Contacts of the helix formed by residues 75 - 101 (chain B) in PDB entry 3RFU
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 SER 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B VAL* 1.3 81.9 - - - +
76B PRO* 1.3 70.6 - - - +
77B GLU* 3.9 4.5 + - - +
78B TYR* 3.3 33.6 + - - +
79B LEU* 3.2 26.7 - - - +
206B LEU* 5.2 0.9 - - - +
210B GLU* 3.6 23.5 + - - -
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Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL 4.4 2.5 - - - +
75B SER* 1.3 95.1 - - - +
77B GLU* 1.3 71.9 + - + +
78B TYR 3.4 0.2 - - - -
79B LEU* 3.9 4.0 + - - +
80B ASP* 3.7 13.9 + - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 4.4 5.2 - - - +
76B PRO* 1.3 85.5 - - + +
78B TYR* 1.3 69.1 + - - +
79B LEU 3.3 0.2 - - - -
80B ASP* 2.9 26.8 - - + +
81B MET* 3.0 20.8 + - + +
136B ARG* 3.5 24.9 + - - -
206B LEU* 4.2 23.3 - - + +
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 3.3 22.8 + - - +
76B PRO 3.4 0.4 - - - -
77B GLU* 1.3 80.3 - - - +
79B LEU* 1.3 92.8 + - + +
81B MET* 3.0 7.4 + - - +
82B ARG* 2.9 44.3 + - + +
203B VAL* 3.5 35.4 - - + +
206B LEU* 3.2 40.4 - - + -
207B LYS* 3.8 30.0 - - + +
210B GLU* 4.3 18.6 - - - -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 4.9 9.9 - - + -
75B SER 3.2 25.4 - - - +
76B PRO 3.9 8.2 + - - +
77B GLU 3.3 0.4 - - - -
78B TYR* 1.3 101.7 - - + +
80B ASP* 1.3 52.4 + - - +
82B ARG* 3.0 13.0 + - - +
83B ARG* 2.5 40.5 + - + +
210B GLU* 5.3 0.7 - - - +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PRO 3.7 6.1 + - - +
77B GLU* 2.9 26.2 + - - +
79B LEU* 1.3 76.1 - - - +
81B MET* 1.3 75.5 + - - +
83B ARG* 3.0 35.5 + - - +
84B ARG* 3.0 48.3 + - - +
132B PRO* 4.8 3.5 - - - +
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.6 20.4 - - + +
78B TYR* 3.0 6.2 + - - +
80B ASP* 1.3 87.4 - - - +
82B ARG* 1.3 56.2 + - - +
84B ARG* 3.0 10.2 + - - +
85B PHE* 2.7 36.7 + - - +
132B PRO* 4.4 17.3 - - + -
133B PHE* 5.3 1.8 - - + -
136B ARG* 3.7 27.1 - - - +
199B LEU* 3.9 24.9 - - + +
202B GLN* 4.0 28.9 - - + +
203B VAL* 3.9 18.4 - - + +
206B LEU* 4.3 10.1 - - + -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 2.9 39.3 + - + +
79B LEU* 3.4 16.6 - - - +
81B MET* 1.3 76.2 - - - +
83B ARG* 1.3 61.6 + - - +
84B ARG 3.6 0.2 + - - -
85B PHE* 4.4 1.8 - - - -
86B TRP* 2.9 60.2 + - - +
203B VAL* 3.9 18.7 - - + +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 2.5 19.3 + - + +
80B ASP* 3.3 28.8 + - - +
82B ARG* 1.3 76.8 - - - +
84B ARG* 1.3 60.8 + - - +
86B TRP* 4.6 1.9 - - - +
87B ILE* 3.2 28.6 + - + +
128B TRP* 4.0 32.2 - - - -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 3.0 41.8 + - - +
81B MET* 3.4 14.1 - - - +
83B ARG* 1.3 76.7 - - + +
85B PHE* 1.3 59.2 + - - +
86B TRP 3.3 0.2 - - - -
87B ILE* 3.0 7.6 + - - +
88B ALA* 2.6 36.9 + - - +
128B TRP* 3.0 70.3 + - + +
129B GLY 3.4 13.5 - - - +
130B GLY 4.4 0.2 - - - +
131B TRP* 4.1 5.1 - - - +
132B PRO* 3.0 35.2 - - - +
199B LEU* 3.9 22.9 - - + -
