Contacts of the helix formed by residues 103 - 128 (chain N) in PDB entry 3V3K
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 THR 103 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N LEU* 3.9 9.2 - - - +
101N GLY 5.9 1.1 - - - -
102N MET* 1.3 77.1 - - - +
104N ILE* 1.3 65.0 + - - +
105N GLU* 3.5 30.3 + - - +
106N ASP* 3.1 30.7 + - - +
107N ARG 3.7 3.3 + - - -
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Residues in contact with ILE 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N THR 5.6 0.2 - - - +
26N PRO* 4.6 27.4 - - + +
98N LEU* 4.7 4.9 - - + -
103N THR* 1.3 72.4 - - - +
105N GLU* 1.3 63.9 + - + +
106N ASP 3.3 0.2 - - - -
107N ARG* 3.2 40.1 + - - +
108N ASP* 3.2 27.2 + - - +
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Residues in contact with GLU 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N THR* 3.2 18.6 + - - +
104N ILE* 1.3 76.6 - - + +
106N ASP* 1.3 62.4 + - - +
108N ASP* 3.6 8.5 + - - +
109N SER* 3.2 23.9 + - - -
112N ARG* 5.1 2.4 + - - -
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Residues in contact with ASP 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N LYS* 4.7 0.2 - - - -
83N VAL* 4.0 13.0 - - + +
101N GLY 5.1 0.3 - - - +
102N MET* 3.6 39.1 - - + +
103N THR* 3.1 37.3 + - - +
104N ILE 3.3 0.8 - - - -
105N GLU* 1.3 74.8 - - - +
107N ARG* 1.3 63.5 + - - +
109N SER* 2.7 22.3 + - - -
110N TYR* 3.4 10.0 + - - +
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Residues in contact with ARG 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N THR 3.0 27.9 + - - -
26N PRO* 3.4 19.3 + - - +
27N GLU 3.6 11.7 - - - +
28N SER* 3.6 6.1 + - - +
29N VAL* 3.2 27.1 - - - +
33N ASN* 4.9 6.3 - - - +
36N HIS* 4.3 2.6 + - - -
83N VAL* 4.4 2.5 - - - +
84N PHE* 3.9 27.0 - - + -
98N LEU* 4.2 13.5 - - + -
103N THR 3.7 2.4 + - - -
104N ILE* 3.2 36.1 + - - +
106N ASP* 1.3 78.6 - - - +
108N ASP* 1.3 87.2 + - - +
110N TYR* 3.3 6.8 + - - +
111N ILE* 3.1 33.3 + - + +
177N PRO* 4.7 0.9 - - + -
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Residues in contact with ASP 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ASN* 5.7 0.7 + - - -
35N ASN* 4.0 31.8 + - + +
36N HIS* 3.1 24.8 + - + +
104N ILE* 3.2 21.2 + - - +
105N GLU* 4.1 7.2 - - - +
106N ASP 3.4 0.4 - - - -
107N ARG* 1.3 106.5 + - - +
109N SER* 1.3 59.3 + - - +
111N ILE* 3.3 7.8 + - - +
112N ARG* 2.9 36.9 + - - +
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Residues in contact with SER 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N LYS* 3.3 24.1 + - - -
105N GLU 3.2 13.7 + - - -
106N ASP* 2.7 30.0 + - - -
108N ASP* 1.3 74.1 - - - +
110N TYR* 1.3 61.5 + - - +
112N ARG* 3.6 29.4 + - - +
113N ASP* 3.2 26.7 + - - +
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Residues in contact with TYR 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N LEU* 3.4 55.7 - - + +
79N LYS* 3.9 17.0 - - + +
80N ARG* 3.7 32.4 - - + -
83N VAL* 5.2 0.9 - - + -
84N PHE* 3.8 26.2 - + + -
106N ASP 3.4 7.4 + - - +
107N ARG 3.3 9.5 + - - +
109N SER* 1.3 82.8 + - - +
111N ILE* 1.3 66.5 + - + +
113N ASP* 3.1 5.7 + - - +
114N LEU* 2.8 42.0 + - + +
150N LEU* 4.7 2.4 - - - +
153N ASP* 2.6 29.4 + - - +
177N PRO* 4.4 8.5 - - + -
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Residues in contact with ILE 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 4.3 0.2 - - + -
32N LEU* 4.3 9.0 - - + -
36N HIS* 3.2 47.1 - - + +
107N ARG* 3.1 37.5 + - + +
108N ASP* 3.3 9.2 + - - +
110N TYR* 1.3 81.1 - - + +
112N ARG* 1.3 56.0 + - - +
114N LEU* 3.3 9.0 + - + +
115N PHE* 2.8 33.2 + - + +
157N MET* 4.8 5.1 - - - +
176N VAL* 3.5 33.0 - - + +
177N PRO* 4.4 7.2 - - + -
