Contacts of the helix formed by residues 64 - 88 (chain A) 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 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 1.3 76.0 - - - +
65A GLU* 1.3 62.0 + - + +
67A PHE* 2.9 3.9 + - - +
68A LYS* 2.8 46.0 + - + +
115A TYR* 6.3 0.6 - - - -
116A PHE* 4.3 25.8 - - + -
175A LEU* 3.7 41.8 + - + +
177A LEU* 5.1 3.2 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.6 2.6 - - + +
64A LYS* 1.3 78.6 - - + +
66A LEU* 1.3 61.1 + - - +
68A LYS* 2.8 45.8 + - - +
69A LEU* 3.2 34.3 + - + +
117A PHE* 5.6 1.6 - - - -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.6 23.5 - - + -
62A ILE* 3.6 30.1 - - + +
63A LYS* 3.7 6.6 + - + +
64A LYS 3.2 0.6 - - - -
65A GLU* 1.3 78.6 - - - +
67A PHE* 1.3 57.5 + - - +
69A LEU* 4.0 8.3 - - + +
70A ALA* 3.2 23.9 + - - +
237A LEU* 3.3 47.1 - - + +
238A ASP* 5.2 1.1 - - - -
240A ALA* 3.7 15.9 - - + -
241A GLY* 5.1 8.7 - - - +
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.9 28.9 - + - -
62A ILE* 4.6 5.2 - - + -
63A LYS 3.3 13.8 + - - +
64A LYS* 2.9 9.3 + - - +
66A LEU* 1.3 76.4 - - - +
68A LYS* 1.3 59.7 + - - +
69A LEU 3.1 1.8 - - - -
70A ALA* 3.5 8.7 - - + +
71A THR* 2.9 41.4 + - - -
116A PHE* 3.5 38.1 - + - -
171A ALA* 3.9 21.5 - - + -
175A LEU* 3.4 26.7 - - + -
177A LEU* 4.6 2.7 - - + -
183A GLY 4.1 6.1 - - - -
184A THR* 4.9 0.4 - - + -
187A TYR* 3.7 33.4 - + - -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 2.8 31.2 + - + +
65A GLU* 2.8 37.3 + - - +
67A PHE* 1.3 78.3 - - - +
69A LEU* 1.3 50.1 + - + +
71A THR* 3.9 4.4 - - - -
72A THR* 2.7 34.9 + - - -
116A PHE* 3.8 40.2 + - + +
117A PHE* 3.4 49.9 - - + +
124A GLN* 5.8 0.2 + - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 3.2 25.2 + - + +
66A LEU* 4.2 12.8 - - + +
67A PHE 3.1 0.2 - - - -
68A LYS* 1.3 78.3 - - + +
70A ALA* 1.3 65.5 + - - +
71A THR 3.2 0.2 - - - -
72A THR* 3.2 10.9 + - + +
73A ALA* 2.8 25.3 + - - +
117A PHE* 5.8 2.9 - - + -
126A GLN* 3.9 25.8 - - + +
128A PRO* 4.9 7.8 - - + +
237A LEU* 4.3 14.0 - - + +
240A ALA* 5.5 6.7 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.6 10.5 - - + -
66A LEU 3.2 19.7 + - - +
67A PHE* 3.2 17.9 + - + +
69A LEU* 1.3 77.9 - - - +
71A THR* 1.3 57.4 + - - +
73A ALA* 3.2 4.1 + - - +
74A LEU* 2.9 36.8 + - + +
187A TYR* 5.7 2.0 - - - +
237A LEU* 4.2 23.0 - - + +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 2.9 36.0 + - - -
68A LYS* 3.9 6.0 - - - -
70A ALA* 1.3 73.1 - - - +
72A THR* 1.3 68.2 + - - +
74A LEU* 2.8 13.8 + - + +
75A TYR* 2.7 22.5 + - - +
109A LEU* 3.7 22.7 - - + -
112A ASP* 4.4 18.8 - - + +
113A MET* 3.8 21.5 - - + +
116A PHE* 4.6 6.7 - - + -
183A GLY 5.5 0.2 + - - -
186A PHE* 5.9 0.7 - - + -
187A TYR* 5.2 3.0 + - - -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS 2.7 19.1 + - - -
69A LEU* 3.4 16.4 - - + +
71A THR* 1.3 78.5 - - - +
