Contacts of the helix formed by residues 85 - 114 (chain E) in PDB entry 6T7B
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 GLN 85 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E PHE* 1.3 78.4 - - - +
86E SER* 1.3 65.4 + - - +
87E SER 3.3 3.4 - - - +
88E ALA* 3.2 12.9 + - - +
89E VAL* 3.3 9.9 + - - -
81F VAL 3.3 17.0 + - - +
82F THR* 5.6 2.7 - - - +
49J G 4.7 2.9 - - - -
50J C 3.3 9.4 - - - -
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Residues in contact with SER 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E PHE 3.8 0.6 + - - -
85E GLN* 1.3 69.9 - - - +
87E SER* 1.3 60.1 + - - +
89E VAL* 3.5 1.9 + - - +
90E MET* 3.0 24.3 + - - -
50J C 2.5 20.4 + - - -
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Residues in contact with SER 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E GLN* 3.3 1.0 - - - +
86E SER* 1.3 78.5 - - - +
88E ALA* 1.3 55.5 + - - +
90E MET* 3.4 1.9 + - - +
91E ALA* 2.9 25.3 + - - -
83F ALA* 4.8 6.5 - - - +
50J C 4.5 0.6 + - - -
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Residues in contact with ALA 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E GLN* 3.2 10.9 + - - +
87E SER* 1.3 77.0 - - - +
89E VAL* 1.3 58.4 + - - +
91E ALA* 3.3 2.2 + - - +
92E LEU* 2.9 23.7 + - - -
81F VAL 4.8 3.4 - - - -
82F THR 4.4 7.2 - - - -
83F ALA* 4.1 22.8 - - - +
86F VAL* 6.5 0.7 - - - +
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Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLN* 6.4 1.8 - - - +
85E GLN 3.3 11.6 + - - -
86E SER* 3.5 2.6 + - - +
87E SER 3.4 0.2 - - - -
88E ALA* 1.3 73.4 - - - +
90E MET* 1.3 58.9 + - - +
92E LEU* 3.8 1.9 - - - +
93E GLN* 2.9 25.5 + - - -
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Residues in contact with MET 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E SER 3.0 15.2 + - - -
87E SER* 3.4 4.0 + - - +
89E VAL* 1.3 78.1 - - - +
91E ALA* 1.3 55.7 + - - +
93E GLN* 3.3 1.7 + - - +
94E GLU* 2.9 25.6 + - - -
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Residues in contact with ALA 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E SER 2.9 15.8 + - - -
88E ALA* 3.3 4.0 + - - +
90E MET* 1.3 72.8 - - - +
92E LEU* 1.3 61.1 + - - +
94E GLU* 3.8 1.5 - - - +
95E ALA* 2.9 26.5 + - - -
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ALA 2.9 14.4 + - - -
89E VAL* 3.4 4.0 + - - +
91E ALA* 1.3 76.2 - - - +
93E GLN* 1.3 56.1 + - - +
95E ALA* 5.2 0.7 - - - +
96E SER* 2.9 26.7 + - - -
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Residues in contact with GLN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E VAL 2.9 15.7 + - - -
90E MET* 3.8 2.9 - - - +
91E ALA 3.3 0.2 - - - -
92E LEU* 1.3 76.3 - - - +
94E GLU* 1.3 55.8 + - - +
96E SER* 3.8 0.8 - - - +
97E GLU* 2.9 25.8 + - - -
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Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E MET 2.9 16.5 + - - -
91E ALA* 3.8 1.6 - - - +
92E LEU 3.3 0.2 - - - -
93E GLN* 1.3 76.9 - - - +
95E ALA* 1.3 55.7 + - - +
97E GLU* 3.3 2.0 + - - +
98E ALA* 2.9 24.6 + - - -
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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
