Contacts of the helix formed by residues 82 - 107 (chain B) in PDB entry 4TXQ
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 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B GLU* 2.8 54.8 + - - +
79B ALA 3.7 4.0 - - - +
80B ILE 3.3 1.1 - - - -
81B THR* 1.3 90.8 + - - +
83B GLU* 1.3 67.1 + - - +
84B ILE* 3.1 10.6 - - + +
85B VAL* 3.0 27.2 + - + +
86B GLY 3.0 9.5 + - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 4.7 6.5 - - + +
80B ILE 4.7 7.8 - - - +
81B THR 4.3 6.2 - - - +
82B GLN* 1.3 75.6 - - - +
84B ILE* 1.3 58.1 + - - +
87B CYS* 2.9 32.1 + - - +
131B PHE* 3.6 29.9 - - + -
196D ARG* 3.9 33.9 + - - +
198D GLN 5.6 0.9 - - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B GLN* 4.5 10.8 - - + +
83B GLU* 1.3 78.6 - - - +
85B VAL* 1.3 76.2 + - + +
87B CYS* 4.1 4.4 - - + +
88B ALA* 3.2 21.8 + - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 3.6 20.6 - - + +
79B ALA* 3.6 22.9 - - + +
82B GLN* 3.0 38.0 + - + +
84B ILE* 1.3 84.1 - - + +
86B GLY* 1.3 58.7 + - - +
88B ALA* 3.3 6.3 + - + +
89B HIS* 3.0 26.7 + - + +
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 4.0 10.1 - - - -
79B ALA* 3.3 27.7 + - - -
82B GLN 3.0 10.9 + - - -
83B GLU 3.9 2.2 - - - -
85B VAL* 1.3 74.1 - - - +
87B CYS* 1.3 63.7 + - - +
89B HIS* 3.2 4.2 + - - +
90B LEU* 3.1 27.9 + - - +
131B PHE* 3.6 7.2 - - - -
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Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU 2.9 18.4 + - - +
84B ILE* 4.1 5.4 - - + +
86B GLY* 1.3 76.1 - - - +
88B ALA* 1.3 62.5 + - - +
90B LEU* 3.3 1.9 + - - +
91B GLU* 2.9 49.3 + - - +
128B ILE* 4.5 7.6 - - - -
131B PHE* 3.5 40.1 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE 3.2 17.3 + - - +
85B VAL* 3.6 8.1 - - + +
86B GLY 3.3 0.2 - - - -
87B CYS* 1.3 78.3 - - - +
89B HIS* 1.3 58.3 + - - +
91B GLU* 4.0 6.6 - - - +
92B ASN* 3.0 34.5 + - - +
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Residues in contact with HIS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 2.7 36.6 + - - -
33B VAL* 3.5 30.5 - - + +
34B VAL* 4.0 10.8 - - + -
79B ALA* 4.6 6.0 - - + +
85B VAL* 3.0 15.3 + - + +
86B GLY* 3.4 12.1 - - - +
87B CYS 3.2 0.2 - - - -
88B ALA* 1.3 76.7 - - - +
90B LEU* 1.3 62.0 + - + +
92B ASN* 4.0 3.5 + - - +
93B TYR* 3.2 26.2 + - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.3 1.8 - - + -
34B VAL* 4.3 19.3 - - + +
37B TYR* 3.8 27.1 - - + -
86B GLY 3.1 19.8 + - - +
87B CYS 3.8 2.0 - - - +
89B HIS* 1.3 91.1 - - + +
91B GLU* 1.3 54.5 + - - +
93B TYR* 3.1 8.2 + - - +
94B ALA* 2.8 34.3 + - - +
124B LEU* 4.8 11.5 - - + +
127B VAL* 3.5 32.5 - - + -
128B ILE* 3.8 20.6 - - + -
131B PHE* 3.8 14.8 - - + -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B CYS* 2.9 36.2 + - - +
88B ALA* 4.0 6.3 - - - +
90B LEU* 1.3 74.7 - - - +
92B ASN* 1.3 55.7 + - - +
94B ALA* 3.3 3.0 + - - +
95B LEU* 2.8 36.9 + - - +
128B ILE* 3.8 21.6 - - + +
135B THR* 5.3 4.3 - - - +
138B ASN* 3.5 28.3 + - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ALA 3.0 21.4 + - - +
89B HIS* 4.0 4.7 + - - +
91B GLU* 1.3 76.4 - - - +
93B TYR* 1.3 58.2 + - - +
95B LEU* 3.6 12.7 + - - +
96B LYS* 3.0 45.8 + - - +
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Residues in contact with TYR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 2.6 41.8 + + - -
31B ASP* 5.0 6.3 - - - +
34B VAL* 3.9 24.2 - - + -
89B HIS* 3.2 19.1 + - + +
90B LEU* 3.1 5.4 + - - +
92B ASN* 1.3 78.9 - - - +
94B ALA* 1.3 63.0 + - - +
96B LYS* 3.4 8.4 + - + +
97B MET* 3.2 48.1 + - + +
124B LEU* 3.6 22.0 - - + -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU 2.8 19.8 + - - +
91B GLU* 3.7 7.6 - - - +
93B TYR* 1.3 72.8 - - - +
95B LEU* 1.3 57.7 + - - +
97B MET* 3.4 5.4 + - - +
98B PHE* 2.9 32.1 + - - +
121B ALA* 3.9 12.5 - - + +
124B LEU* 3.8 30.2 - - + +