73A ALA* 1.3 66.2 + - - +
75A TYR* 3.2 15.8 - - - +
76A PHE* 3.4 12.1 + - + -
113A MET* 3.4 23.1 - - + +
117A PHE* 3.7 8.5 - - - -
125A VAL* 3.4 33.3 - - + -
126A GLN 3.7 22.9 - - - +
127A ALA* 4.5 0.4 - - - +
128A PRO* 5.3 0.4 - - + -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 2.8 15.8 + - - +
70A ALA* 3.4 10.5 - - - +
72A THR* 1.3 74.5 - - - +
74A LEU* 1.3 66.9 + - - +
75A TYR 3.2 0.9 + - - -
76A PHE* 3.3 11.2 + - - +
77A THR* 3.5 13.7 + - - -
128A PRO* 3.8 30.9 - - + +
131A ALA* 4.3 9.1 - - + +
233A ILE* 4.2 23.0 - - + +
237A LEU* 5.5 0.7 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 2.9 18.8 + - + +
71A THR* 2.8 21.1 + - + +
73A ALA* 1.3 73.7 - - + +
75A TYR* 1.3 67.1 + - - +
77A THR* 3.7 1.9 + - + -
78A TYR* 3.0 32.8 + - + -
109A LEU* 4.1 7.9 - - + -
156A ARG* 3.6 29.2 - - - +
186A PHE* 3.3 40.6 - - + -
187A TYR* 3.9 13.9 - - + +
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR 2.7 14.3 + - - +
72A THR* 3.2 13.5 - - - +
74A LEU* 1.3 73.2 - - - +
76A PHE* 1.3 88.3 + + - +
78A TYR* 2.9 1.4 + - - +
79A SER* 2.6 44.4 + - - -
106A LYS* 3.5 39.6 + - + -
109A LEU* 3.8 29.9 - - + +
110A THR* 4.0 15.5 - - - -
113A MET* 4.9 12.1 - - + -
121A TRP* 4.0 31.0 - + - -
122A GLU* 5.5 1.9 + - - -
125A VAL* 5.5 3.4 - - + -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 3.4 16.5 + - + -
73A ALA* 3.3 7.2 + - - +
75A TYR* 1.3 94.9 - + - +
77A THR* 1.3 54.4 + - - +
79A SER* 2.7 10.9 + - - -
80A ALA* 2.7 34.0 + - + +
125A VAL* 3.4 34.1 - - + -
126A GLN* 5.4 0.4 - - - -
127A ALA* 3.2 39.7 - - + -
131A ALA* 5.2 2.9 - - + -
135A VAL* 3.9 19.7 - - + -
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 3.5 12.4 + - - -
74A LEU* 4.2 2.5 - - + -
76A PHE* 1.3 77.5 - - - +
78A TYR* 1.3 60.8 + - + +
80A ALA* 4.4 0.2 - - - -
81A LEU* 2.8 32.9 + - + +
131A ALA* 4.1 2.6 + - - -
134A TYR* 2.9 56.6 - - + +
135A VAL* 3.6 13.7 - - - +
138A ILE* 3.5 14.4 - - + +
156A ARG* 4.1 17.5 - - + -
233A ILE* 4.7 2.5 - - - +
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Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.0 43.7 + - + +
75A TYR 2.9 3.7 + - - +
76A PHE 2.8 1.0 + - - -
77A THR* 1.3 75.8 - - + +
79A SER* 1.3 62.1 + - - +
81A LEU* 3.8 4.7 - - + -
82A GLU* 2.8 39.9 + - - +
105A ARG* 3.8 20.2 - - + -
106A LYS* 5.1 2.7 - - - +
109A LEU* 4.3 11.7 - - + -
156A ARG* 2.6 60.7 + - + +
157A TYR* 3.7 31.2 - + - -
160A ASP* 2.4 33.4 + - - -
186A PHE* 4.3 5.4 - + - -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 2.6 38.0 + - - -
76A PHE* 2.7 5.8 + - - -
78A TYR* 1.3 69.4 - - - +
80A ALA* 1.3 59.9 + - - -
82A GLU* 3.3 3.0 + - - +
83A GLU* 2.9 31.9 + - - +
106A LYS* 2.8 50.2 + - - +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 2.7 18.9 + - + +
77A THR* 4.0 2.9 - - - +
79A SER* 1.3 75.1 + - - +
81A LEU* 1.3 56.6 + - - +
83A GLU* 3.2 7.1 + - - +
