Contacts of the helix formed by residues 62 - 91 (chain A) in PDB entry 4AL1
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 ASP 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 2.7 48.4 + - - +
43A ALA* 3.4 21.6 - - + +
60A ARG* 4.1 0.7 + - - -
61A SER* 1.3 77.4 - - - +
63A PRO* 1.4 69.0 - - - +
64A ASP* 2.9 26.0 + - - +
65A VAL* 3.1 16.9 + - + +
66A GLU* 2.8 32.8 + - - +
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Residues in contact with PRO 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.6 4.3 - - - +
61A SER 4.9 0.4 - - - +
62A ASP* 1.4 94.3 - - - +
64A ASP* 1.3 60.3 + - - +
66A GLU* 3.8 8.0 - - + +
67A ARG* 2.9 29.9 + - - +
70A ARG* 4.6 3.5 + - - -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.9 17.5 - - + -
41A LYS* 3.0 27.4 + - - +
62A ASP* 2.9 9.8 + - - +
63A PRO* 1.3 79.5 - - - +
65A VAL* 1.3 66.1 + - - +
67A ARG* 3.5 6.7 + - - +
68A CYS* 3.1 26.9 + - - -
120A LYS* 2.8 36.0 + - - -
203A PLM 3.9 14.5 - - - +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 4.6 4.3 - - + -
37A VAL* 3.7 22.9 - - + +
38A ARG* 3.6 62.4 - - + +
43A ALA* 4.2 6.7 - - + -
62A ASP* 3.1 28.8 + - + +
64A ASP* 1.3 76.5 - - - +
66A GLU* 1.3 67.0 + - - +
68A CYS* 3.1 7.6 + - - +
69A LEU* 3.0 28.8 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 5.4 0.9 + - - -
61A SER* 4.4 17.4 - - - -
62A ASP 2.8 29.5 + - - +
63A PRO* 3.8 7.4 - - + +
65A VAL* 1.3 76.4 - - - +
67A ARG* 1.3 57.1 + - - +
69A LEU* 3.3 26.1 + - - +
70A ARG* 3.0 48.7 + - - +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO 2.9 17.9 + - - +
64A ASP* 3.5 6.6 + - - +
66A GLU* 1.3 73.6 - - - +
68A CYS* 1.3 65.8 + - - +
70A ARG* 3.3 30.5 + - - +
71A ALA* 3.0 22.2 + - - +
117A TYR* 2.9 50.9 + - + +
118A LEU* 4.4 8.1 - - + +
120A LYS* 3.6 48.8 - - - +
126A ARG* 5.5 2.2 - - - +
203A PLM 4.0 9.4 - - - +
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Residues in contact with CYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.9 5.3 - - + +
33A ILE* 3.9 28.3 - - - -
34A THR* 3.3 27.4 - - + +
37A VAL* 4.1 16.2 - - - -
64A ASP 3.1 18.5 + - - -
65A VAL 3.1 8.3 + - - +
67A ARG* 1.3 75.6 - - - +
69A LEU* 1.3 58.7 + - - +
71A ALA* 3.3 3.6 + - - +
72A HIS* 3.0 28.1 + - - +
118A LEU* 3.9 14.1 - - + -
203A PLM 4.1 10.3 - - - -
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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
----------------------------------------------------------
34A THR* 4.2 17.3 - - + +
38A ARG* 3.8 23.3 - - - +
65A VAL* 3.0 19.2 + - + +
66A GLU* 3.6 33.9 - - - +
68A CYS* 1.3 77.9 - - - +
70A ARG* 1.3 55.9 + - - +
72A HIS* 3.3 11.3 + - + +
73A ARG* 2.8 30.2 + - - +
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO 4.6 2.4 + - - -
66A GLU* 3.0 34.7 + - - +
67A ARG* 3.6 47.3 - - - +
68A CYS 3.3 0.2 - - - -
69A LEU* 1.3 73.7 - - + +
71A ALA* 1.3 59.5 + - - +
73A ARG* 3.8 5.8 - - - +
74A ASN* 2.9 31.0 + - - +
117A TYR* 3.0 34.4 + - - +
1153A 48T 3.5 11.7 + - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.7 6.3 - - + -
67A ARG 3.0 13.1 + - - +
68A CYS 3.6 8.1 - - - +
70A ARG* 1.3 75.3 - - - +
72A HIS* 1.3 57.9 + - - +
74A ASN* 3.3 3.8 + - - +
75A ASP* 3.0 34.6 + - - +
113A HIS* 5.2 1.6 - - + +
114A THR* 5.1 9.4 - - + +
117A TYR* 3.5 27.5 - - + -
118A LEU* 3.8 21.3 - - + -
