Contacts of the helix formed by residues 67 - 93 (chain A) in PDB entry 3Q0U
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 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 5.2 2.0 - - - -
61A PHE* 3.7 11.9 - - - -
62A TYR* 4.8 3.1 - - - -
65A PHE* 3.3 2.8 + - - +
66A PRO* 1.3 82.6 - - - +
68A LYS* 1.3 62.5 + - - +
69A GLU* 3.4 20.7 + - - +
70A ALA* 3.1 29.8 + - - +
71A VAL* 3.4 14.6 + - - +
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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
----------------------------------------------------------
42A LEU* 3.0 39.0 + - + +
43A ALA* 3.6 17.3 + - - +
45A ILE* 2.7 31.4 + - + +
46A SER* 4.7 2.2 - - - +
47A VAL* 4.4 19.0 - - + +
50A LEU* 3.8 21.8 - - + -
61A PHE* 4.2 2.0 - - - -
67A SER* 1.3 71.1 - - - +
69A GLU* 1.3 88.3 + - - +
71A VAL* 3.1 21.4 + - - +
72A LEU* 3.1 12.6 + - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.2 17.4 - - + +
67A SER* 3.2 20.6 - - - +
68A LYS* 1.3 101.2 - - - +
70A ALA* 1.3 55.7 + - - +
72A LEU* 3.3 5.2 + - - +
73A LEU* 3.0 27.4 + - - +
131A SER* 6.1 6.5 - - - -
134A VAL* 5.5 2.3 - - - +
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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
----------------------------------------------------------
65A PHE* 4.0 7.4 - - + -
66A PRO* 3.7 29.2 - - + -
67A SER* 3.1 23.9 + - - +
68A LYS 3.3 0.2 - - - -
69A GLU* 1.3 72.9 - - - +
71A VAL* 1.3 66.2 + - - +
73A LEU* 3.5 11.3 + - + +
74A THR* 3.1 26.7 + - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.0 9.4 - - + +
30A LEU* 3.8 14.8 - - + +
33A ALA* 3.5 32.5 - - + -
42A LEU* 6.1 0.4 - - + -
50A LEU* 4.2 4.7 - - + -
61A PHE* 3.6 22.4 - - + -
65A PHE* 3.6 28.0 - - + -
67A SER 3.5 14.4 - - - +
68A LYS* 3.1 11.5 + - - +
70A ALA* 1.3 76.6 - - - +
72A LEU* 1.3 56.2 + - - +
74A THR* 3.2 4.7 + - - -
75A LEU* 3.0 27.6 + - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.0 15.5 - - + -
42A LEU* 3.9 29.8 - - + +
68A LYS 3.1 11.1 + - - +
69A GLU* 3.3 8.0 + - - +
71A VAL* 1.3 73.2 - - - +
73A LEU* 1.3 59.7 + - - +
75A LEU* 3.1 11.8 + - + -
76A LEU* 2.8 29.8 + - + +
120A VAL* 4.4 8.5 - - + +
123A ALA* 3.7 45.3 - - + +
124A GLY* 4.0 12.3 - - - +
127A ALA* 3.9 18.8 - - + -
134A VAL* 5.5 2.5 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU 3.0 15.0 + - - +
70A ALA* 3.6 14.1 - - + +
72A LEU* 1.3 76.4 - - - +
74A THR* 1.3 58.4 + - - +
76A LEU* 3.4 2.7 + - - +
77A ASP* 2.9 31.8 + - + +
131A SER* 5.6 0.2 - - - +
133A GLU* 3.6 38.1 - - + +
134A VAL* 4.0 26.6 - - + +
137A LEU* 3.8 22.9 - - + -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU* 4.6 6.1 - - - +
30A LEU* 3.7 25.1 - - + -
65A PHE* 3.5 15.6 - - + -
70A ALA 3.1 15.3 + - - -
71A VAL 3.2 8.0 + - - -
73A LEU* 1.3 73.4 - - - +
75A LEU* 1.3 65.9 + - - +
77A ASP* 3.3 7.0 + - + +
78A ARG* 3.0 36.1 + - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.6 35.2 - - + +
33A ALA* 3.8 28.0 - - + -
34A GLU* 3.8 26.0 - - - +
37A LEU* 4.2 11.0 - - + -
