Contacts of the helix formed by residues 86 - 109 (chain E) in PDB entry 2PWZ
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 86 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E GLY 4.0 2.8 + - - +
85E MET* 1.3 78.8 - - - +
87E ARG* 1.3 64.2 + - - +
88E SER* 3.7 11.7 + - - +
89E ASP* 3.2 32.0 + - + +
90E LEU* 3.0 22.0 + - - +
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Residues in contact with ARG 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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85E MET 4.0 0.2 + - - -
86E ASP* 1.3 73.5 - - - +
88E SER* 1.3 56.6 + - - +
90E LEU* 3.4 13.2 - - + +
91E PHE* 3.1 24.1 + - - +
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Residues in contact with SER 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ASP* 3.1 13.2 + - - +
87E ARG* 1.3 76.7 - - - +
89E ASP* 1.3 60.5 + - - +
90E LEU 3.2 0.9 - - - -
91E PHE* 3.7 11.3 - - - +
92E ASN* 2.8 45.0 + - - -
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Residues in contact with ASP 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E GLY 4.2 4.3 - - - +
85E MET* 3.9 21.7 - - + +
86E ASP* 3.2 38.5 + - - +
88E SER* 1.3 81.6 + - - +
90E LEU* 1.3 63.2 + - - +
92E ASN* 3.3 6.6 + - - +
93E VAL* 3.2 31.2 + - + +
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Residues in contact with LEU 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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79E VAL* 3.3 34.5 - - + +
80E ALA 3.6 12.3 - - - +
81E ARG* 3.8 31.0 - - + +
82E LYS 4.9 0.4 - - - +
85E MET* 4.4 14.3 - - + -
86E ASP 3.0 11.6 + - - +
87E ARG* 3.4 16.2 - - + +
89E ASP* 1.3 76.3 - - - +
91E PHE* 1.3 61.9 + - - +
93E VAL* 4.1 1.9 - - - +
94E ASN* 3.2 38.1 + - - +
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Residues in contact with PHE 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 ARG 3.1 16.0 + - - +
88E SER* 3.8 11.4 - - - +
89E ASP 3.2 0.4 - - - -
90E LEU* 1.3 75.0 - - - +
92E ASN* 1.3 65.0 + - - +
93E VAL 3.2 0.2 - - - -
94E ASN* 3.2 2.9 + - - -
95E ALA* 2.7 60.9 + - + +
120E PRO* 3.9 29.8 - - + -
123E THR* 3.5 33.4 - - + -
124E THR* 5.4 0.7 - - + -
127E ILE* 4.5 3.8 - - + -
305E LEU* 3.8 31.9 - - + -
309E PHE* 4.3 16.8 - + + -
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Residues in contact with ASN 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E SER* 2.8 35.8 + - - +
89E ASP* 3.3 8.2 + - - +
91E PHE* 1.3 85.0 - - - +
93E VAL* 1.3 60.1 + - + +
95E ALA* 4.1 2.7 - - - -
96E GLY* 3.2 22.0 + - - -
309E PHE* 4.0 22.9 - - - -
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Residues in contact with VAL 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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79E VAL* 4.0 23.3 - - + -
85E MET* 4.3 17.9 - - + -
89E ASP* 3.2 17.9 + - + +
90E LEU 4.1 2.7 - - - +
91E PHE 3.2 0.4 - - - -
92E ASN* 1.3 81.1 - - + +
94E ASN* 1.3 58.2 + - - +
96E GLY* 3.4 1.2 + - - -
97E ILE* 3.0 44.0 + - + +
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Residues in contact with ASN 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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78E GLY* 3.1 12.2 - - - -
79E VAL* 2.9 46.7 + - - +
90E LEU* 3.2 26.1 + - - +
91E PHE* 4.1 3.1 - - - +
93E VAL* 1.3 78.2 - - - +
95E ALA* 1.3 59.1 + - - +
97E ILE* 3.3 7.5 + - - +
98E VAL* 2.9 34.2 + - - +