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Residues in contact with PHE 85 (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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81B MET 2.7 22.7 + - - +
82B ARG* 4.0 2.9 - - + +
84B ARG* 1.3 74.9 - - - +
86B TRP* 1.3 99.5 + + - +
88B ALA* 3.0 2.9 + - - +
89B LEU* 2.7 53.5 + - + +
196B THR* 3.4 26.1 - - - -
199B LEU* 4.0 14.6 - - + -
200B LEU* 3.4 51.8 - - + -
203B VAL* 4.3 14.8 - - + -
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Residues in contact with TRP 86 (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 ARG* 2.9 58.9 + - + +
83B ARG 4.6 2.2 - - - +
84B ARG 3.3 0.4 - - - -
85B PHE* 1.3 100.0 - + - +
87B ILE* 1.3 68.3 + - + +
89B LEU* 3.0 25.2 + - + +
90B MET* 2.7 35.3 + - + +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 3.2 20.9 - - + +
84B ARG* 3.0 11.7 + - - +
86B TRP* 1.3 80.1 - - + +
88B ALA* 1.3 64.8 + - - +
90B MET* 3.0 21.6 + - - +
91B LEU* 2.9 47.0 + - + +
128B TRP* 4.6 19.3 - - + +
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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 ARG 2.6 15.4 + - - +
85B PHE 3.2 9.4 - - - +
87B ILE* 1.3 75.6 - - - +
89B LEU* 1.3 53.1 + - - +
91B LEU* 3.0 2.8 + - - +
92B THR* 2.6 40.0 + - - -
125B VAL* 3.2 30.7 - - + +
128B TRP* 6.1 1.1 - - + -
129B GLY 5.7 1.3 - - - +
196B THR* 3.4 14.4 - - + -
199B LEU* 4.2 13.2 - - + -
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Residues in contact with LEU 89 (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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85B PHE* 2.7 37.6 + - + +
86B TRP* 3.3 33.9 - - + +
88B ALA* 1.3 70.3 - - - +
90B MET* 1.3 69.0 + - + +
92B THR* 3.1 10.2 + - + -
93B ILE* 2.9 27.3 + - + +
196B THR* 4.1 13.3 - - - +
197B LEU* 6.6 0.2 - - + -
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Residues in contact with MET 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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86B TRP* 2.7 29.2 + - + +
87B ILE* 3.2 27.1 - - + +
89B LEU* 1.3 77.0 - - + +
91B LEU* 1.3 60.6 + - + +
93B ILE* 3.1 8.8 - - - +
94B PRO* 2.7 35.5 - - - +
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Residues in contact with LEU 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 ILE* 2.9 35.1 + - + +
88B ALA* 3.7 5.8 - - - +
90B MET* 1.3 85.3 - - + +
92B THR* 1.3 56.9 + - - +
94B PRO* 3.4 9.3 - - - +
95B VAL* 3.1 22.7 - - - +
121B LEU* 3.7 35.8 - - + +
124B PRO* 4.0 29.4 - - + -
125B VAL* 4.5 9.6 - - + +
128B TRP* 6.1 1.3 - - + -
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Residues in contact with THR 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 2.6 23.3 + - - -
89B LEU* 3.5 8.5 - - + +
90B MET 2.8 1.4 + - - -
91B LEU* 1.3 74.7 - - - +
93B ILE* 1.3 65.0 + - - +
95B VAL* 3.0 9.7 + - + +
96B VAL* 2.9 34.8 + - + -
125B VAL* 3.4 5.8 - - - +
192B ALA* 3.3 27.0 - - + +
193B VAL* 4.0 16.2 - - + +
196B THR* 3.1 23.4 - - + +
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Residues in contact with ILE 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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89B LEU* 2.9 22.2 + - + +
