Contacts of the helix formed by residues 77 - 100 (chain E) in PDB entry 5LF4
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 LEU 77 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.0 17.7 - - + -
19D GLY 4.4 14.8 - - - +
20D ARG* 5.4 4.9 - - + -
21D LEU* 4.0 27.6 - - + +
121D LEU* 4.2 12.8 - - + -
159D SER* 6.3 2.5 - - - -
28E ALA* 4.6 3.6 - - + -
76E GLY* 1.3 70.4 - - - -
78E THR* 1.3 61.2 + - - +
79E ALA 3.2 1.6 - - - +
80E ASP* 3.1 29.7 + - + +
81E ALA* 2.9 26.4 + - - +
126E ARG* 4.3 0.2 - - - +
129E GLY* 2.8 21.2 + - - +
130E VAL* 4.1 1.7 - - - +
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Residues in contact with THR 78 (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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159D SER 4.7 0.9 + - - -
160D GLY 4.1 0.7 + - - -
161D THR* 2.7 39.8 + - + +
60E GLN* 3.7 28.3 - - + +
61E LYS* 4.6 4.8 + - - -
74E ILE* 4.6 12.6 - - + -
76E GLY 3.2 8.2 + - - +
77E LEU* 1.3 70.7 - - - +
79E ALA* 1.3 57.8 + - - +
81E ALA* 3.1 11.3 + - - +
82E ARG* 2.9 41.3 + - - +
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Residues in contact with ALA 79 (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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117D SER 5.3 1.3 - - - +
118D ASN* 5.5 0.6 - - - +
121D LEU* 3.5 35.4 - - + +
159D SER 3.6 16.0 + - - +
160D GLY* 4.6 1.8 - - - -
77E LEU* 3.2 0.8 - - - +
78E THR* 1.3 79.3 + - - +
80E ASP* 1.4 62.4 + - - +
82E ARG* 3.4 24.9 + - - +
83E LEU* 3.1 22.6 + - - +
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Residues in contact with ASP 80 (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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121D LEU* 3.7 7.3 - - - +
77E LEU* 3.1 21.5 + - + +
79E ALA* 1.4 75.2 - - - +
81E ALA* 1.3 63.5 + - - +
83E LEU* 3.4 12.5 + - - +
84E LEU* 3.0 27.0 + - - +
126E ARG* 2.6 46.6 + - - -
128E TYR* 3.5 14.0 - - + -
129E GLY* 2.8 18.8 + - - +
130E VAL* 4.0 16.2 - - + +
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Residues in contact with ALA 81 (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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64E LEU* 4.9 2.6 - - + +
72E ILE* 4.9 2.3 - - - +
74E ILE* 3.7 38.1 - - + -
77E LEU 2.9 12.6 + - - +
78E THR* 3.1 9.8 + - - +
80E ASP* 1.3 77.6 - - - +
82E ARG* 1.3 56.8 + - + +
84E LEU* 3.4 2.9 + - - +
85E CYS* 2.9 31.1 + - - +
130E VAL* 3.8 22.2 - - + +
132E LEU* 5.1 1.9 - - - +
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Residues in contact with ARG 82 (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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114D GLN* 4.6 13.9 - - - +
117D SER* 3.0 33.5 + - - -
118D ASN* 2.7 31.2 + - - +
160D GLY 2.9 26.5 + - - -
161D THR* 4.7 0.8 - - - +
162D PHE* 3.6 19.5 - - - -
61E LYS* 3.6 28.3 - - - +
64E LEU* 5.1 7.0 - - + -
78E THR* 2.9 24.9 + - - +
79E ALA* 3.4 20.7 + - - +
80E ASP 3.3 0.2 - - - -
81E ALA* 1.3 75.5 - - + +
83E LEU* 1.3 59.5 + - - +
85E CYS* 3.3 6.6 + - - +
86E ASN* 2.8 42.0 + - - +
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Residues in contact with LEU 83 (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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122D GLN* 6.5 0.9 - - + -
79E ALA 3.1 14.1 + - - +
80E ASP* 3.6 16.2 - - - +
82E ARG* 1.3 74.0 - - - +
84E LEU* 1.3 58.7 + - - +
86E ASN* 3.2 10.9 + - + +
87E PHE* 3.0 27.0 + - - +
115E LYS* 6.1 2.0 - - - -
128E TYR* 4.1 28.0 - - + +