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.9 35.6 + - + +
30A VAL* 3.7 17.2 - - + +
31A ALA* 3.8 31.9 - - + -
34A THR* 4.8 4.0 + - - +
68A CYS 3.0 16.8 + - - +
69A LEU* 3.6 13.0 - - + +
71A ALA* 1.3 76.0 - - - +
73A ARG* 1.3 64.4 + - - +
75A ASP* 3.2 10.5 + - + +
76A MET* 3.0 31.8 + - + +
80A TYR* 5.2 1.6 + - - -
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Residues in contact with ARG 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 18.6 + - - +
70A ARG* 3.8 6.5 - - - +
72A HIS* 1.3 77.5 - - - +
74A ASN* 1.3 56.6 + - - +
76A MET* 3.0 23.0 + - + +
77A GLU* 2.8 53.3 + - + +
1153A 48T 4.9 5.5 + - - -
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG 2.9 18.3 + - - +
71A ALA 3.7 4.5 - - - +
73A ARG* 1.3 75.6 - - - +
75A ASP* 1.3 61.1 + - - +
77A GLU* 3.2 20.5 + - - +
78A THR* 2.9 19.1 + - - +
110A ARG* 2.8 35.5 + - - -
113A HIS* 3.3 18.9 - - + -
130A TYR* 3.4 10.1 - - - -
1153A 48T 2.8 54.5 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.5 36.4 + - - -
27A MET* 3.5 24.2 - - + +
30A VAL* 4.0 8.8 - - - +
71A ALA 3.0 17.8 + - - +
72A HIS* 3.2 13.0 + - - +
74A ASN* 1.3 74.9 - - - +
76A MET* 1.3 57.2 + - - +
78A THR* 3.8 0.9 - - - -
79A ILE* 2.7 46.7 + - + +
110A ARG* 3.0 21.7 + - - +
113A HIS* 4.8 0.9 + - - -
114A THR* 3.7 6.8 + - - -
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.7 8.1 - - + -
72A HIS* 3.0 19.8 + - + +
73A ARG* 3.0 31.6 + - + +
75A ASP* 1.3 74.9 - - - +
77A GLU* 1.3 62.3 + - + +
78A THR 3.4 0.7 + - - -
80A TYR* 3.4 62.9 - - + +
81A PRO* 3.8 1.7 - - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 2.8 53.8 + - + +
74A ASN* 3.2 18.2 + - - +
76A MET* 1.3 79.6 - - + +
78A THR* 1.3 63.0 + - + +
81A PRO* 3.5 15.9 - - - +
130A TYR* 5.2 3.3 + - - +
134A GLN* 5.3 1.7 + - - -
1153A 48T 2.9 39.9 + - - +
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN 2.9 15.8 + - - +
75A ASP 3.1 1.4 + - - -
76A MET 3.2 0.2 - - - -
77A GLU* 1.3 84.1 - - + +
79A ILE* 1.3 70.5 + - - +
80A TYR 3.4 1.3 - - - -
81A PRO* 3.4 7.2 - - - +
82A PHE* 3.2 16.1 + - - +
106A PHE* 3.6 11.4 - - - -
110A ARG* 3.0 25.0 + - - +
130A TYR* 3.4 39.7 - - + +
134A GLN* 3.5 27.6 + - - +
137A CYS* 4.8 2.8 - - - -
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 29.2 - - + +
24A VAL* 5.0 1.1 - - + +
26A LYS* 3.8 13.9 - - - -
27A MET* 3.8 28.0 - - + -
75A ASP* 2.7 46.3 + - - +
78A THR* 1.3 76.9 + - - +
80A TYR* 1.3 64.6 + - - +
82A PHE* 3.2 3.3 + - + +
83A LEU* 3.0 37.5 + - + +
106A PHE* 3.9 23.8 - - + -
110A ARG* 4.2 7.9 - - + +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 6.1 1.3 - - + -
27A MET* 3.5 38.4 - - + +
72A HIS* 5.2 1.6 + - - -
75A ASP 3.8 1.4 + - - -
76A MET* 3.4 46.9 - - + +
79A ILE* 1.3 77.4 - - - +
81A PRO* 1.4 70.3 - - + +
83A LEU* 3.2 36.7 + - + +
84A PHE* 3.4 7.1 + - - +
----------------------------------------------------------
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Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET 3.8 3.8 - - - +
77A GLU 3.5 20.6 - - - +
78A THR* 3.4 14.6 - - - +
80A TYR* 1.4 94.5 - - + +
82A PHE* 1.3 56.0 + - - +
84A PHE* 3.2 8.3 + - + +
85A LEU* 2.9 44.0 + - + +
134A GLN* 6.3 0.7 - - - +
137A CYS* 6.1 1.3 - - + -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.7 8.7 - + - -
19A CYS* 4.8 3.4 - - + -
20A SER* 3.5 26.9 - - - -