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Residues in contact with ARG 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N ASN 3.2 22.9 + - - +
36N HIS 3.8 10.1 + - - +
37N PHE 3.5 22.9 - - - +
38N LEU* 3.5 8.6 - - - +
39N SER* 4.9 16.5 + - - +
42N LEU* 4.0 22.5 - - + +
79N LYS* 6.0 0.2 - - - +
105N GLU 5.1 1.6 + - - -
108N ASP* 2.9 18.7 + - - +
109N SER* 3.6 30.2 + - - +
111N ILE* 1.3 76.5 - - - +
113N ASP* 1.3 57.6 + - - +
115N PHE* 3.2 4.3 + - - +
116N PHE* 3.0 24.3 + - - +
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Residues in contact with ASP 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N LEU* 3.9 18.6 - - - +
72N PHE* 3.6 27.4 - - + -
76N LEU* 3.5 20.4 - - + +
79N LYS* 3.3 25.4 + - - +
109N SER 3.2 14.4 + - - +
110N TYR 3.1 9.0 + - - +
112N ARG* 1.3 77.6 + - - +
114N LEU* 1.3 60.3 + - - +
116N PHE* 3.5 6.5 - - - +
117N LEU* 3.4 24.6 + - - +
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Residues in contact with LEU 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N LEU* 4.4 1.7 - - + +
110N TYR* 2.8 33.8 + - + +
111N ILE* 3.5 13.9 - - + +
112N ARG 3.2 0.2 - - - -
113N ASP* 1.3 73.5 - - - +
115N PHE* 1.3 63.5 + - - +
117N LEU* 3.3 10.9 + - + +
118N HIS* 3.2 20.8 + - - +
150N LEU* 3.8 23.6 - - + -
153N ASP* 3.6 31.2 - - + +
154N LEU* 4.3 10.2 - - + +
157N MET* 3.4 28.0 - - + -
176N VAL 3.4 20.0 - - - +
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Residues in contact with PHE 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N LEU* 4.4 13.5 - - + -
36N HIS 4.0 17.3 - - - +
37N PHE* 4.8 20.0 - + - -
38N LEU* 3.6 32.3 - - + -
111N ILE* 2.8 20.7 + - + +
112N ARG 3.2 6.5 + - - +
114N LEU* 1.3 71.0 - - - +
116N PHE* 1.3 53.7 + - - +
118N HIS* 3.2 4.3 + - - +
119N SER* 2.7 51.0 + - - -
157N MET* 3.4 34.9 - - + +
161N VAL* 4.1 18.4 - - + -
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Residues in contact with PHE 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N LEU* 3.6 10.4 - - + +
42N LEU* 3.8 25.8 - - + -
45N LYS* 4.1 10.5 - - + -
46N LEU* 3.6 36.8 - - + -
49N MET* 3.7 19.3 - - + -
69N LEU* 4.3 10.5 - - + -
72N PHE* 3.6 35.4 - + + -
112N ARG 3.0 12.7 + - - +
113N ASP* 3.5 11.7 - - - +
115N PHE* 1.3 75.0 - - - +
117N LEU* 1.3 60.8 + - + +
119N SER* 3.1 6.6 + - - -
120N LEU* 2.9 62.9 + - + +
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Residues in contact with LEU 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N LEU* 4.4 9.0 - - + -
72N PHE* 3.9 23.1 - - + -
73N VAL* 4.0 15.3 - - + -
76N LEU* 4.0 23.3 - - + -
113N ASP 3.4 15.4 + - - +
114N LEU* 3.3 11.4 + - + +
115N PHE 3.3 0.4 - - - -
116N PHE* 1.3 78.3 - - + +
118N HIS* 1.3 58.1 + - - +
120N LEU* 4.0 1.5 - - - -
121N LYS* 3.1 28.4 + - - +
142N LEU* 3.5 31.3 - - + +
150N LEU* 4.1 26.0 - - + -
154N LEU* 4.0 13.0 - - + +
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Residues in contact with HIS 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N LEU 3.2 8.9 + - - +
115N PHE* 3.2 9.0 + - - +
117N LEU* 1.3 76.2 - - - +
119N SER* 1.3 60.9 + - - +
121N LYS* 3.4 13.8 + - + +
122N VAL* 3.0 49.1 + - + +
154N LEU* 4.2 17.8 - - + +
157N MET* 3.8 20.0 - - + +
158N LYS* 3.8 34.4 - - + +
161N VAL* 3.5 39.2 - - + +
162N GLU* 3.8 16.5 + - + -
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Residues in contact with SER 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N LEU* 3.9 2.0 - - - +
46N LEU* 3.2 21.0 - - - +
115N PHE* 2.7 42.6 + - - -
116N PHE* 3.1 13.0 + - - -
118N HIS* 1.3 76.3 + - - +
120N LEU* 1.3 60.8 + - - +
122N VAL* 3.4 9.3 + - - +
123N LYS* 3.3 31.1 + - - +