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Residues in contact with LEU 84 (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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80E ASP 3.0 16.6 + - - +
81E ALA* 3.8 3.8 - - - +
83E LEU* 1.3 72.3 - - - +
85E CYS* 1.3 66.1 + - - +
87E PHE* 3.2 19.7 + - + +
88E MET* 2.9 29.5 + - - +
112E ILE* 4.3 16.8 - - + -
115E LYS* 4.6 4.3 - - + -
116E THR* 3.7 32.8 - - + -
128E TYR* 4.0 17.4 - - + -
130E VAL* 3.9 23.8 - - + +
132E LEU* 4.0 27.1 - - + -
147E THR* 4.9 2.5 - - - +
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Residues in contact with CYS 85 (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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64E LEU* 4.0 14.6 - - + -
65E HIS 4.0 6.7 - - - -
66E VAL* 4.2 3.8 - - - -
72E ILE* 3.8 28.7 - - + +
81E ALA 2.9 19.4 + - - +
82E ARG* 3.6 7.6 - - - +
84E LEU* 1.3 76.0 - - - +
86E ASN* 1.3 58.7 + - - +
88E MET* 3.2 7.2 + - - +
89E ARG* 2.9 64.6 + - - +
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Residues in contact with ASN 86 (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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118D ASN* 4.5 18.2 - - - +
82E ARG* 2.8 29.3 + - - +
83E LEU* 3.7 9.6 - - + +
85E CYS* 1.3 76.5 - - - +
87E PHE* 1.3 61.4 + - - +
89E ARG* 3.3 31.5 + - - +
90E GLN* 3.0 24.4 + - - +
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Residues in contact with PHE 87 (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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83E LEU 3.0 13.3 + - - +
84E LEU* 3.2 18.4 + - + +
86E ASN* 1.3 75.2 - - - +
88E MET* 1.3 70.5 + - + +
90E GLN* 3.2 7.1 + - + +
91E GLU* 2.9 58.6 + - + +
108E LEU* 5.1 0.9 - - + -
111E LEU* 3.9 36.3 - - + -
112E ILE* 4.2 7.4 - - + -
115E LYS* 3.5 49.4 - - + -
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Residues in contact with MET 88 (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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66E VAL* 3.8 15.7 - - + -
70E ILE* 4.6 0.9 - - + -
72E ILE* 3.5 35.7 - - + -
84E LEU* 2.9 18.9 + - + +
85E CYS* 3.5 6.5 - - - +
87E PHE* 1.3 77.0 - - + +
89E ARG* 1.3 57.9 + - - +
91E GLU* 3.3 2.8 + - - +
92E CYS* 3.0 34.1 + - - -
108E LEU* 3.8 29.7 - - + +
112E ILE* 3.5 39.0 - - + -
132E LEU* 3.8 19.7 - - - -
134E ILE* 3.9 13.2 - - + -
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Residues in contact with ARG 89 (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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114D GLN* 6.0 0.2 + - - -
64E LEU* 4.4 9.1 - - - +
65E HIS* 2.9 36.5 + - - +
66E VAL* 3.5 29.8 + - - +
85E CYS* 2.9 32.0 + - - +
86E ASN* 3.4 28.9 + - - +
88E MET* 1.3 76.4 - - - +
90E GLN* 1.3 57.7 + - - +
92E CYS* 3.4 4.0 + - - +
93E LEU* 2.9 37.9 + - + +
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Residues in contact with GLN 90 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E ASN 3.0 14.3 + - - +
87E PHE* 3.6 7.2 - - + +
88E MET 3.2 0.2 - - - -
89E ARG* 1.3 77.9 - - - +
91E GLU* 1.3 62.5 + - + +
93E LEU* 3.2 20.5 + - - +
94E ASP* 2.9 65.0 + - - +
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Residues in contact with GLU 91 (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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87E PHE* 2.9 55.9 + - + +
88E MET 3.7 4.7 - - - +
90E GLN* 1.3 78.7 - - - +
92E CYS* 1.3 61.5 + - - +
94E ASP* 3.6 13.9 - - - +
95E SER* 3.1 23.9 + - - -
103E LEU* 3.8 10.1 - - + +
108E LEU* 3.9 14.1 - - + -
111E LEU* 3.4 25.3 - - + +
