Contacts of the helix formed by residues 63 - 88 (chain B) in PDB entry 2RGZ
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 LYS 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 5.5 2.7 - - - +
62B ILE* 1.3 83.3 - - - +
64B LYS* 1.3 50.4 + - - +
65B GLU 2.6 3.5 + - - +
66B LEU* 2.3 45.2 + - + +
67B PHE 4.3 2.0 - - - -
241B GLY* 5.9 0.7 - - - +
244B LEU* 3.9 35.4 - - + +
245B ALA* 5.8 5.4 - - + +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 1.3 66.7 - - - +
65B GLU* 1.3 64.6 + - + +
66B LEU 3.0 0.2 + - - -
67B PHE* 3.0 8.4 + - - +
68B LYS* 2.9 39.9 + - + +
115B TYR* 5.4 11.0 + - - -
116B PHE* 3.9 37.0 + - + +
175B LEU* 3.3 37.2 - - + +
177B LEU* 5.8 2.5 - - + -
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 2.6 6.1 + - - +
64B LYS* 1.3 81.4 - - + +
66B LEU* 1.3 57.5 + - - +
68B LYS* 2.7 45.0 + - - +
69B LEU* 3.5 21.4 + - - +
117B PHE* 4.9 6.4 - - - -
244B LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 4.2 11.2 - - + -
62B ILE* 3.4 29.6 - - + -
63B LYS* 2.3 38.4 + - + +
65B GLU* 1.3 65.0 - - - +
67B PHE* 1.3 54.3 + - - +
68B LYS 2.8 4.7 - - - -
69B LEU* 2.6 49.7 + - + +
70B ALA* 3.0 11.3 + - - +
237B LEU* 3.2 35.0 - - + +
238B ASP* 5.1 2.5 - - - +
241B GLY* 3.6 27.1 - - - +
244B LEU* 4.6 4.1 - - + +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 5.6 0.9 - - - -
57B PHE* 3.4 42.2 - + - -
62B ILE* 4.5 12.2 - - + +
63B LYS 3.5 2.0 + - - -
64B LYS* 3.3 11.0 - - - +
66B LEU* 1.3 80.0 - - - +
68B LYS* 1.3 51.9 + - - +
70B ALA* 3.5 10.1 + - + +
71B THR* 2.7 51.8 + - - -
112B ASP* 6.3 0.2 - - + -
116B PHE* 3.5 35.9 - + - -
171B ALA* 3.7 18.4 - - + -
175B LEU* 3.6 21.8 - - + -
184B THR* 3.8 17.7 - - + -
187B TYR* 4.0 17.7 - + - -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 2.9 27.3 + - + +
65B GLU* 2.7 45.4 + - - +
66B LEU 2.8 0.2 - - - -
67B PHE* 1.3 77.5 - - - +
69B LEU* 1.3 57.3 + - - +
71B THR* 4.3 5.4 - - - -
72B THR* 2.7 34.3 + - - -
113B MET* 3.4 1.0 - - - +
116B PHE* 3.1 61.4 + - + -
117B PHE* 3.1 40.8 - - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLU 3.6 11.4 - - - +
66B LEU* 2.6 38.3 + - + +
68B LYS* 1.3 73.8 - - - +
70B ALA* 1.3 62.1 + - - +
72B THR* 3.0 10.8 + - - -
73B ALA* 2.9 20.3 + - - +
117B PHE* 5.6 5.4 - - + -
128B PRO* 4.7 11.9 - - + +
236B GLU* 5.6 0.7 - - - +
237B LEU* 3.4 17.8 - - + +
240B ALA* 3.7 23.1 - - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 4.2 15.5 - - + -
57B PHE* 6.2 0.4 - - + -
66B LEU 3.0 8.4 + - - +
67B PHE* 3.6 13.9 - - + +
69B LEU* 1.3 76.4 - - - +
71B THR* 1.3 58.2 + - - +
73B ALA* 2.8 24.3 + - - +
74B LEU* 2.9 19.7 + - + +
237B LEU* 3.4 28.6 - - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 2.7 43.2 + - + -
68B LYS* 4.0 1.7 - - - -
70B ALA* 1.3 76.8 - - - +
72B THR* 1.3 55.6 + - - +
74B LEU* 3.3 13.8 + - + +
75B TYR* 3.0 26.3 + - - +
109B LEU* 3.8 20.7 - - + +
112B ASP* 4.0 20.2 - - + +
113B MET* 3.1 31.8 - - + +