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Residues in contact with LEU 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N LEU* 4.1 15.6 - - + +
49N MET* 3.7 31.0 - - + -
50N VAL* 5.2 6.0 - - + +
69N LEU* 4.1 15.5 - - + -
116N PHE* 2.9 53.6 + - + +
117N LEU* 4.1 3.8 - - - +
119N SER* 1.3 73.8 + - - +
121N LYS* 1.3 59.7 + - - +
123N LYS* 3.7 4.6 + - - +
124N ILE* 3.2 57.4 + - + +
142N LEU* 3.3 15.5 - - + -
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Residues in contact with LYS 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N LEU 3.1 19.7 + - - +
118N HIS* 3.5 13.2 - - + +
119N SER 3.3 0.2 - - - -
120N LEU* 1.3 74.8 - - - +
122N VAL* 1.3 59.5 + - + +
124N ILE* 3.4 3.1 + - - +
125N GLU* 3.0 51.2 + - - +
139N TYR* 4.2 7.6 - - + -
142N LEU* 3.4 47.0 + - + +
143N CYS* 3.8 19.0 - - - +
144N PRO* 5.9 0.4 - - - +
154N LEU* 5.6 12.7 - - + +
158N LYS* 5.7 8.9 - - - +
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Residues in contact with VAL 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N HIS* 3.0 45.2 + - + +
119N SER* 3.6 9.6 - - - +
120N LEU 3.4 0.4 - - - -
121N LYS* 1.3 76.7 - - + +
123N LYS* 1.3 59.5 + - + +
125N GLU* 3.3 14.2 + - - +
126N GLU* 3.0 45.3 + - + +
162N GLU* 4.0 12.6 - - - +
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Residues in contact with LYS 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N GLN* 4.6 5.7 - - - +
46N LEU* 3.2 26.5 - - + +
47N ASP* 4.1 8.7 + - - -
50N VAL* 3.5 44.2 - - + +
119N SER* 3.3 16.3 + - - +
120N LEU 4.2 1.6 - - - +
122N VAL* 1.3 75.6 - - + +
124N ILE* 1.3 60.8 + - - +
126N GLU* 3.4 19.4 + - - +
127N SER* 3.0 30.2 + - - -
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Residues in contact with ILE 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N VAL* 6.1 3.8 - - + -
53N TYR* 3.6 42.0 - - + +
65N ILE* 6.4 0.2 - - + -
120N LEU* 3.2 42.8 + - + +
121N LYS* 3.8 4.9 - - - +
123N LYS* 1.3 72.6 - - + +
125N GLU* 1.3 60.4 + - - +
127N SER* 3.3 7.9 + - - -
128N ARG* 2.9 30.4 + - - +
138N VAL* 4.4 19.5 - - + -
139N TYR* 3.6 29.8 - - + -
142N LEU* 4.0 9.4 - - + -
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Residues in contact with GLU 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LYS* 3.0 39.5 + - - +
122N VAL* 3.3 13.9 + - - +
124N ILE* 1.3 77.6 - - - +
126N GLU* 1.3 57.1 + - - +
128N ARG* 3.1 26.0 - - - +
129N GLN* 4.0 5.5 + - - +
139N TYR* 3.1 34.1 + - + +
158N LYS* 5.6 5.1 + - - -
162N GLU* 5.8 0.3 - - - +
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Residues in contact with GLU 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122N VAL* 3.0 36.1 + - + +
123N LYS* 3.5 19.7 - - - +
124N ILE 3.3 0.2 - - - -
125N GLU* 1.3 76.6 - - - +
127N SER* 1.3 60.2 - - - +
129N GLN* 3.0 39.3 + - - +
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Residues in contact with SER 127 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N VAL* 4.9 7.1 + - - +
53N TYR* 4.2 21.9 - - - -
54N SER* 3.9 23.6 - - - -
123N LYS 3.0 15.3 + - - -
124N ILE 3.3 9.1 + - - -
126N GLU* 1.3 79.3 - - - +
128N ARG* 1.3 58.2 + - - +
129N GLN* 3.2 6.2 + - - +
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Residues in contact with ARG 128 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N TYR* 3.4 25.6 - - + +
124N ILE* 2.9 20.5 + - - +
125N GLU* 3.1 15.1 - - - +
126N GLU 3.5 0.2 - - - -
127N SER* 1.3 73.8 - - - +
129N GLN* 1.3 59.1 + - - +
130N GLY 3.8 0.9 - - - +
131N LYS 4.2 13.4 + - - +
132N GLU* 2.8 30.9 + - - +
134N SER* 3.6 29.5 + - - +
135N LYS* 3.9 5.1 - - - +
136N CYS* 3.5 15.3 - - - +
139N TYR* 3.3 46.0 - - - +
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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