Contacts of the helix formed by residues 81 - 104 (chain E) in PDB entry 4R3O
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 81 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 4.1 12.6 - - + -
16D LEU* 3.9 28.5 - - + -
152D THR* 6.0 0.2 - - - -
30E ALA* 4.9 12.3 - - + +
79E SER 4.1 0.6 + - - -
80E GLY* 1.3 72.1 - - - +
82E ILE* 1.3 65.4 + - - +
83E ALA* 3.2 3.8 - - + +
84E ASP* 3.0 31.0 + - - +
85E ALA* 3.2 9.8 + - - +
138E GLY* 2.9 35.6 + - - +
139E VAL* 4.1 4.4 - - - +
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Residues in contact with ILE 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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152D THR* 5.2 11.7 - - + +
154D HIS* 6.5 0.9 - - + -
65E GLU 4.8 9.0 - - - +
66E LYS* 4.1 36.3 - - + +
78E MET* 4.3 35.7 - - + +
79E SER* 4.8 0.9 - - - -
80E GLY 3.3 18.6 + - - +
81E LEU* 1.3 71.0 - - - +
83E ALA* 1.3 56.0 + - - +
85E ALA* 2.8 24.4 + - - +
86E LYS* 3.0 15.6 + - + +
139E VAL* 6.0 0.2 - - + -
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Residues in contact with ALA 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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116D GLN* 3.5 21.5 - - + +
150D SER* 3.6 25.8 - - - +
151D GLY 3.8 21.5 - - - -
152D THR* 4.0 12.0 - - + +
81E LEU* 3.2 2.2 - - + -
82E ILE* 1.3 77.5 - - - +
84E ASP* 1.3 65.1 + - - +
86E LYS* 3.6 17.2 + - - +
87E THR* 3.9 5.2 + - - -
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Residues in contact with ASP 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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16D LEU* 5.4 0.5 - - - +
116D GLN* 3.6 18.2 + - - +
119D THR* 5.0 0.9 + - - -
120D GLN* 4.4 1.6 + - - -
150D SER 5.2 0.5 - - - +
81E LEU* 3.0 26.5 + - + +
83E ALA* 1.3 79.9 - - - +
85E ALA* 1.3 64.4 + - - +
86E LYS 3.6 0.2 + - - -
87E THR* 3.6 8.5 + - - -
88E LEU* 3.7 2.3 - - - +
135E ARG* 2.2 36.9 + - - -
137E PHE* 3.4 36.1 - - + -
138E GLY 3.4 21.4 + - - +
139E VAL* 4.5 2.9 - - + -
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Residues in contact with ALA 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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78E MET* 3.5 27.8 - - + -
81E LEU 3.2 3.6 + - - -
82E ILE* 2.8 15.4 + - - +
84E ASP* 1.3 77.3 - - - +
86E LYS* 1.3 64.5 + - - +
88E LEU* 3.0 8.5 + - - +
89E ILE* 2.9 25.8 + - - +
139E VAL* 3.7 30.9 - - + +
141E LEU* 4.7 3.1 - - + -
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Residues in contact with LYS 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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153D TYR* 6.6 0.4 - - + -
78E MET* 5.0 2.1 - - - -
82E ILE* 3.0 11.5 + - + +
83E ALA* 3.7 13.5 - - - +
84E ASP 3.4 0.4 - - - -
85E ALA* 1.3 75.5 - - - +
87E THR* 1.3 56.1 + - - +
89E ILE* 3.4 9.6 + - - +
90E ASP* 3.0 29.8 + - - +
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Residues in contact with THR 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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116D GLN* 3.7 21.7 + - - +
83E ALA 3.9 4.5 + - - -
84E ASP 3.7 11.3 + - - -
85E ALA 3.2 0.6 - - - -
86E LYS* 1.3 79.0 - - - +
88E LEU* 1.3 57.3 + - + +
90E ASP* 3.3 6.5 + - - +
91E LYS* 2.9 29.8 + - + +
119E LEU* 6.1 2.2 - - + -
133E MET* 4.5 15.4 - - + +
137E PHE* 4.0 17.8 - - + -
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Residues in contact with LEU 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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84E ASP 3.7 10.3 - - - +
85E ALA* 3.0 6.0 + - - +
87E THR* 1.3 73.2 - - + +
89E ILE* 1.3 61.5 + - - +
91E LYS* 3.3 5.7 + - - +
92E ALA* 2.9 29.5 + - - +
116E VAL* 3.9 24.2 - - + +
119E LEU* 4.2 21.1 - - + -
137E PHE* 3.6 41.3 - - + -
139E VAL* 3.6 31.0 - - + -
141E LEU* 3.9 21.1 - - + -
143E PHE* 6.3 0.2 - - - -
156E MET* 4.7 7.0 - - + -
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Residues in contact with ILE 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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68E VAL* 3.6 29.6 - - + -
70E ILE* 4.0 8.7 - - + -
76E CYS* 3.7 30.5 - - - -
78E MET* 4.2 12.1 - - + -
85E ALA 2.9 22.6 + - - +
86E LYS* 3.6 9.2 - - - +
88E LEU* 1.3 76.6 - - + +
90E ASP* 1.3 63.0 + - - +
92E ALA* 3.1 6.9 + - - +
93E ARG* 3.0 56.9 + - - +
141E LEU* 4.4 11.7 - - + -
143E PHE* 5.3 2.0 - - + -
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Residues in contact with ASP 90 (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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86E LYS 3.0 17.6 + - - +
87E THR* 3.7 5.8 - - - +
89E ILE* 1.3 76.8 - - - +
91E LYS* 1.3 58.3 + - - +
93E ARG* 3.3 17.3 + - - +
94E VAL* 2.9 48.5 + - - +
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Residues in contact with LYS 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 THR* 2.9 19.2 + - + +
88E LEU 3.6 5.6 - - - +
89E ILE 3.3 0.2 - - - -
90E ASP* 1.3 77.5 + - - +
