Contacts of the helix formed by residues 72 - 93 (chain A) in PDB entry 4PK5
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.7 8.4 - - - +
71A THR* 1.3 83.7 + - - +
73A HIS* 1.3 64.9 + - - +
74A LYS* 3.5 6.9 + - - +
75A SER* 3.0 27.6 + - - -
76A GLN* 2.9 27.8 + - - +
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Residues in contact with HIS 73 (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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16A HIS* 5.7 17.9 + + - -
25A LEU* 4.3 15.5 - - + +
72A ASP* 1.3 73.8 - - - +
74A LYS* 1.3 68.0 + - + +
76A GLN* 3.0 10.9 + - - +
77A ARG* 2.9 60.9 + - + +
118A LEU* 3.8 24.2 - - + +
300A PRO* 6.4 2.0 - - + -
301A PRO* 6.4 1.6 - - + -
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Residues in contact with LYS 74 (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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25A LEU* 4.6 19.0 - - + +
26A PRO* 4.0 13.8 - - - +
27A ASN* 2.8 56.4 + - - +
28A PRO* 4.6 1.8 - - + +
29A GLN* 3.6 26.5 + - + +
72A ASP* 3.3 7.6 + - + +
73A HIS* 1.3 81.6 - - + +
75A SER* 1.3 57.8 + - - +
77A ARG* 3.2 7.5 + - - +
78A LEU* 2.8 28.6 + - - +
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Residues in contact with SER 75 (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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29A GLN* 3.3 27.1 + - - +
32A LEU* 3.8 5.9 - - - +
33A PRO* 5.0 5.4 - - - -
70A LEU* 3.4 32.0 - - - +
71A THR 3.9 1.2 + - - -
72A ASP* 3.0 21.4 + - - -
74A LYS* 1.3 74.3 - - - +
76A GLN* 1.3 63.5 + - - +
78A LEU* 4.1 4.5 - - - -
79A ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 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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70A LEU* 3.2 30.0 + - + +
71A THR 3.3 15.2 + - - -
72A ASP 2.9 21.1 + - - +
73A HIS* 3.0 10.7 + - - +
75A SER* 1.3 77.3 + - - +
77A ARG* 1.3 62.0 + - - +
79A ALA* 3.2 5.2 + - - +
80A ARG* 2.9 32.1 + - - +
114A LEU* 3.6 21.7 - - + +
117A LYS* 3.8 25.9 - - - +
118A LEU* 3.8 32.4 - - + +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE 5.4 2.0 + - - -
25A LEU* 3.8 32.2 - - + +
73A HIS* 2.9 50.0 + - + +
74A LYS 3.4 7.9 - - - +
76A GLN* 1.3 77.6 - - - +
78A LEU* 1.3 60.6 + - - +
80A ARG* 3.2 7.6 + - - +
81A LEU* 3.1 20.6 + - - +
118A LEU* 4.1 12.8 - - + -
120A LEU* 4.9 11.8 - - - +
127A ALA* 2.7 45.0 + - - +
128A ASP* 4.4 12.2 + - - +
131A LEU* 4.0 12.1 + - - +
132A ALA* 3.7 19.9 - - + +
300A PRO* 4.6 13.7 - - - +
303A HIS* 5.8 2.2 - - - -
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Residues in contact with LEU 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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29A GLN* 2.8 39.5 - - + +
30A GLU 3.5 16.2 - - - +
31A ASN 3.6 18.4 - - - +
32A LEU* 3.9 13.0 - - + +
40A MET* 5.3 1.1 - - + -
74A LYS 2.8 19.8 + - - +
75A SER* 3.8 7.9 - - - +
77A ARG* 1.3 67.6 - - - +
79A ALA* 1.3 56.3 + - - +
80A ARG 3.0 1.8 - - - -
81A LEU* 2.9 17.3 + - + +
82A VAL* 2.8 37.6 + - + +
132A ALA* 5.4 2.0 - - - +
151A LEU* 4.3 4.5 - - + -
152A PHE* 3.9 27.6 - - + -
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Residues in contact with ALA 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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32A LEU* 4.0 8.9 - - + +
39A TRP* 4.4 9.6 - - + -
70A LEU* 3.7 22.0 - - + -
75A SER 2.9 19.5 + - - +
78A LEU* 1.3 76.4 - - - +
80A ARG* 1.3 56.8 + - - +
82A VAL* 3.4 5.6 + - - +
83A LEU* 2.9 34.0 + - - +
114A LEU* 3.4 23.3 - - + -
