Contacts of the helix formed by residues 93 - 116 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E GLN* 3.3 3.0 + - - -
91E SER* 2.9 12.6 + - - +
92E THR* 1.3 80.5 + - - +
94E PRO* 1.4 70.6 - - - +
95E ALA* 2.7 32.8 + - - +
96E THR* 2.7 33.6 + - + +
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Residues in contact with PRO 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LYS* 3.7 9.7 - - + +
25E GLN* 3.5 16.2 - - + +
26E GLU* 4.0 43.1 - - + +
29E ALA* 5.3 7.9 - - + -
92E THR 3.4 6.5 - - - +
93E ASP* 1.4 89.8 - - - +
95E ALA* 1.3 56.1 + - - +
96E THR 3.1 0.2 - - - -
97E GLY* 3.1 3.3 + - - -
98E GLN* 2.9 28.9 + - - +
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ASP* 2.7 30.2 + - - +
94E PRO* 1.3 73.3 - - - +
96E THR* 1.3 57.2 + - + +
98E GLN* 3.6 8.3 - - - +
99E LYS* 3.0 26.9 + - - +
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Residues in contact with THR 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLN* 2.8 21.0 + - - -
84E ALA* 4.2 7.1 - - - +
87E ALA* 4.4 11.4 - - + +
88E ALA* 3.6 18.7 - - - +
91E SER* 3.6 24.3 + - - +
93E ASP* 2.7 24.3 + - + +
95E ALA* 1.3 75.0 - - + +
97E GLY* 1.3 64.7 + - - +
99E LYS* 3.4 9.2 + - - +
100E ALA* 3.3 19.6 + - - +
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Residues in contact with GLY 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA* 5.0 2.2 - - - +
21E VAL* 4.7 4.5 - - - -
22E LYS* 4.1 14.8 - - - -
25E GLN* 3.2 18.8 + - - -
88E ALA* 4.4 9.0 - - - -
94E PRO 3.1 4.7 + - - -
96E THR* 1.3 82.0 + - - +
98E GLN* 1.3 62.5 + - - +
100E ALA* 3.3 6.3 + - - +
101E LEU* 3.1 25.5 + - - +
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Residues in contact with GLN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LYS* 2.6 39.1 + - + +
94E PRO 2.9 15.5 + - - +
95E ALA* 3.6 9.9 - - - +
96E THR 3.2 0.2 - - - -
97E GLY* 1.3 74.1 - - - +
99E LYS* 1.3 59.8 + - - +
101E LEU* 3.2 12.9 + - - +
102E ASP* 2.8 64.6 + - - +
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Residues in contact with LYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E ALA* 4.5 9.0 - - + +
95E ALA 3.0 17.4 + - - +
96E THR* 3.6 9.2 - - - +
97E GLY 3.3 0.2 - - - -
98E GLN* 1.3 76.6 - - - +
100E ALA* 1.3 63.2 + - - +
102E ASP* 3.3 12.0 + - + +
103E TYR* 3.1 58.0 + - + -
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Residues in contact with ALA 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA* 5.2 2.2 - - + -
81E ALA* 4.6 1.7 - - - +
84E ALA* 3.9 20.1 - - + +
85E LEU* 3.6 36.6 - - + -
88E ALA* 5.3 0.4 - - + -
96E THR 3.3 9.6 + - - +
97E GLY* 3.3 10.9 + - - +
98E GLN 3.2 0.6 - - - -
99E LYS* 1.3 79.2 - - - +
101E LEU* 1.3 56.6 + - - +
103E TYR* 3.3 4.9 + - - +
104E ILE* 3.0 35.5 + - + +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG* 4.0 13.5 - - + +
18E ALA* 3.5 29.6 - - + +
19E GLU* 3.9 26.7 - - + -
22E LYS* 3.8 44.0 - - + +
97E GLY 3.1 12.7 + - - +
98E GLN* 3.2 16.1 + - - +
100E ALA* 1.3 73.2 - - - +
102E ASP* 1.3 65.2 + - - +
104E ILE* 3.3 6.7 + - + +
105E ALA* 3.0 24.3 + - - +
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Residues in contact with ASP 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E GLN* 2.8 48.0 + - - +
99E LYS* 3.5 11.8 - - + +
101E LEU* 1.3 77.3 - - - +
103E TYR* 1.3 64.9 + - + +
105E ALA* 3.2 16.4 + - - +
106E GLN* 3.2 19.4 + - - +
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Residues in contact with TYR 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 3.7 19.8 - - + +
80E GLU* 3.7 51.9 + - + +
81E ALA* 3.7 17.9 - - + -
84E ALA* 3.9 15.5 - - + -
99E LYS* 3.1 54.1 + - + -
100E ALA 3.7 5.4 - - - +
102E ASP* 1.3 78.0 - - + +
104E ILE* 1.3 61.6 + - - +
106E GLN* 3.3 16.3 + - - +
107E ILE* 3.1 27.3 + - - +
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Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PRO* 4.5 11.2 - - + +
14E ALA* 4.2 13.0 - - + +
15E ARG* 4.2 28.5 - - + +
18E ALA* 3.5 31.9 - - + -
51E ALA* 5.4 0.2 - - + -
55E LEU* 4.2 32.3 - - + -
81E ALA* 4.7 2.7 - - + -
85E LEU* 4.8 7.0 - - + -
100E ALA* 3.0 22.7 + - + +
101E LEU* 3.7 7.4 - - + +
102E ASP 3.2 0.4 - - - -
103E TYR* 1.3 72.9 - - - +
105E ALA* 1.3 56.2 + - - +
107E ILE* 3.1 9.5 + - + +
108E ASP* 2.8 34.1 + - + +
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG* 6.6 0.2 - - - +
101E LEU 3.0 14.2 + - - +