90B MET* 3.1 20.4 - - - +
92B THR* 1.3 73.8 - - - +
94B PRO* 1.3 73.2 - - + +
96B VAL* 3.0 10.2 + - + +
97B ILE* 2.9 37.3 + - + +
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Residues in contact with PRO 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 MET 2.7 29.8 - - - +
91B LEU* 3.4 11.9 - - - +
93B ILE* 1.3 85.3 - - + +
95B VAL* 1.3 50.8 + - - +
97B ILE* 3.0 14.3 + - + +
98B LEU* 2.8 48.9 + - + +
117B ILE* 6.1 0.4 - - + -
121B LEU* 4.0 18.2 - - + -
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Residues in contact with VAL 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 LEU 3.1 21.5 - - - +
92B THR* 3.0 14.8 + - - +
94B PRO* 1.3 76.1 - - - +
96B VAL* 1.3 63.0 + - + +
98B LEU* 3.0 19.8 + - - +
99B GLU* 3.2 9.7 + - - +
118B GLN* 3.7 22.5 - - + +
121B LEU* 3.7 22.2 - - + +
122B ALA* 4.2 13.7 - - + +
188B PHE 4.5 3.6 - - - -
189B GLU* 3.9 31.4 - - + +
192B ALA* 4.6 7.4 - - + -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 2.9 23.3 + - + +
93B ILE* 3.0 11.2 + - + +
95B VAL* 1.3 73.8 - - - +
97B ILE* 1.3 66.1 + - + +
99B GLU* 3.0 4.5 + - - +
100B MET* 2.9 40.5 + - + +
189B GLU* 4.0 21.3 - - + +
193B VAL* 3.9 28.0 - - + -
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 35.6 + - + +
94B PRO* 3.2 14.1 - - + +
96B VAL* 1.3 76.8 - - + +
98B LEU* 1.3 65.1 + - + +
99B GLU 2.9 0.3 + - - -
100B MET* 3.0 5.3 + - - -
101B GLY* 2.6 37.8 + - - +
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Residues in contact with LEU 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 PRO* 2.8 28.7 + - + +
95B VAL* 3.0 10.7 + - - +
97B ILE* 1.3 80.6 - - + +
99B GLU* 1.3 60.4 + - - +
101B GLY* 5.3 0.7 - - - -
102B GLY 3.9 16.1 + - - +
103B HIS* 4.2 2.1 + - - -
114B SER* 4.0 20.5 + - - +
117B ILE* 3.5 44.0 - - + -
118B GLN* 3.5 30.3 - - + +
121B LEU* 5.5 0.9 - - + -
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Residues in contact with GLU 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 VAL 3.2 6.3 + - - +
96B VAL 3.0 7.4 + - - +
98B LEU* 1.3 75.4 - - - +
100B MET* 1.3 69.5 - - + +
102B GLY* 3.1 25.9 + - - +
118B GLN* 3.0 22.4 + - - +
186B VAL* 3.3 29.7 - - - +
189B GLU* 3.9 32.3 - - + +
710B PRO* 3.9 17.6 - - - +
711B MET* 5.5 10.6 - - - +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 2.9 32.6 + - + +
97B ILE* 3.9 3.8 - - - +
99B GLU* 1.3 74.9 - - - +
101B GLY* 1.3 67.1 + - - +
102B GLY* 3.1 2.3 + - - -
189B GLU* 3.8 17.5 - - - +
711B MET* 5.4 12.1 - - - +
714B ALA* 4.7 15.3 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 2.6 26.0 + - - +
98B LEU* 4.7 0.9 - - - -
100B MET* 1.3 72.4 - - - +
102B GLY* 1.3 55.9 + - - +
103B HIS* 4.1 2.2 - - - +
104B GLY* 3.7 13.3 + - - -
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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
------------------------------------------------------------
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