125B ILE* 4.7 7.0 - - + -
128B ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU 2.8 23.2 + - - +
92B ASN* 3.7 15.9 - - - +
93B TYR 3.3 0.2 - - - -
94B ALA* 1.3 70.1 - - - +
96B LYS* 1.3 62.9 + - + +
98B PHE* 3.2 11.0 + - + +
99B LEU* 2.8 63.6 + - + +
141B HIS* 5.5 11.2 - - + +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASN* 3.0 45.1 + - - +
93B TYR* 3.7 12.1 - - + +
95B LEU* 1.3 82.7 - - + +
97B MET* 1.3 57.9 + - - +
99B LEU* 3.3 8.9 + - + +
100B TYR* 2.9 27.0 + - - +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TYR* 3.2 53.6 + - + +
94B ALA* 3.6 9.4 - - - +
96B LYS* 1.3 76.9 - - + +
98B PHE* 1.3 62.7 + - - +
100B TYR* 3.5 8.0 - - + +
101B ALA* 2.9 29.8 + - - +
117B SER* 3.6 31.7 - - - +
120B THR* 3.6 34.5 - - + -
121B ALA* 3.6 8.3 - - + -
124B LEU* 3.7 9.6 - - + -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA 2.9 20.2 + - - +
95B LEU* 3.4 12.8 - - + +
97B MET* 1.3 78.6 - - - +
99B LEU* 1.3 74.6 + - + +
101B ALA* 3.2 4.9 + - - +
102B ASP* 2.9 39.3 + - + +
117B SER 5.0 0.4 - - - -
118B PHE* 4.2 7.7 - + - -
121B ALA* 4.3 11.4 - - + -
125B ILE* 6.2 1.1 - - + -
141B HIS* 4.2 38.8 - + + -
144B TYR* 3.7 37.9 - + - -
145B ALA* 4.0 24.7 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 2.8 50.9 + - + +
96B LYS* 3.9 8.1 - - + +
98B PHE* 1.3 85.7 - - + +
100B TYR* 1.3 61.3 - - - +
102B ASP* 3.8 12.5 - - - +
103B ASN* 2.9 29.3 + - - +
106B ARG* 5.1 1.1 + - - +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS 2.9 17.2 + - - +
97B MET* 3.5 7.0 - - + +
99B LEU* 1.3 76.3 - - - +
101B ALA* 1.3 64.4 + - - +
103B ASN* 3.3 8.0 + - + +
104B GLU* 3.2 41.6 + - + +
111B HIS* 3.3 23.4 - - - -
113B ASN* 3.9 18.8 + - - -
114B MET* 3.9 15.5 - - - -
117B SER* 3.3 28.0 - - - -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B MET 2.9 17.6 + - - +
98B PHE 3.8 0.7 - - - +
100B TYR* 1.3 82.3 - - - +
102B ASP* 1.3 57.8 + - - +
104B GLU* 3.3 1.9 + - - +
105B ASP* 3.0 23.4 + - - +
114B MET* 3.3 41.2 - - - +
117B SER* 3.8 2.9 - - - -
118B PHE* 3.6 32.1 - - + +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PHE* 2.9 31.3 + - + +
99B LEU* 3.8 15.2 - - - +
101B ALA* 1.3 78.6 - - - +
103B ASN* 1.3 56.1 + - - +
105B ASP* 3.3 5.3 + - - +
106B ARG* 2.9 64.7 + - - +
118B PHE* 3.6 13.1 - - + -
144B TYR* 4.1 17.2 + - - -
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU 2.9 19.5 + - - +
100B TYR* 3.6 8.4 - - + +
102B ASP* 1.3 76.8 + - - +
104B GLU* 1.3 63.8 + - - +
106B ARG* 3.2 30.9 + - - +
107B ALA* 3.1 23.5 + - - +
109B ARG* 4.0 16.0 - - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.2 43.6 + - + +
101B ALA 3.5 7.4 - - - +
103B ASN* 1.3 80.0 + - - +
105B ASP* 1.3 63.1 + - - +
107B ALA* 3.0 12.3 + - - +
109B ARG* 2.8 76.9 + - - +
111B HIS* 2.7 26.5 + - - +
114B MET* 3.8 11.0 - - + -
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS* 2.7 50.5 + - - -
101B ALA 3.0 13.1 + - - +
102B ASP* 3.4 14.4 - - - +
104B GLU* 1.3 76.4 - - - +
106B ARG* 1.3 62.4 + - - +
108B GLY* 3.0 10.9 + - - -
110B PHE* 3.2 17.7 - - - -
114B MET* 3.6 15.9 - - + +
118B PHE* 4.3 2.4 - - + -
144B TYR* 4.4 4.5 + - - -
148B LYS* 2.8 38.6 + - - -
152B ILE* 4.6 1.8 - - - +
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS* 4.4 4.9 + - - +
99B LEU* 5.1 1.2 + - - +
102B ASP* 2.9 45.0 + - - +
103B ASN* 3.2 34.6 + - - +
104B GLU 3.3 0.2 - - - -
105B ASP* 1.3 79.0 - - + +
107B ALA* 1.3 57.9 + - - +
108B GLY 3.3 0.9 + - - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASN* 3.1 15.6 + - - +
104B GLU 3.0 7.1 + - - +
106B ARG* 1.3 77.4 - - - +
108B GLY* 1.3 62.7 + - - +
109B ARG* 3.3 36.3 + - - +
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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
------------------------------------------------------------
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