102E ASP* 3.2 11.9 + - - +
104E ILE* 1.3 75.7 - - - +
106E GLN* 1.3 58.9 + - + +
108E ASP* 3.3 9.3 + - - +
109E LYS* 3.0 27.0 + - - +
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Residues in contact with GLN 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 3.3 31.9 - - + +
102E ASP* 3.2 13.6 + - + +
103E TYR* 3.5 19.7 - - - +
104E ILE 3.2 0.4 - - - -
105E ALA* 1.3 75.8 - - + +
107E ILE* 1.3 65.6 + - - +
109E LYS* 3.2 12.4 + - + +
110E ILE* 3.2 25.7 + - + +
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Residues in contact with ILE 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PRO* 5.2 2.9 - - + -
55E LEU* 4.1 18.4 - - + -
58E LEU* 4.3 24.0 - - + -
63E PHE* 4.4 17.7 - - + -
74E LEU* 5.2 1.6 - - + -
77E LEU* 3.6 21.3 - - + +
78E VAL* 3.8 26.2 - - + -
81E ALA* 3.7 29.4 - - + -
103E TYR 3.1 12.5 + - - +
104E ILE* 3.1 8.3 + - - +
106E GLN* 1.3 75.4 - - - +
108E ASP* 1.3 57.9 + - - +
110E ILE* 3.2 6.2 + - - +
111E PHE* 2.9 26.7 + - - +
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Residues in contact with ASP 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ASP* 4.8 0.9 - - - +
11E PRO* 3.6 25.4 - - + +
12E ALA* 4.8 2.1 + - - +
15E ARG* 5.7 4.7 + - - -
104E ILE* 2.8 19.1 + - + +
105E ALA* 3.5 10.2 - - - +
107E ILE* 1.3 76.0 - - - +
109E LYS* 1.3 66.7 + - - +
111E PHE* 3.4 5.7 + - - +
112E TRP* 3.1 49.2 + - - -
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Residues in contact with LYS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ALA 3.0 12.7 + - - +
106E GLN* 3.2 14.5 + - + +
108E ASP* 1.3 82.1 + - - +
110E ILE* 1.3 64.8 + - + +
112E TRP* 3.5 3.8 + - - +
113E GLU* 3.2 45.5 + - + +
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Residues in contact with ILE 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E PHE* 4.3 11.4 - - + -
71E TYR* 3.8 50.3 - - + -
73E GLU* 4.5 11.7 - - + +
74E LEU* 3.9 31.4 - - + -
77E LEU* 4.0 18.6 - - + -
106E GLN* 3.2 8.6 + - + +
107E ILE* 3.6 6.5 - - - +
109E LYS* 1.3 78.1 - - + +
111E PHE* 1.3 65.9 + - - +
113E GLU* 3.0 20.2 + - - +
114E THR* 3.0 13.5 + - + +
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Residues in contact with PHE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 3.7 30.7 - - + -
11E PRO* 3.4 33.9 - - + -
58E LEU* 4.2 9.4 - - + -
62E TYR* 3.4 45.3 - + - -
63E PHE* 4.2 11.7 - + + -
107E ILE* 2.9 17.0 + - + +
108E ASP 3.5 4.7 - - - +
109E LYS 3.3 0.2 - - - -
110E ILE* 1.3 76.6 - - - +
112E TRP* 1.3 91.7 + + - +
114E THR* 2.5 25.8 + - - -
115E LYS* 3.1 35.7 + - + +
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Residues in contact with TRP 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR 5.1 2.9 - - - -
10E ASP* 3.9 26.6 + - - -
11E PRO* 4.5 0.8 - - - +
108E ASP* 3.1 50.6 + - - +
109E LYS* 4.2 4.3 - - - +
111E PHE* 1.3 104.3 - + - +
113E GLU* 1.3 59.7 + - - +
115E LYS* 3.2 37.2 + - + +
116E LYS* 3.1 31.7 + - - +
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Residues in contact with GLU 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E TYR* 2.4 47.7 + - - +
109E LYS* 3.2 42.7 + - + +
110E ILE* 3.0 11.7 + - - +
112E TRP* 1.3 76.5 - - + +
114E THR* 1.3 58.6 + - - +
115E LYS 3.0 1.3 - - - -
116E LYS* 3.1 33.5 + - + +
117E ALA* 3.9 4.2 + - - +
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Residues in contact with THR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E TYR* 2.6 27.6 + - - -
63E PHE* 4.3 9.9 - - + -
67E HIS* 3.4 42.9 + - + -
71E TYR* 4.3 19.1 - - + -
110E ILE* 3.0 13.6 + - + +
111E PHE 2.5 19.4 + - - -
113E GLU* 1.3 77.1 - - - +
115E LYS* 1.3 59.1 + - - +
116E LYS 3.2 0.4 - - - -
117E ALA* 3.5 21.0 - - - +
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Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLY 4.8 11.7 + - - -
9E TYR* 5.6 4.6 + - - +
62E TYR* 3.1 26.5 - - + +
111E PHE* 3.1 42.2 + - + +
112E TRP* 3.4 34.8 - - + +
113E GLU 3.0 0.4 - - - -
114E THR* 1.3 75.3 - - - +
116E LYS* 1.3 57.0 + - + +
117E ALA* 3.1 12.3 + - - +
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Residues in contact with LYS 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E TRP* 3.1 25.4 - - - +
113E GLU* 3.1 19.9 + - + +
115E LYS* 1.3 79.2 - - + +
117E ALA* 1.3 61.4 + - - +
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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