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Residues in contact with ARG 80 (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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76A GLN 2.9 15.9 + - - +
77A ARG* 3.3 12.9 - - - +
78A LEU 3.0 0.2 - - - -
79A ALA* 1.3 73.6 - - - +
81A LEU* 1.3 61.0 + - - +
83A LEU* 4.9 0.2 - - - -
84A GLY* 2.9 26.9 + - - -
111A TYR* 3.8 23.2 + - - -
114A LEU* 3.9 16.4 - - + -
115A SER* 3.2 26.8 + - - +
118A LEU* 4.0 11.9 - - + +
120A LEU* 3.5 30.5 - - - +
121A PRO 2.7 28.5 + - - -
123A ILE 3.5 8.3 + - - -
124A LEU* 4.5 2.6 - - - +
125A VAL* 3.2 19.0 - - - +
128A ASP* 2.7 38.3 + - - +
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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
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77A ARG 3.1 8.6 + - - +
78A LEU* 2.9 16.1 + - + +
80A ARG* 1.3 78.0 - - - +
82A VAL* 1.3 66.7 + - - +
84A GLY* 3.1 1.2 + - - -
85A CYS* 2.9 41.5 + - - -
124A LEU* 4.2 3.5 - - + +
128A ASP* 3.6 33.8 + - + +
129A CYS* 4.2 5.4 - - - +
132A ALA* 3.4 28.7 - - + +
133A ASN* 3.6 28.9 - - + +
151A LEU* 4.5 1.3 - - + -
152A PHE* 3.8 20.9 - - + -
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Residues in contact with VAL 82 (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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32A LEU* 4.4 7.2 - - + -
39A TRP* 3.9 33.7 - - + +
40A MET* 3.9 16.6 - - - -
43A ALA* 3.6 21.0 - - + +
78A LEU* 2.8 25.9 + - + +
79A ALA* 3.7 9.0 - - - +
81A LEU* 1.3 75.5 - - - +
83A LEU* 1.3 63.9 + - - +
85A CYS* 3.2 4.7 + - - +
86A ILE* 3.2 29.8 + - + +
152A PHE* 3.8 26.2 - - + -
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Residues in contact with LEU 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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39A TRP* 3.6 54.3 - - + +
79A ALA 2.9 21.9 + - - +
82A VAL* 1.3 74.3 - - - +
84A GLY* 1.3 53.4 + - - +
86A ILE* 3.6 8.1 + - + +
87A THR* 2.7 37.7 + - - -
107A ILE* 3.8 25.9 - - + +
110A PRO* 4.1 2.2 - - + -
111A TYR* 3.4 51.1 - - + +
114A LEU* 4.6 9.6 - - + -
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Residues in contact with GLY 84 (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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80A ARG 2.9 20.6 + - - -
83A LEU* 1.3 77.0 - - - +
85A CYS* 1.3 57.3 + - - +
87A THR* 3.3 3.5 + - - -
88A MET* 3.1 33.6 + - - +
111A TYR* 3.4 22.8 - - - -
124A LEU* 3.6 14.6 - - - -
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Residues in contact with CYS 85 (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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43A ALA* 5.2 3.8 - - + -
46A LEU* 3.7 22.0 - - + +
81A LEU* 2.9 37.3 + - - -
82A VAL* 3.5 8.3 - - - +
84A GLY* 1.3 74.2 - - - +
86A ILE* 1.3 60.2 - - + +
88A MET* 3.3 5.5 + - - +
89A ALA* 2.9 28.2 + - - +
124A LEU* 4.3 8.5 - - - -
129A CYS* 5.7 1.1 - - - -
133A ASN* 6.2 0.2 - - - -
152A PHE* 4.1 22.9 - - + -
153A SER 6.4 0.2 - - - -
154A PHE* 3.9 17.7 - - + -
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Residues in contact with ILE 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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39A TRP* 3.9 27.4 - - + +
42A ILE* 4.1 23.1 - - + -
43A ALA* 4.2 9.6 - - - +
46A LEU* 4.1 2.7 - - - +
55A LEU* 4.7 1.3 - - + +
59A VAL* 3.5 31.4 - - + -
62A LEU* 5.7 0.2 - - + -
82A VAL* 3.2 24.6 + - + +
83A LEU* 3.7 16.4 - - + +
85A CYS* 1.3 71.5 - - - +
87A THR* 1.3 57.5 + - - +
89A ALA* 3.1 7.3 + - - +
90A TYR* 2.7 38.5 + - + +
107A ILE* 4.6 18.8 - - + -