116B PHE* 4.8 1.0 - - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS 2.7 18.8 + - - -
69B LEU* 3.0 14.4 + - + -
71B THR* 1.3 74.9 - - - +
73B ALA* 1.3 66.5 + - - +
75B TYR* 3.2 8.4 + - - +
76B PHE* 3.1 47.5 + - + -
113B MET* 3.3 12.7 - - - +
117B PHE* 3.0 22.2 - - + -
125B VAL* 4.4 11.9 - - + +
126B GLN 3.8 14.4 - - - +
128B PRO* 3.9 6.1 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 2.9 10.1 + - - +
70B ALA* 2.8 13.1 + - - +
72B THR* 1.3 79.5 - - - +
74B LEU* 1.3 58.7 + - + +
76B PHE* 3.3 2.1 + - - +
77B THR* 2.9 33.8 + - - -
128B PRO* 4.0 22.2 - - + +
131B ALA* 4.1 8.1 - - + +
233B ILE* 4.1 27.6 - - + -
237B LEU* 5.5 1.8 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 2.9 18.5 + - + +
71B THR* 3.4 14.6 - - + +
73B ALA* 1.3 78.8 - - + +
75B TYR* 1.3 56.8 + - - +
77B THR* 4.4 4.0 - - + -
78B TYR* 2.8 60.2 + - + +
109B LEU* 3.6 19.1 - - + -
156B ARG* 3.8 19.1 - - - +
186B PHE* 3.6 31.9 - - + -
187B TYR* 4.7 8.7 - - - +
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 3.0 13.4 + - - +
72B THR* 3.2 9.4 + - - +
74B LEU* 1.3 76.0 - - - +
76B PHE* 1.3 88.1 + + - +
78B TYR* 4.5 0.3 - - - +
79B SER* 3.1 32.6 + - - -
106B LYS* 3.7 30.7 + - + +
109B LEU* 3.7 13.4 - - + +
110B THR* 3.3 43.5 + - + +
113B MET* 4.4 11.4 - - + -
121B TRP* 4.3 11.2 - + - -
122B GLU* 3.5 30.4 + - - -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.1 44.4 + - + +
73B ALA* 4.0 3.1 - - - +
75B TYR* 1.3 100.9 - + - +
77B THR* 1.3 67.6 + - - +
79B SER* 3.6 4.3 + - - -
80B ALA* 3.3 15.9 + - - +
121B TRP* 5.8 0.2 - + - -
122B GLU* 4.9 4.5 - - - -
125B VAL* 3.9 21.8 - - + -
126B GLN* 3.8 1.3 - - - -
127B ALA* 3.4 47.6 - - + -
128B PRO* 4.4 0.4 - - + -
131B ALA* 5.3 2.2 - - + -
135B VAL* 3.4 20.2 - - + +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA 2.9 21.8 + - - -
74B LEU* 3.8 6.5 - - + -
76B PHE* 1.3 79.1 - - - +
78B TYR* 1.3 71.4 + - + +
80B ALA* 3.3 2.9 + - - +
81B LEU* 3.0 27.9 + - + +
131B ALA* 4.3 12.1 + - - +
134B TYR* 3.7 39.1 - - + -
135B VAL* 3.9 10.0 - - - +
138B ILE* 4.0 7.7 - - + +
156B ARG* 4.8 8.7 - - + -
233B ILE* 4.4 4.7 - - - +
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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
----------------------------------------------------------
74B LEU* 2.8 59.9 + - + +
75B TYR 4.5 0.7 - - - +
77B THR* 1.3 75.6 - - + +
79B SER* 1.3 59.8 + - - +
81B LEU* 4.4 5.8 - - + -
82B GLU* 2.8 43.7 + - - +
105B ARG* 3.6 15.0 - - + -
106B LYS* 4.8 2.7 - - - +
109B LEU* 4.1 15.5 - - + -
156B ARG* 2.9 34.1 + - + +
157B TYR* 3.3 43.1 - + - -
160B ASP* 2.6 34.9 + - - -
186B PHE* 4.0 8.1 - + - -
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.1 29.4 + - - -
76B PHE* 4.0 6.5 - - - -
77B THR 3.3 0.4 - - - -
78B TYR* 1.3 77.7 - - - +
80B ALA* 1.3 62.2 + - - +
82B GLU* 4.1 1.9 - - - +
83B GLU* 3.1 23.6 + - - +
106B LYS* 3.2 46.2 + - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE 3.3 16.1 + - - +
77B THR 3.6 4.0 - - - +
78B TYR 3.1 0.2 - - - -