71A VAL* 3.0 16.5 + - + +
72A LEU* 3.5 10.8 - - + +
74A THR* 1.3 77.3 - - - +
76A LEU* 1.3 62.7 + - - +
78A ARG* 3.3 14.8 + - + +
79A VAL* 3.1 26.5 + - - +
120A VAL* 3.8 25.1 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 2.8 16.8 + - + +
73A LEU* 3.7 6.3 - - - +
75A LEU* 1.3 77.6 - - - +
77A ASP* 1.3 56.4 + - - +
79A VAL* 3.2 6.6 + - + -
80A VAL* 2.9 47.7 + - + +
114A PHE* 5.7 1.3 - - + -
120A VAL* 3.9 19.7 - - + +
121A THR* 5.2 5.2 - - - +
124A GLY* 3.9 24.5 - - - +
125A GLN* 5.5 1.6 - - - +
128A ARG* 6.0 0.2 - - + -
134A VAL* 3.7 33.2 - - + +
137A LEU* 3.8 20.4 - - + -
138A TRP* 4.8 18.6 - - + +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 2.9 20.3 + - + +
74A THR* 3.6 9.6 - - + +
76A LEU* 1.3 76.7 - - - +
78A ARG* 1.3 64.6 + - - +
80A VAL* 4.7 0.9 - - - -
81A ASN* 2.9 47.2 + - - +
137A LEU* 3.4 32.0 - - + +
141A PHE* 5.0 0.3 - - - -
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Residues in contact with ARG 78 (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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27A LEU* 3.7 32.0 - - - +
30A LEU* 4.1 18.1 - - - +
74A THR* 3.0 35.7 + - + +
75A LEU* 3.3 16.5 + - + +
77A ASP* 1.3 79.1 - - - +
79A VAL* 1.3 58.9 + - + +
81A ASN* 3.8 3.9 - - - +
82A GLN* 2.9 30.7 + - - +
85A MET* 5.3 1.0 - - - +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 5.3 0.7 - - - +
75A LEU* 3.1 16.6 + - + +
76A LEU* 3.8 6.1 - - + +
78A ARG* 1.3 74.2 - - + +
80A VAL* 1.3 61.9 + - + +
82A GLN* 3.2 9.5 + - - +
83A ALA* 2.9 27.2 + - - +
113A THR* 3.7 9.2 - - + +
114A PHE* 3.4 30.5 - - + -
117A HIS* 3.9 37.7 - - + +
120A VAL* 3.9 22.2 - - + -
121A THR* 4.8 2.9 - - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 2.9 32.5 + - + +
77A ASP* 4.1 4.5 - - - +
79A VAL* 1.3 76.2 - - - +
81A ASN* 1.3 58.1 + - - +
83A ALA* 3.3 3.6 + - - +
84A ASP* 2.9 26.9 + - - +
114A PHE* 4.2 13.9 - - + -
137A LEU* 5.0 5.4 - - + +
138A TRP* 3.7 32.5 - - + -
141A PHE* 3.1 50.0 - - + -
145A TRP* 3.8 4.9 - - + -
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Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 2.9 49.5 + - - +
78A ARG* 3.9 4.7 - - - +
80A VAL* 1.3 75.8 - - - +
82A GLN* 1.3 59.3 + - - +
84A ASP* 3.7 7.2 - - - +
85A MET* 2.8 50.5 + - + +
141A PHE* 3.5 26.3 - - - -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG 2.9 20.2 + - - +
79A VAL* 3.2 9.5 + - - +
81A ASN* 1.3 74.5 - - - +
83A ALA* 1.3 64.1 + - - +
85A MET* 3.4 15.0 + - + +
86A ALA* 3.1 23.7 + - + +
113A THR* 3.8 22.4 + - + +
116A SER* 6.1 0.6 - - - -
117A HIS* 4.0 24.1 + - - -
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Residues in contact with ALA 83 (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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79A VAL 2.9 13.7 + - - +
80A VAL 3.6 7.4 - - - +
82A GLN* 1.3 76.8 - - - +
84A ASP* 1.3 62.1 + - - +
86A ALA 3.3 1.7 + - - -
87A LEU* 3.0 21.3 + - - +
109A VAL* 3.5 9.9 - - + +
110A PHE* 3.7 30.0 - - + -