92E ALA* 1.3 58.1 - - - +
94E VAL* 3.8 6.6 - - + +
95E GLU* 2.9 62.7 + - + +
115E ALA* 3.9 21.7 + - - +
116E VAL* 5.4 2.7 - - + -
118E ASN* 5.3 2.8 - - - +
119E LEU* 3.6 43.4 - - + +
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Residues in contact with ALA 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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70E ILE* 3.9 26.2 - - + -
88E LEU 2.9 14.1 + - - +
89E ILE* 3.4 8.7 - - - +
91E LYS* 1.3 74.7 - - - +
93E ARG* 1.3 60.1 + - - +
95E GLU* 3.2 8.7 + - - +
96E THR* 2.9 32.9 + - - +
112E VAL* 4.1 7.2 - - + +
116E VAL* 3.6 24.0 - - + +
143E PHE* 4.7 1.8 - - + -
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Residues in contact with ARG 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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68E VAL* 3.5 27.9 - - - +
69E GLU* 2.9 26.6 + - - +
70E ILE* 3.5 23.6 - - - +
89E ILE* 3.0 34.7 + - + +
90E ASP* 3.3 17.5 + - - +
92E ALA* 1.3 74.9 - - - +
94E VAL* 1.3 62.1 + - + +
96E THR* 2.5 25.3 + - - -
97E GLN* 3.0 15.6 + - + +
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Residues in contact with VAL 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 ASP* 2.9 36.7 + - - +
91E LYS* 3.8 7.6 - - + +
93E ARG* 1.3 76.3 - - + +
95E GLU* 1.3 58.8 + - + +
97E GLN* 3.3 7.1 + - - +
98E ASN* 2.9 54.7 + - - +
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Residues in contact with GLU 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 LYS* 2.9 52.3 + - + +
92E ALA* 3.2 8.9 + - - +
94E VAL* 1.3 73.9 - - + +
96E THR* 1.3 65.2 + - - +
98E ASN* 3.3 14.3 + - - +
99E HIS* 3.0 24.4 + - - +
107E MET* 4.1 20.0 - - + +
112E VAL* 6.0 0.4 - - + -
115E ALA* 4.1 18.3 - - + +
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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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70E ILE* 3.9 20.9 + - + -
71E ASP* 4.2 19.8 + - + +
73E HIS* 5.6 0.9 - - + -
74E ILE* 5.1 2.0 - - + -
92E ALA 2.9 17.2 + - - +
93E ARG* 2.5 24.9 + - - -
95E GLU* 1.3 74.4 - - - +
97E GLN* 1.3 68.7 + - - +
99E HIS* 3.3 3.6 + - - +
100E TRP* 2.9 28.4 + - - +
106E THR* 6.1 0.3 - - - -
107E MET* 3.9 16.5 + - + +
112E VAL* 3.6 29.2 - - + -
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Residues in contact with GLN 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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70E ILE 5.6 0.6 + - - -
71E ASP* 3.8 28.7 + - - -
93E ARG* 3.0 16.1 + - + +
94E VAL* 3.7 7.0 - - - +
96E THR* 1.3 86.3 + - - +
98E ASN* 1.3 59.4 + - - +
100E TRP* 3.4 30.3 + - - +
101E PHE* 2.9 27.9 + - - +
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Residues in contact with ASN 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 VAL* 2.9 41.8 + - - +
95E GLU* 3.7 14.8 + - - +
96E THR 3.3 0.2 - - - -
97E GLN* 1.3 75.2 - - - +
99E HIS* 1.3 61.6 + - - +
101E PHE* 3.2 7.4 + - - +
102E THR* 2.9 36.6 + - - +
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Residues in contact with HIS 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 GLU* 3.0 12.3 + - - +
96E THR 3.3 0.9 + - - +
98E ASN* 1.3 77.4 - - - +
100E TRP* 1.3 57.0 + - - +
102E THR* 4.8 0.2 - - - -
103E TYR* 2.9 61.9 + + - +
105E GLU* 3.1 48.4 + - + -
106E THR 3.8 6.9 + - - -
107E MET* 3.4 44.8 - - + +
111E SER* 6.0 1.0 + - - -
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Residues in contact with TRP 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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71E ASP* 6.2 0.2 - - - +
96E THR 2.9 13.9 + - - +
97E GLN* 3.6 32.1 - - - +
99E HIS* 1.3 77.6 + - - +
101E PHE* 1.3 87.0 + + + +
104E ASN* 2.8 58.5 + - - +
105E GLU* 3.9 15.2 + - - +
106E THR* 5.4 5.8 - - + -
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Residues in contact with PHE 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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97E GLN 2.9 18.4 + - - +
98E ASN* 3.2 8.9 + - - +
100E TRP* 1.3 98.9 - + + +
102E THR* 1.3 71.2 + - - +
104E ASN* 4.5 1.9 + - - +
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Residues in contact with THR 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 ASN* 2.9 18.1 + - - +
101E PHE* 1.3 87.7 - - - +
103E TYR* 1.3 96.2 + - + +
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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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99E HIS* 2.9 48.8 + + - +
102E THR* 1.3 103.5 - - + +
104E ASN* 1.3 70.8 + - - +
105E GLU* 3.2 25.2 + - + +
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Residues in contact with ASN 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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100E TRP* 2.8 43.5 + - - +
101E PHE 4.5 1.9 + - - +
102E THR 3.7 0.8 - - - -
103E TYR* 1.3 80.3 - - - +
105E GLU* 1.3 59.7 + - - +
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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