118E THR* 4.3 8.4 - - + +
119E ASN 4.1 22.6 + - - +
120E PRO* 5.6 1.1 - - + -
124E THR* 5.2 1.3 - - - -
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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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91E PHE* 2.7 34.5 + - + +
94E ASN* 1.3 73.2 - - - +
96E GLY* 1.3 57.1 + - - +
98E VAL* 3.5 4.3 + - - +
99E LYS* 3.1 22.5 + - - +
124E THR* 5.0 3.5 - - - +
127E ILE* 3.7 26.9 - - + +
309E PHE* 3.4 35.1 - - + -
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Residues in contact with GLY 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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92E ASN 3.2 17.0 + - - -
93E VAL* 3.9 1.6 - - - -
94E ASN 3.3 0.2 - - - -
95E ALA* 1.3 73.9 - - - +
97E ILE* 1.3 60.9 + - - +
99E LYS* 4.0 3.1 - - - +
100E ASN* 3.1 30.1 + - - +
309E PHE* 3.5 15.6 - - - -
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Residues in contact with ILE 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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77E ALA* 3.5 32.3 - - + -
78E GLY* 3.8 25.6 - - - +
79E VAL* 4.2 9.6 - - + -
93E VAL* 3.0 33.7 + - + +
94E ASN* 3.5 11.0 - - - +
96E GLY* 1.3 75.1 - - - +
98E VAL* 1.3 70.2 + - + +
100E ASN* 3.5 4.0 + - - +
101E LEU* 3.1 30.7 + - + +
118E THR* 5.6 0.2 - - + -
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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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75E ILE* 5.0 7.2 - - + -
94E ASN 2.9 21.2 + - - +
95E ALA 3.5 4.2 + - - +
96E GLY 3.5 0.2 - - - -
97E ILE* 1.3 76.0 - - + +
99E LYS* 1.3 58.6 + - - +
101E LEU* 3.9 3.9 - - - +
102E VAL* 2.9 52.4 + - + +
116E ILE* 4.6 10.8 - - + -
118E THR* 3.6 33.9 - - + +
124E THR* 3.7 37.0 - - + +
127E ILE* 4.1 9.4 - - + -
128E ALA 4.4 0.7 - - - +
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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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95E ALA 3.1 18.1 + - - +
96E GLY* 4.0 4.5 - - - +
97E ILE 3.4 0.2 - - - -
98E VAL* 1.3 77.4 - - - +
100E ASN* 1.3 62.7 + - - +
102E VAL* 4.2 1.4 - - - +
103E GLN* 3.1 55.6 + - - +
127E ILE* 4.0 14.5 - - + +
131E VAL* 3.8 14.9 - - + +
309E PHE* 4.2 20.2 + - + -
310E VAL* 4.5 33.0 + - + +
312E LYS* 4.6 12.7 - - - +
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Residues in contact with ASN 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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61E GLU 5.1 0.9 - - - +
96E GLY 3.1 19.5 + - - +
97E ILE* 3.9 4.3 - - - +
98E VAL 3.3 0.2 - - - -
99E LYS* 1.3 76.1 - - - +
101E LEU* 1.3 71.4 + - - +
103E GLN* 3.3 16.9 + - - +
104E GLN* 3.1 44.7 + - - +
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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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6E LEU* 3.9 26.4 - - + +
33E TYR* 3.8 29.4 - - + +
63E ALA* 4.4 3.8 - - + -
75E ILE* 4.2 17.3 - - + -
77E ALA* 3.5 31.9 - - + -
97E ILE* 3.1 23.7 + - + +
98E VAL 4.0 1.6 - - - +
100E ASN* 1.3 82.4 - - - +
102E VAL* 1.3 56.1 + - - +
104E GLN* 3.0 21.7 + - - +
105E VAL* 2.9 32.0 + - - +
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Residues in contact with VAL 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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75E ILE* 3.9 17.3 - - + -
98E VAL* 2.9 31.4 + - + +