79B SER* 1.3 77.8 - - - +
81B LEU* 1.3 66.2 + - - +
83B GLU* 3.2 3.3 + - - +
84B GLU* 3.1 26.9 + - - +
135B VAL* 4.0 14.8 - - + -
138B ILE* 3.8 12.3 - - + -
139B HIS* 3.2 33.6 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 3.0 19.0 + - + +
78B TYR* 4.0 8.3 - - + +
80B ALA* 1.3 76.5 - - - +
82B GLU* 1.3 61.3 + - - +
84B GLU* 3.5 1.4 + - - +
85B MET* 3.1 34.7 + - + +
134B TYR* 5.4 1.1 - - - +
138B ILE* 3.4 28.6 - - + +
149B LEU* 3.7 15.7 - - + -
152B HIS* 3.7 42.4 - - + +
153B ALA* 4.5 1.1 - - - +
156B ARG* 4.5 13.0 - - + -
157B TYR* 3.6 31.9 - - + +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TYR* 2.8 22.7 + - - +
79B SER* 4.1 4.3 - - - +
81B LEU* 1.3 75.5 - - - +
83B GLU* 1.3 64.7 + - - +
85B MET* 3.5 6.8 + - - +
86B GLU* 3.1 21.8 + - - +
104B HIS* 3.2 46.6 + - + +
105B ARG* 2.6 26.6 + - - -
106B LYS* 2.9 30.6 + - + +
157B TYR* 3.2 22.3 + - - +
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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
----------------------------------------------------------
79B SER 3.1 20.2 + - - +
80B ALA* 3.2 5.1 + - - +
82B GLU* 1.3 76.3 - - - +
84B GLU* 1.3 60.9 + - - +
86B GLU* 3.0 11.3 + - + +
87B ARG* 2.8 55.7 + - + +
139B HIS* 4.3 12.6 - - + -
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 3.1 16.5 + - - +
81B LEU 3.8 5.2 - - - +
83B GLU* 1.3 79.0 - - - +
85B MET* 1.3 56.6 + - - +
87B ARG* 2.6 48.2 + - - +
88B ASN* 2.8 34.7 + - - -
138B ILE* 3.1 26.0 - - + +
139B HIS* 2.8 33.3 + - - +
142B GLY* 3.2 22.8 - - - -
143B GLN* 3.3 4.0 + - - -
149B LEU* 3.8 11.7 - - + -
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.1 25.2 + - + +
82B GLU* 3.9 6.7 - - - +
84B GLU* 1.3 73.5 - - - +
86B GLU* 1.3 62.5 + - - +
88B ASN 3.4 1.1 - - - +
89B LYS* 2.8 31.2 + - - +
94B PHE* 3.1 39.0 - - + -
97B LEU 4.6 6.7 - - - +
98B TYR* 3.8 13.9 - - + -
99B PHE 6.3 0.4 - - - -
103B LEU* 6.5 0.7 - - + -
104B HIS* 4.5 10.3 - - - +
149B LEU* 3.8 16.4 - - + +
153B ALA* 3.2 30.7 - - + -
157B TYR* 4.0 29.2 - - + -
202B TYR* 4.9 0.4 - - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU 3.1 14.3 + - - +
83B GLU* 3.0 15.0 + - + +
85B MET* 1.3 77.6 - - - +
87B ARG* 1.3 61.9 + - - +
89B LYS* 3.1 41.1 + - - +
98B TYR* 3.0 28.4 + - + +
104B HIS* 5.7 2.9 - - + -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 2.8 33.3 + - - +
84B GLU* 2.6 48.8 + - - +
86B GLU* 1.3 78.6 - - - +
88B ASN* 1.3 59.6 + - - +
89B LYS* 3.4 2.6 + - - +
90B ASP 4.9 1.0 + - - -
139B HIS* 4.8 0.6 + - - -
142B GLY 3.9 16.4 - - - -
143B GLN* 3.7 25.1 - - - +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 2.8 27.2 + - - +
85B MET 3.2 2.7 + - - +
87B ARG* 1.3 81.4 - - - +
89B LYS* 1.3 64.8 + - - +
90B ASP 3.2 3.1 - - - -
91B HIS* 2.8 34.7 + - + +
94B PHE* 3.8 16.2 - - + +
142B GLY* 2.9 35.3 + - - +
146B PRO* 3.3 26.7 - - - +
149B LEU* 3.8 15.0 - - + +
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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