113A THR* 3.7 25.4 - - + +
114A PHE* 4.0 11.7 - - + -
145A TRP* 4.5 0.2 - - + -
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL 2.9 16.6 + - - +
81A ASN* 3.3 7.7 + - - +
83A ALA* 1.3 76.2 - - - +
85A MET* 1.3 58.8 + - + +
87A LEU* 3.3 8.9 + - - +
88A GLN* 2.9 54.6 + - - +
141A PHE* 3.8 23.1 - - + -
144A LYS* 3.5 23.6 - - - +
145A TRP* 3.0 29.4 + - - +
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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
----------------------------------------------------------
78A ARG 5.3 0.4 - - - +
81A ASN* 2.8 47.8 + - + +
82A GLN* 3.7 14.1 - - + +
84A ASP* 1.3 72.6 - - + +
86A ALA* 1.3 60.1 + - - +
88A GLN* 3.2 19.1 + - - +
89A THR* 3.0 32.4 + - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 3.1 17.1 + - + +
83A ALA* 3.3 0.9 + - - -
85A MET* 1.3 72.1 - - - +
87A LEU* 1.3 64.8 + - - +
89A THR* 3.3 8.2 + - - -
90A LEU* 3.0 24.8 + - - +
109A VAL* 3.5 26.9 - - + +
113A THR* 4.7 5.4 - - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 3.0 13.3 + - - +
84A ASP* 3.5 11.7 - - - +
86A ALA* 1.3 77.6 - - - +
88A GLN* 1.3 57.8 + - + +
90A LEU* 3.4 9.3 + - + +
91A ALA* 2.9 27.1 + - + +
106A GLY* 4.7 7.0 - - - +
109A VAL* 3.8 4.6 - - + +
110A PHE* 4.0 22.2 - - + -
145A TRP* 4.0 15.7 - - + -
148A TYR* 4.1 22.2 - - + -
217A LL3 3.8 58.6 - - + +
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Residues in contact with GLN 88 (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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84A ASP* 2.9 45.0 + - - +
85A MET* 3.2 20.0 + - - +
87A LEU* 1.3 76.4 - - + +
89A THR* 1.3 56.4 + - - +
91A ALA* 3.2 8.2 + - - +
92A GLU* 3.0 42.7 + - - +
144A LYS* 5.6 1.4 - - - +
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET 3.0 14.4 + - - -
86A ALA* 3.6 11.3 - - - -
87A LEU 3.3 0.2 - - - -
88A GLN* 1.3 72.2 - - - +
90A LEU* 1.3 66.4 + - - +
92A GLU* 3.3 23.0 + - - +
93A ASN* 3.2 27.4 + - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 3.0 10.7 + - - +
87A LEU* 3.5 11.4 - - + +
89A THR* 1.3 78.2 - - - +
91A ALA* 1.3 62.6 + - - +
92A GLU 3.3 0.7 + - - -
93A ASN* 3.4 29.9 + - + +
105A THR* 3.5 48.0 - - + +
106A GLY* 3.6 17.3 - - - +
109A VAL* 3.7 15.3 - - + -
217A LL3 3.9 23.5 - - + +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 2.9 18.0 + - - +
88A GLN* 3.2 9.6 + - - +
90A LEU* 1.3 76.4 - - - +
92A GLU* 1.3 61.1 + - + +
93A ASN 3.6 6.6 - - - +
148A TYR* 3.2 40.3 + - + +
217A LL3 4.6 8.7 - - - -
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 3.0 29.7 + - - +
89A THR* 3.6 15.9 + - - +
90A LEU 3.2 0.4 - - - -
91A ALA* 1.3 75.0 - - - +
93A ASN* 1.3 69.9 + - - +
94A PRO* 3.9 1.4 - - - +
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.2 26.2 + - - +
90A LEU* 3.4 25.8 + - + +
91A ALA* 3.6 8.8 - - - +
92A GLU* 1.3 83.5 - - - +
94A PRO* 1.4 78.3 - - + +
95A ALA* 3.7 15.2 - - + +
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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