----------------------------------------------------------
91E ALA 2.9 16.5 + - - -
92E LEU 4.0 0.7 - - - -
94E GLU* 1.3 74.3 - - - +
96E SER* 1.3 60.4 + - - +
98E ALA* 3.4 1.6 + - - +
99E TYR* 2.8 26.3 + - - -
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Residues in contact with SER 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LEU 2.9 17.5 + - - -
93E GLN* 3.9 0.9 - - - +
95E ALA* 1.3 72.4 - - - +
97E GLU* 1.3 59.9 + - - +
99E TYR* 4.4 1.1 - - - +
100E LEU* 2.9 27.0 + - - -
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Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E GLN 2.9 16.6 + - - -
94E GLU* 3.6 3.8 - - - +
95E ALA 3.3 0.2 - - - -
96E SER* 1.3 75.5 - - - +
98E ALA* 1.3 55.6 + - - +
100E LEU* 3.4 1.1 + - - +
101E VAL* 2.9 26.0 + - - -
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU 2.9 14.2 + - - -
95E ALA* 3.4 2.9 + - - +
96E SER 3.3 0.2 - - - -
97E GLU* 1.3 75.5 - - - +
99E TYR* 1.3 57.2 + - - +
101E VAL* 3.4 1.1 + - - +
102E GLY* 2.9 26.2 + - - -
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Residues in contact with TYR 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 2.8 17.1 + - - -
96E SER* 4.0 1.6 - - - +
98E ALA* 1.3 74.8 - - - +
100E LEU* 1.3 57.7 + - - +
102E GLY* 3.5 1.7 + - - -
103E LEU* 2.9 23.7 + - - -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E SER 2.9 17.9 + - - -
97E GLU* 3.8 1.1 - - - +
99E TYR* 1.3 76.4 - - - +
101E VAL* 1.3 59.9 + - - +
103E LEU* 3.7 1.9 - - - +
104E PHE* 2.9 24.4 + - - -
37F LEU 5.2 3.7 - - - +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E GLU 2.9 16.3 + - - -
98E ALA* 4.0 1.3 - - - +
100E LEU* 1.3 74.6 - - - +
102E GLY* 1.3 60.1 + - - +
104E PHE* 3.8 1.5 - - - +
105E GLU* 2.9 25.1 + - - -
37F LEU* 4.5 14.5 + - - +
40F ARG 5.9 0.2 - - - -
41F GLY* 4.4 11.8 - - - +
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Residues in contact with GLY 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ALA 2.9 16.0 + - - -
99E TYR* 3.8 1.8 - - - -
101E VAL* 1.3 74.2 - - - +
103E LEU* 1.3 63.3 + - - +
105E GLU* 3.4 1.3 + - - -
106E ASP* 3.1 21.0 + - - -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E TYR 2.9 16.9 + - - -
100E LEU* 3.7 2.5 - - - +
101E VAL 3.4 0.2 - - - -
102E GLY* 1.3 76.7 - - - +
104E PHE* 1.3 56.4 + - - +
106E ASP* 3.5 1.3 + - - +
107E THR* 2.9 24.8 + - - -
124E ILE* 6.0 1.0 - - - -
127E ALA* 6.1 0.2 - - - -
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Residues in contact with PHE 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 LEU 2.9 16.7 + - - -
101E VAL* 3.8 2.0 - - - +
102E GLY 3.2 0.2 - - - -
103E LEU* 1.3 75.9 - - - +
105E GLU* 1.3 59.7 + - - +
107E THR* 3.7 1.7 - - - +
108E ASN* 2.9 25.1 + - - -
38F ALA* 6.0 5.6 - - - +
41F GLY* 4.7 8.8 - - - +
42F GLY 6.1 0.3 - - - -
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Residues in contact with GLU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E VAL 2.9 16.5 + - - -
102E GLY* 4.0 1.1 - - - -
104E PHE* 1.3 75.9 - - - +
106E ASP* 1.3 57.5 + - - +
108E ASN* 3.4 1.5 + - - +
109E LEU* 2.9 24.4 + - - -
41F GLY* 4.0 15.4 + - - -
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Residues in contact with ASP 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 6.0 6.1 - - - +