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Residues in contact with CYS 92 (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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66E VAL* 3.8 13.5 - - - +
67E ASP* 3.5 33.8 - - + +
69E HIS* 4.4 0.2 - - - -
70E ILE* 4.0 9.6 - - - -
88E MET 3.0 20.7 + - - +
89E ARG* 3.6 6.3 - - - +
91E GLU* 1.3 74.5 - - - +
93E LEU* 1.3 66.2 + - + +
95E SER* 3.4 3.1 + - - -
96E ARG* 3.1 25.6 + - - +
103E LEU* 4.3 16.8 + - + +
108E LEU* 3.7 23.3 - - - -
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Residues in contact with LEU 93 (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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66E VAL 6.2 0.2 - - - +
67E ASP* 5.6 6.1 - - - +
89E ARG* 2.9 26.7 + - + +
90E GLN* 3.7 25.8 - - - +
92E CYS* 1.3 75.9 - - + +
94E ASP* 1.3 58.6 + - - +
96E ARG* 3.2 10.8 + - - +
97E PHE* 2.8 30.7 + - - +
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Residues in contact with ASP 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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90E GLN* 2.9 48.0 + - - +
91E GLU* 3.6 18.3 - - - +
93E LEU* 1.3 74.5 - - - +
95E SER* 1.3 58.8 + - - +
97E PHE* 3.2 6.0 + - - +
98E VAL* 2.9 38.0 + - + +
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Residues in contact with SER 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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91E GLU 3.1 13.9 + - - -
92E CYS 4.1 0.9 - - - -
93E LEU 3.3 0.4 - - - -
94E ASP* 1.3 78.8 - - - +
96E ARG* 1.3 58.5 + - - +
98E VAL* 4.8 0.4 - - - -
99E PHE* 2.9 38.6 + - - +
100E ASP 3.5 0.9 + - - -
101E ARG* 2.9 41.6 + - - +
103E LEU* 3.5 27.5 + - - -
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Residues in contact with ARG 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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67E ASP* 2.8 38.3 + - - -
68E ASN* 4.2 17.4 - - - +
69E HIS* 3.4 20.6 + - - +
92E CYS 3.1 14.5 + - - +
93E LEU* 3.8 11.2 - - + +
95E SER* 1.3 73.0 + - - +
97E PHE* 1.3 63.0 + - - +
100E ASP* 2.9 33.6 + - - +
101E ARG* 3.8 18.7 - - - +
102E PRO* 3.5 31.5 - - + +
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Residues in contact with PHE 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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93E LEU 2.8 20.5 + - - +
94E ASP* 3.6 8.3 - - - +
96E ARG* 1.3 75.4 - - - +
98E VAL* 1.3 73.9 + - + +
100E ASP* 4.6 1.2 + - - +
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Residues in contact with VAL 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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94E ASP* 2.9 23.2 + - + +
95E SER* 4.8 0.2 - - - -
97E PHE* 1.3 89.0 - - + +
99E PHE* 1.3 95.3 + - + +
100E ASP* 5.5 0.3 - - - +
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Residues in contact with PHE 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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95E SER* 2.9 18.6 + - - +
98E VAL* 1.3 99.6 - - + +
100E ASP* 1.3 73.1 + - - +
101E ARG* 3.2 48.0 + - + +
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Residues in contact with ASP 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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95E SER 3.5 0.6 + - - -
96E ARG* 2.9 26.0 + - - +
97E PHE 5.6 0.9 - - - +
98E VAL 3.7 1.0 - - - +
99E PHE* 1.3 80.0 - - - +
101E ARG* 1.3 59.8 + - - +
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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