
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 ASP 93 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F GLN* 3.5 3.1 + - - -
91F SER* 2.9 11.9 + - - +
92F THR* 1.3 79.0 + - - +
94F PRO* 1.3 71.2 - - - +
95F ALA* 2.8 31.6 + - - +
96F THR* 2.7 33.8 + - + +
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Residues in contact with PRO 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LYS* 4.1 7.9 - - + +
25F GLN* 3.5 29.4 - - + +
26F GLU* 3.4 41.1 - - + +
29F ALA* 5.7 6.3 - - + -
92F THR 3.4 6.5 - - - +
93F ASP* 1.3 89.5 - - - +
95F ALA* 1.3 55.6 + - - +
96F THR 3.2 0.2 - - - -
97F GLY* 3.2 3.0 + - - -
98F GLN* 2.9 28.1 + - - +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ASP* 2.8 23.8 + - - +
94F PRO* 1.3 79.8 - - - +
96F THR* 1.3 58.2 + - + +
98F GLN* 3.2 8.7 + - - +
99F LYS* 2.9 28.6 + - - +
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Residues in contact with THR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F GLN* 2.8 21.1 + - - -
84F ALA* 4.1 5.1 - - - +
87F ALA* 4.3 11.0 - - + +
88F ALA* 3.5 21.2 - - - +
91F SER* 3.5 24.8 + - - +
93F ASP* 2.7 24.3 + - + +
95F ALA* 1.3 78.3 - - + +
97F GLY* 1.3 60.6 + - - +
99F LYS* 3.5 7.8 + - - +
100F ALA* 3.4 19.9 + - - +
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Residues in contact with GLY 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ALA* 4.8 2.0 - - - +
21F VAL* 4.5 6.5 - - - -
22F LYS* 4.4 8.5 - - - +
25F GLN* 3.2 22.0 + - - -
88F ALA* 4.2 9.4 - - - -
94F PRO 3.2 1.7 + - - -
96F THR* 1.3 83.5 + - - +
98F GLN* 1.3 61.3 + - - +
100F ALA* 3.4 6.0 + - - +
101F LEU* 3.1 30.4 + - - +
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Residues in contact with GLN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LYS* 2.5 39.9 + - + +
94F PRO 2.9 13.5 + - - +
95F ALA* 3.2 13.2 + - - +
97F GLY* 1.3 75.3 - - - +
99F LYS* 1.3 60.8 + - - +
101F LEU* 3.1 17.7 + - - +
102F ASP* 2.9 61.6 + - - +
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Residues in contact with LYS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ALA* 4.5 9.2 - - + -
95F ALA 2.9 15.2 + - - +
96F THR* 3.7 9.2 - - - +
97F GLY 3.3 0.2 - - - -
98F GLN* 1.3 75.4 - - - +
100F ALA* 1.3 63.5 + - - +
102F ASP* 3.3 11.4 + - + +
103F TYR* 3.2 57.6 + - + -
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Residues in contact with ALA 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ALA* 5.1 1.8 - - + -
81F ALA* 4.6 2.5 - - - +
84F ALA* 3.8 17.7 - - + +
85F LEU* 3.5 39.7 - - + +
88F ALA* 5.3 0.7 - - + -
96F THR 3.4 9.5 + - - +
97F GLY* 3.6 10.3 - - - +
98F GLN 3.2 0.4 - - - -
99F LYS* 1.3 78.6 - - - +
101F LEU* 1.3 57.6 + - - +
103F TYR* 3.3 4.8 + - - +
104F ILE* 3.0 35.1 + - + +
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ARG* 3.9 15.2 - - + +
18F ALA* 3.7 27.4 - - + +
19F GLU* 3.7 28.5 - - + +
22F LYS* 3.7 35.7 - - + +
97F GLY 3.1 18.7 + - - +
98F GLN* 3.1 18.3 + - - +
100F ALA* 1.3 76.9 - - - +
102F ASP* 1.3 56.8 + - - +
104F ILE* 3.4 8.0 + - + +
105F ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F GLN* 2.9 48.6 + - - +
99F LYS* 3.6 11.8 - - + +
100F ALA 3.2 0.2 - - - -
101F LEU* 1.3 75.6 - - - +
103F TYR* 1.3 65.5 + - + +
105F ALA* 3.3 9.1 + - - +
106F GLN* 3.2 28.8 + - - +
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Residues in contact with TYR 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LEU* 3.8 14.7 - - + +
80F GLU* 3.8 55.0 + - + +
81F ALA* 3.7 23.1 - - + -
84F ALA* 4.0 7.2 - - + -
99F LYS* 3.2 52.5 + - + -
100F ALA 3.7 3.1 - - - +
102F ASP* 1.3 74.2 - - + +
104F ILE* 1.3 65.6 + - - +
106F GLN* 3.1 24.1 + - - +
107F ILE* 2.9 27.9 + - - +
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Residues in contact with ILE 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F PRO* 4.3 11.9 - - + +
14F ALA* 4.0 17.3 - - + +
15F ARG* 4.1 30.1 - - + +
18F ALA* 3.6 31.9 - - + -
55F LEU* 4.0 29.6 - - + -
81F ALA* 4.9 1.8 - - + -
85F LEU* 4.7 9.2 - - + -
100F ALA 3.0 22.4 + - - +
101F LEU* 3.6 6.1 - - - +
103F TYR* 1.3 76.6 - - - +
105F ALA* 1.3 57.1 + - - +
107F ILE* 3.2 9.3 + - + +
108F ASP* 2.8 29.2 + - + +
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Residues in contact with ALA 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ARG* 6.4 2.0 - - - +
101F LEU 3.0 13.8 + - - +
102F ASP* 3.5 11.7 - - - +