102E GLY 3.1 15.1 + - - -
103E LEU* 3.8 3.1 - - - +
105E GLU* 1.3 76.6 - - - +
107E THR* 1.3 57.2 + - - +
109E LEU* 3.3 2.2 + - - +
110E ALA* 2.9 24.8 + - - -
127E ALA* 5.4 9.4 - - - +
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Residues in contact with THR 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU 2.9 17.8 + - - -
104E PHE* 3.7 3.1 - - - +
105E GLU 3.3 0.4 - - - -
106E ASP* 1.3 76.1 - - - +
108E ASN* 1.3 56.3 + - - +
110E ALA* 3.3 2.6 + - - +
111E ALA* 2.9 24.8 + - - -
119E ILE* 6.0 2.6 - - - -
123E ASP* 4.5 23.8 - - - -
124E ILE* 5.3 2.9 - - - +
127E ALA* 5.7 1.5 - - - +
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Residues in contact with ASN 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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104E PHE 2.9 16.0 + - - -
105E GLU* 3.8 1.8 - - - +
107E THR* 1.3 73.7 - - - +
109E LEU* 1.3 59.4 + - - +
111E ALA* 4.3 1.8 - - - +
112E ILE* 2.9 26.7 + - - -
118E THR 5.6 4.9 - - - -
42F GLY 5.8 3.8 - - - -
43F VAL* 6.3 2.5 - - - +
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Residues in contact with LEU 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 GLU 2.9 15.1 + - - -
106E ASP* 3.3 4.2 + - - +
107E THR 3.3 0.2 - - - -
108E ASN* 1.3 76.6 - - - +
110E ALA* 1.3 56.0 + - - +
112E ILE* 3.9 0.7 - - - +
113E HIS* 2.9 26.0 + - - -
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Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ASP 2.9 14.6 + - - -
107E THR* 3.3 4.5 + - - +
109E LEU* 1.3 75.3 - - - +
111E ALA* 1.3 59.7 + - - +
113E HIS* 3.6 2.2 + - - +
114E ALA* 3.3 16.5 + - - -
123E ASP* 5.7 8.1 - - - +
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Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E THR 2.9 15.5 + - - -
108E ASN* 3.8 1.6 - - - +
109E LEU 3.2 0.2 - - - -
110E ALA* 1.3 76.9 - - - +
112E ILE* 1.3 61.0 + - - +
113E HIS 3.2 0.2 - - - -
114E ALA* 3.3 7.9 + - - +
115E LYS 3.6 0.2 + - - -
116E ARG* 2.9 33.6 + - - +
118E THR 4.7 10.8 - - - -
119E ILE* 6.2 0.4 - - - +
123E ASP* 6.0 2.5 - - - +
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Residues in contact with ILE 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ASN 2.9 16.5 + - - -
109E LEU* 3.9 1.6 - - - +
111E ALA* 1.3 74.3 - - - +
113E HIS* 1.3 63.4 + - - +
115E LYS* 3.1 14.2 + - - -
116E ARG 3.5 11.7 + - - +
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Residues in contact with HIS 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA* 5.6 0.7 - - - -
109E LEU 2.9 17.6 + - - -
110E ALA* 3.9 3.6 - - - +
111E ALA 3.2 0.4 - - - -
112E ILE* 1.3 77.5 - - - +
114E ALA* 1.3 55.6 + - - +
115E LYS 3.2 3.2 + - - -
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Residues in contact with ALA 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS 5.6 0.4 - - - -
114A ALA* 4.5 23.2 - - - +
110E ALA 3.3 10.5 + - - -
111E ALA* 3.3 6.5 + - - +
112E ILE 3.2 1.0 - - - -
113E HIS* 1.3 74.7 - - - +
115E LYS* 1.3 63.9 + - - +
116E ARG* 3.5 2.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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