99E LYS 4.2 0.4 - - - +
101E LEU* 1.3 74.8 - - - +
103E GLN* 1.3 57.3 + - - +
105E VAL* 3.2 9.1 + - + +
106E ALA* 2.8 27.9 + - - +
114E ILE* 5.1 4.5 - - + -
116E ILE* 4.4 2.0 - - + -
128E ALA* 3.6 38.8 - - + +
131E VAL* 3.6 20.4 - - + -
132E LEU* 3.7 20.0 - - + -
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Residues in contact with GLN 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 LYS* 3.1 56.1 + - - +
100E ASN* 3.4 19.0 + - - +
101E LEU 3.2 0.2 - - - -
102E VAL* 1.3 75.8 - - - +
104E GLN* 1.3 58.2 + - + +
106E ALA* 3.5 5.6 + - - +
107E LYS* 3.1 27.0 + - - +
131E VAL* 3.5 19.3 - - + +
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Residues in contact with GLN 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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33E TYR* 5.1 1.2 + - - -
61E GLU 3.3 19.7 + - - -
62E ASP* 3.5 9.8 - - - +
63E ALA* 2.8 34.2 + - + +
64E THR* 4.0 3.4 + - - +
67E LEU* 3.7 13.0 - - + +
100E ASN* 3.1 41.0 + - - +
101E LEU* 3.0 17.9 + - - +
103E GLN* 1.3 74.8 - - + +
105E VAL* 1.3 58.0 + - - +
107E LYS* 3.4 6.1 + - - +
108E THR* 3.0 35.7 + - - +
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Residues in contact with VAL 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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6E LEU* 4.3 3.6 - - + -
67E LEU* 3.8 28.5 - - + -
73E VAL* 3.9 16.8 - - + -
75E ILE* 4.6 4.9 - - + -
101E LEU 2.9 19.1 + - - +
102E VAL* 3.2 12.8 + - + +
104E GLN* 1.3 75.1 - - - +
106E ALA* 1.3 60.8 + - - +
109E CYS* 2.8 57.3 + - - +
110E PRO* 4.9 1.3 - - + -
114E ILE* 3.8 32.8 - - + -
132E LEU* 5.1 0.4 - - + -
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Residues in contact with ALA 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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102E VAL 2.8 20.5 + - - +
103E GLN* 3.7 9.4 - - - +
104E GLN 3.4 0.2 - - - -
105E VAL* 1.3 74.1 - - - +
107E LYS* 1.3 60.9 + - - +
110E PRO* 3.4 26.8 - - - +
131E VAL* 5.0 2.0 - - + -
132E LEU* 4.1 11.2 - - + -
135E ALA* 3.9 28.2 - - + +
137E VAL* 4.0 14.9 - - + +
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Residues in contact with LYS 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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64E THR* 6.0 0.7 - - - +
103E GLN 3.1 17.7 + - - +
104E GLN* 3.7 7.9 - - - +
106E ALA* 1.3 79.8 - - - +
108E THR* 1.3 68.3 + - - +
110E PRO* 4.1 4.7 - - - +
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Residues in contact with THR 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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64E THR* 3.7 29.6 + - + +
67E LEU* 3.7 13.8 - - + +
68E GLU* 3.7 53.6 - - - +
69E GLY 5.4 0.9 + - - -
104E GLN* 3.0 16.3 + - - -
107E LYS* 1.3 84.8 - - - +
109E CYS* 1.3 58.3 + - - +
110E PRO* 3.4 7.2 - - - +
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Residues in contact with CYS 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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67E LEU* 3.2 40.6 - - - +
69E GLY* 5.2 1.1 - - - +
70E ALA* 3.8 19.7 - - - +
73E VAL* 3.6 30.3 - - - -
105E VAL* 2.8 26.2 + - - +
108E THR* 1.3 72.9 - - - +
110E PRO* 1.4 59.9 - - - +
111E LYS 3.2 2.7 - - - -
112E ALA* 3.1 20.5 + - - +
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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