104F ILE* 1.3 77.8 - - - +
106F GLN* 1.3 57.3 + - + +
108F ASP* 3.4 8.9 + - - +
109F LYS* 3.0 28.4 + - - +
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Residues in contact with GLN 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F LEU* 3.8 26.4 - - + +
102F ASP* 3.2 14.9 + - - +
103F TYR* 3.1 31.4 + - - +
105F ALA* 1.3 73.7 - - + +
107F ILE* 1.3 67.4 + - - +
109F LYS* 3.3 8.1 + - - +
110F ILE* 3.2 26.2 + - + +
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Residues in contact with ILE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F PRO* 4.9 2.7 - - + -
55F LEU* 4.0 17.7 - - + -
58F LEU* 4.2 25.4 - - + -
63F PHE* 4.3 17.2 - - + -
74F LEU* 5.1 1.6 - - + -
77F LEU* 3.7 22.4 - - + +
78F VAL* 4.0 24.5 - - + -
81F ALA* 3.7 30.3 - - + -
103F TYR 2.9 16.8 + - - +
104F ILE* 3.4 7.6 - - - +
106F GLN* 1.3 75.1 - - - +
108F ASP* 1.3 57.9 + - - +
110F ILE* 3.1 7.7 + - - +
111F PHE* 2.8 27.2 + - - +
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Residues in contact with ASP 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASP* 4.5 1.6 - - - +
11F PRO* 3.4 26.0 - - + +
12F ALA* 4.5 4.9 + - - +
15F ARG* 5.9 4.2 + - - -
104F ILE* 2.8 18.2 + - + +
105F ALA* 3.5 10.5 - - - +
107F ILE* 1.3 77.1 - - - +
109F LYS* 1.3 61.8 + - - +
111F PHE* 3.2 6.3 + - - +
112F TRP* 3.0 61.7 + - - -
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Residues in contact with LYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ALA 3.0 14.4 + - - +
106F GLN* 3.5 11.2 - - - +
107F ILE 3.2 0.2 - - - -
108F ASP* 1.3 78.0 + - - +
110F ILE* 1.3 65.2 + - + +
112F TRP* 3.4 6.0 + - + +
113F GLU* 3.2 44.0 + - + +
116F LYS* 5.9 5.2 - - - +
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Residues in contact with ILE 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F PHE* 4.2 17.0 - - + -
71F TYR* 3.9 49.4 - - + -
73F GLU* 4.2 14.1 - - + +
74F LEU* 4.0 14.6 - - + -
77F LEU* 3.6 30.3 - - + -
106F GLN* 3.2 7.6 + - + +
107F ILE* 3.1 7.7 + - - +
109F LYS* 1.3 77.4 - - + +
111F PHE* 1.3 64.1 + - - +
113F GLU* 3.2 12.2 + - - +
114F THR* 3.1 21.5 + - + +
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Residues in contact with PHE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F TYR* 3.4 40.2 - - + -
11F PRO* 3.5 35.7 - - + -
58F LEU* 4.2 5.2 - - + -
62F TYR* 3.4 39.9 - + - -
63F PHE* 4.3 11.2 - + + -
107F ILE 2.8 13.2 + - - +
108F ASP 3.4 7.6 - - - +
109F LYS 3.2 0.2 - - - -
110F ILE* 1.3 77.3 - - - +
112F TRP* 1.3 90.7 + + - +
114F THR* 2.6 24.2 + - - -
115F LYS* 3.1 37.4 + - + +
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Residues in contact with TRP 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F TYR 5.5 2.2 - - - -
10F ASP* 4.2 22.6 + - - -
11F PRO* 4.9 0.2 - - - +
108F ASP* 3.0 55.1 + - - +
109F LYS* 4.1 6.1 - - + +
111F PHE* 1.3 99.8 - + - +
113F GLU* 1.3 61.3 + - - +
115F LYS* 3.6 22.3 - - + +
116F LYS* 3.0 51.0 + - + +
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F TYR* 2.6 45.3 + - - +
109F LYS* 3.2 34.1 + - + +
110F ILE* 3.5 8.2 - - - +
111F PHE 3.2 0.6 - - - -
112F TRP* 1.3 77.5 - - - +
114F THR* 1.3 61.9 + - - +
116F LYS* 4.1 15.4 - - + +
117F ALA* 3.2 25.7 + - - +
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Residues in contact with THR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F TYR* 2.6 31.5 + - - -
63F PHE* 4.3 4.7 - - + -
67F HIS* 3.7 37.4 + - + -
71F TYR* 3.9 21.5 - - + -
110F ILE* 3.1 19.0 + - + +
111F PHE* 2.6 18.7 + - - -
113F GLU* 1.3 75.6 - - - +
115F LYS* 1.3 59.1 - - - +
117F ALA* 3.6 17.5 - - - +
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLY 4.5 13.9 + - - -
9F TYR* 5.6 3.6 + - - +
62F TYR* 3.0 33.3 - - + +
111F PHE* 3.1 44.9 + - + +
112F TRP* 3.6 25.1 - - + +
113F GLU 3.1 0.6 - - - -
114F THR* 1.3 74.7 - - - +
116F LYS* 1.3 59.3 + - + +
117F ALA 2.8 19.1 - - - +
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Residues in contact with LYS 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LYS* 5.8 5.1 + - - +
112F TRP* 3.0 38.8 + - + +
113F GLU* 4.1 14.9 - - + +
115F LYS* 1.3 76.9 - - + +
117F ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLU 3.2 17.0 + - - +
114F THR* 3.6 13.1 - - - +
115F LYS 2.8 18.5 - - - +
116F LYS* 1.3 80.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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