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Residues in contact with THR 87 (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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83A LEU 2.7 22.3 + - - -
84A GLY 3.5 6.3 - - - -
85A CYS 3.2 0.4 - - - -
86A ILE* 1.3 76.7 - - - +
88A MET* 1.3 57.8 + - + +
90A TYR* 3.6 0.7 - - - +
91A VAL* 2.8 38.9 + - + +
103A LEU* 3.8 36.9 - - + +
107A ILE* 4.0 5.7 - - - +
111A TYR* 3.8 23.0 - - + -
122A PRO 5.4 0.2 - - - +
237A TRP* 4.0 26.5 - - + -
247A LEU* 4.5 0.4 - - + -
249A TYR* 5.5 0.2 - - + -
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Residues in contact with MET 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 GLY* 3.1 21.6 + - - +
85A CYS 3.5 6.7 - - - +
87A THR* 1.3 77.7 - - + +
89A ALA* 1.3 65.0 + - - +
91A VAL* 4.7 1.3 - - - -
92A TRP* 3.2 35.7 + - + +
123A ILE* 3.6 20.9 - - + -
124A LEU* 3.7 27.8 - - + +
154A PHE* 4.1 10.3 - - + -
233A TYR* 3.1 34.5 - - + +
234A LEU* 5.3 1.1 - - - -
235A SER 3.8 18.4 - - - +
237A TRP* 3.6 30.5 - - + -
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Residues in contact with ALA 89 (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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46A LEU* 3.8 23.1 - - + -
50A ILE* 4.0 14.5 - - + +
55A LEU* 3.4 20.6 - - + +
85A CYS 2.9 13.6 + - - +
86A ILE 3.4 6.5 - - - +
88A MET* 1.3 76.4 - - - +
90A TYR* 1.3 55.6 + - - +
93A GLY* 2.8 35.7 + - - +
154A PHE* 5.3 0.4 - - + -
233A TYR* 4.4 12.3 - - + -
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Residues in contact with TYR 90 (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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55A LEU* 3.4 8.9 - - + +
56A ARG* 2.8 50.2 + - + +
59A VAL* 3.5 28.5 - - + -
60A GLU* 2.9 23.8 + - + +
86A ILE* 2.7 23.1 + - + +
87A THR* 3.6 5.8 - - - +
89A ALA* 1.3 72.4 - - - +
91A VAL* 1.3 66.7 + - + +
100A ARG* 3.2 37.3 - - + +
102A VAL 3.5 16.8 + - - -
103A LEU* 4.3 13.5 - - + -
104A PRO* 3.5 30.5 - - + +
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Residues in contact with VAL 91 (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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56A ARG* 3.1 2.9 + - - -
87A THR* 2.8 24.4 + - + +
88A MET 4.0 2.5 - - - +
90A TYR* 1.3 85.9 - - + +
92A TRP* 1.3 89.9 + - + +
99A VAL* 3.3 9.4 - - + -
100A ARG 2.8 39.7 + - - +
103A LEU* 4.9 2.0 - - + -
237A TRP* 4.2 12.6 - - + -
243A LEU* 4.4 6.3 - - + -
247A LEU* 3.7 34.8 - - + -
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Residues in contact with TRP 92 (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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56A ARG* 3.6 3.5 + - - -
88A MET* 3.2 34.5 + - - +
91A VAL* 1.3 96.5 - - + +
93A GLY* 1.3 54.7 + - - +
94A LYS 2.9 0.5 + - - -
95A GLY* 2.6 34.0 + - - -
98A ASP 4.3 7.3 + - - +
99A VAL* 4.5 13.9 - - + +
232A ILE* 3.5 41.0 + - + -
233A TYR* 4.1 15.3 - - + -
235A SER* 3.2 34.6 + - - -
236A GLY 3.8 12.1 - - - -
237A TRP* 4.1 6.6 - + - -
240A ASN* 3.5 22.9 - - - -
242A GLN* 4.3 31.4 - - + -
243A LEU* 4.3 13.0 - - + -
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Residues in contact with GLY 93 (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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50A ILE* 3.5 14.9 - - - +
55A LEU* 5.5 1.1 - - - -
56A ARG* 3.2 25.1 - - - +
89A ALA 2.8 19.8 + - - +
92A TRP* 1.3 76.3 - - - +
94A LYS* 1.3 57.0 + - - -
98A ASP 5.0 0.2 - - - -
233A TYR* 3.0 24.6 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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