23A LEU* 4.3 11.9 - - + -
78A THR 3.2 3.0 + - - +
79A ILE* 3.2 11.2 + - + +
81A PRO* 1.3 77.4 - - - +
83A LEU* 1.3 62.2 + - + +
85A LEU* 4.5 5.6 - - - +
86A GLY* 2.7 31.4 + - - -
102A HIS 4.8 0.9 - - - -
103A PHE* 3.8 36.3 - + + -
106A PHE* 3.4 61.9 - + + -
137A CYS* 4.1 10.2 - - - -
140A MET* 3.6 28.3 - - + -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.3 22.7 - - + -
20A SER* 3.6 40.2 - - - +
24A VAL* 4.2 20.9 - - + -
79A ILE* 3.0 25.6 + - + +
80A TYR* 3.2 32.5 + - + +
82A PHE* 1.3 77.6 - - + +
84A PHE* 1.3 61.5 + - - +
87A PHE* 3.3 9.5 - - - +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR 3.4 6.6 + - - +
81A PRO* 3.2 9.9 + - + +
83A LEU* 1.3 77.2 - - - +
85A LEU* 1.3 84.5 + - + +
87A PHE* 3.4 4.5 + - - +
88A VAL* 3.1 48.5 + - + +
144A ILE* 5.7 5.2 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 2.9 35.4 + - + +
82A PHE* 4.1 2.5 - - - +
84A PHE* 1.3 90.2 - - + +
86A GLY* 1.3 58.2 + - - +
89A TYR* 2.8 32.4 + - - +
137A CYS* 3.6 36.6 - - + +
140A MET* 4.2 11.9 - - + -
141A ALA* 3.9 21.8 - - + -
144A ILE* 3.4 26.9 - - + +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.4 19.0 - - - -
82A PHE* 2.7 22.1 + - - -
85A LEU* 1.3 74.3 - - - +
87A PHE* 1.3 52.9 + - - +
89A TYR* 3.8 0.9 - - - +
90A SER* 2.8 37.4 + - - -
103A PHE* 4.2 3.3 - - - -
140A MET* 3.8 21.2 - - - +
----------------------------------------------------------
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.4 9.0 - - + -
16A PHE* 3.3 29.8 - + + -
17A LEU* 4.8 8.1 - - + -
83A LEU 3.3 18.6 + - - +
84A PHE* 3.4 4.2 + - - +
85A LEU 3.3 0.4 - - - -
86A GLY* 1.3 73.4 - - - +
88A VAL* 1.3 72.9 + - + +
90A SER* 3.3 9.2 + - - -
91A PHE* 3.2 54.5 - + - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.1 43.3 + - + +
85A LEU 3.8 3.4 - - - +
87A PHE* 1.3 83.2 - - + +
89A TYR* 1.3 65.2 + - - +
91A PHE* 3.0 18.2 + - - +
92A LEU* 3.4 23.3 + - + +
144A ILE* 3.9 31.6 - - + -
----------------------------------------------------------
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 2.8 23.3 + - - +
86A GLY 3.8 1.6 - - - +
88A VAL* 1.3 71.5 - - - +
90A SER* 1.3 61.7 + - - +
91A PHE 3.1 1.0 + - - -
92A LEU* 3.1 24.5 + - + +
94A PRO* 3.3 41.2 - - + +
98A VAL* 3.9 5.0 - - - +
99A ALA* 3.6 31.9 + - + -
102A HIS* 3.5 24.0 + + - -
103A PHE* 3.8 17.5 - + - -
140A MET* 3.5 40.4 - - + -
143A GLN* 3.6 35.1 + - + -
144A ILE* 4.1 7.4 - - + +
----------------------------------------------------------
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.5 20.4 - - - -
11A PRO* 5.6 0.3 - - - +
12A ALA* 4.0 10.8 + - - +
13A LEU* 4.0 29.6 - - - -
16A PHE* 3.3 21.2 - - - +
86A GLY 2.8 22.0 + - - -
87A PHE 3.5 7.2 - - - -
88A VAL 3.2 0.4 - - - -
89A TYR* 1.3 78.0 - - - +
91A PHE* 1.3 60.2 + - - +
92A LEU 3.4 0.4 + - - -
93A GLY* 4.4 0.9 + - - -
94A PRO* 4.1 11.8 - - - +
103A PHE* 3.5 8.7 - - - -
----------------------------------------------------------
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.5 23.1 + - - -
13A LEU* 3.7 30.1 - - + -
87A PHE* 3.2 59.5 - + - -
88A VAL* 3.0 11.3 + - - +
90A SER* 1.3 76.9 - - - +
92A LEU* 1.3 62.6 + - + +
93A GLY 3.4 6.0 + - - -
----------------------------------------------------------
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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