84A GLU* 3.0 34.1 + - - +
135A VAL* 3.6 33.9 - - + -
138A ILE* 3.9 7.9 - - + -
139A HIS* 4.1 12.8 - - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 2.8 23.5 + - + +
78A TYR* 3.9 6.7 - - + +
80A ALA* 1.3 77.3 - - - +
82A GLU* 1.3 58.0 + - - +
84A GLU* 3.5 1.0 + - - +
85A MET* 2.9 53.0 + - + +
138A ILE* 3.5 24.4 - - + +
149A LEU* 4.3 9.2 - - + -
152A HIS* 3.5 46.0 - - + +
153A ALA 4.6 0.4 - - - +
156A ARG* 4.3 14.8 - - + -
157A TYR* 3.8 21.1 - - + +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 2.8 23.4 + - - +
79A SER* 3.8 4.3 - - - +
80A ALA 3.2 0.2 - - - -
81A LEU* 1.3 76.6 - - - +
83A GLU* 1.3 59.7 + - - +
85A MET* 3.7 4.6 - - + -
86A GLU* 2.8 30.1 + - - +
104A HIS* 3.1 40.8 + - + +
105A ARG* 2.7 26.8 + - - -
106A LYS* 3.0 33.0 + - + +
157A TYR* 2.5 30.4 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 2.9 17.7 + - - +
80A ALA* 3.2 7.8 + - - +
82A GLU* 1.3 76.3 - - - +
84A GLU* 1.3 68.3 + - - +
86A GLU* 3.2 11.4 + - + +
87A ARG* 3.0 35.5 + - - +
106A LYS* 5.2 8.4 + - - +
139A HIS* 5.1 6.9 - - + -
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA 3.0 19.1 + - - +
81A LEU 3.7 4.5 - - - +
83A GLU* 1.3 80.1 - - - +
85A MET* 1.3 63.3 + - - +
87A ARG* 2.6 59.4 + - - +
88A ASN* 3.3 15.6 + - - -
138A ILE* 3.2 27.6 - - + +
139A HIS* 2.5 35.1 + - - +
142A GLY* 3.2 19.3 - - - -
143A GLN* 3.7 1.3 - - - +
149A LEU* 4.4 11.2 - - + -
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 2.9 27.2 + - + +
82A GLU* 3.7 18.4 - - + +
84A GLU* 1.3 72.1 - - - +
86A GLU* 1.3 58.9 + - - +
87A ARG 3.0 5.6 - - - -
88A ASN 3.4 1.8 + - - +
89A LYS* 3.0 28.8 + - - -
94A PHE* 3.4 34.2 - - + -
97A LEU 5.4 2.7 - - - +
98A TYR* 3.7 11.3 - - + -
99A PHE 6.2 0.9 - - - -
104A HIS* 3.9 12.6 - - + +
149A LEU* 3.8 16.8 - - + -
153A ALA* 4.0 19.3 - - - -
157A TYR* 3.1 38.8 - - + +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU 2.8 20.9 + - - +
83A GLU* 3.2 14.4 - - + +
85A MET* 1.3 77.0 - - - +
87A ARG* 1.3 59.7 + - - +
89A LYS* 3.6 29.4 + - - +
98A TYR* 2.5 34.3 + - - -
100A PRO* 5.1 0.3 - - - +
104A HIS* 4.5 5.9 - - + -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.0 20.4 + - - +
84A GLU* 2.6 50.9 + - - +
85A MET 3.0 0.4 - - - -
86A GLU* 1.3 80.8 - - - +
88A ASN* 1.3 66.2 + - - +
89A LYS* 3.2 6.8 + - - +
90A ASP 4.9 0.5 + - - -
142A GLY 3.4 14.8 + - - -
143A GLN* 2.9 28.2 + - - -
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Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU 3.3 18.0 + - - +
85A MET 3.4 2.9 + - - -
87A ARG* 1.3 82.1 - - - +
89A LYS* 1.3 51.4 + - - +
90A ASP 2.6 18.5 + - - -
91A HIS* 2.8 45.2 + - + +
94A PHE* 3.7 22.7 - - + +
141A ILE 5.3 0.6 + - - -
142A GLY* 4.0 23.0 + - - +
146A PRO* 4.2 14.8 - - - +
149A LEU* 4.1 13.7 - - + +
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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