Contacts of the helix formed by residues 56 - 78 (chain X) in PDB entry 6CP3
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 56 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57U ASP 4.9 2.2 - - - -
58U GLY* 3.7 16.0 - - - -
47X THR 5.3 4.0 - - - -
49X ASN* 2.4 43.1 + - - -
52X LYS* 4.7 6.2 - - - +
54X ILE* 3.9 1.5 - - - +
55X GLY* 1.3 77.4 + - - +
57X ARG* 1.3 59.6 + - - +
58X TRP* 3.2 4.9 - - - -
59X LEU* 2.7 30.8 + - - +
60X ILE* 3.0 7.7 + - - +
85Z MET* 3.7 11.3 - - - +
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Residues in contact with ARG 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58U GLY* 5.0 7.6 + - - +
59U ASP 4.9 1.2 + - - -
60U ASN 3.9 9.1 + - - -
61U ALA* 3.4 47.9 + - + +
62U SER* 5.0 2.2 + - - +
56X SER* 1.3 76.4 - - - +
58X TRP* 1.3 64.1 + - + +
59X LEU 3.4 0.2 + - - -
60X ILE* 3.6 16.0 + - - +
77Z TYR* 3.3 43.8 + - + -
78Z LYS* 3.0 55.5 + - - +
81Z ALA* 3.7 25.6 - - + +
82Z ASP* 4.9 10.5 - - - +
85Z MET* 4.0 8.0 - - + +
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Residues in contact with TRP 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55U TYR 3.8 1.6 + - - -
56U PHE* 3.6 51.0 - + + -
57U ASP 4.5 4.3 - - - -
61U ALA* 3.4 34.6 - - + +
62U SER 3.2 24.9 - - - -
63U GLY* 3.9 7.6 - - - -
65U PRO* 4.5 1.6 - - + -
66U LEU* 3.6 44.2 - - + -
43X LEU 4.5 3.1 - - - +
47X THR* 3.3 37.7 + - + +
56X SER* 3.2 1.9 - - - -
57X ARG* 1.3 78.3 - - + +
59X LEU* 1.3 59.7 + - - +
60X ILE 3.5 0.2 - - - -
61X SER* 3.8 18.5 - - - -
62X GLN* 4.5 1.6 + - - +
77Z TYR* 6.5 0.4 - + - -
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Residues in contact with LEU 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348 MET* 5.5 5.4 - - + -
358 ILE* 5.2 11.4 - - + -
388 LEU* 3.7 30.5 - - + -
43X LEU 5.3 0.2 - - - +
44X TYR* 5.2 10.8 - - + +
47X THR* 3.6 20.3 + - + +
48X ASN* 4.7 20.2 - - + +
49X ASN* 5.6 2.5 - - - +
52X LYS 5.0 3.4 - - - +
55X GLY* 3.8 21.8 - - - -
56X SER* 2.7 17.4 + - - +
58X TRP* 1.3 76.5 - - - +
60X ILE* 1.3 58.4 + - - +
61X SER 3.1 2.9 + - - -
62X GLN* 3.3 11.7 + - + +
63X GLU* 2.9 31.7 + - + +
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Residues in contact with ILE 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707 LEU* 4.5 14.8 - - + -
55X GLY 3.4 9.4 - - - +
56X SER 3.0 8.3 + - - +
57X ARG* 3.8 12.1 - - - +
58X TRP 3.5 0.4 - - - -
59X LEU* 1.3 74.5 - - - +
61X SER* 1.3 58.8 + - - +
63X GLU* 3.3 9.3 - - + +
64X ALA* 2.9 29.7 + - + +
77Z TYR* 4.2 8.1 - - + +
80Z PHE* 4.7 19.7 - - + -
81Z ALA* 3.7 30.7 - - + +
84Z ARG* 4.8 16.8 - - + -
85Z MET* 3.7 27.6 - - + -
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Residues in contact with SER 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X LEU* 5.4 3.1 - - - +
57X ARG 4.9 0.2 - - - -
58X TRP* 3.8 16.3 + - - -
60X ILE* 1.3 79.0 - - - +
62X GLN* 1.3 67.0 + - - +
64X ALA* 3.2 4.1 + - - +
65X ILE* 3.0 44.0 + - - +
77Z TYR* 3.7 18.5 + - - -
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Residues in contact with GLN 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358 ILE* 4.4 9.5 - - + +
43X LEU* 3.7 44.4 - - + +
44X TYR* 2.4 53.3 + - + -
58X TRP 5.0 2.7 - - - +
59X LEU* 3.3 10.9 + - + +
61X SER* 1.3 80.0 + - - +
63X GLU* 1.3 59.1 + - - +
65X ILE* 3.5 26.0 - - - +
66X TYR* 2.8 30.7 + - - +
90X PHE* 4.1 7.7 - - + -
94X MET* 3.8 11.8 - - - +
97X PHE* 5.8 1.2 - - - -
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Residues in contact with GLU 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637 TYR* 4.0 7.3 + - - -
1707 LEU* 3.7 25.7 - - + +
358 ILE* 3.6 22.0 - - - +
388 LEU* 5.1 6.9 - - - +
398 TYR* 2.8 36.0 + - - +
428 ARG* 4.4 14.4 + - - +
59X LEU* 2.9 18.6 + - - +
60X ILE* 3.3 16.2 - - + +
61X SER 3.2 0.2 - - - -
62X GLN* 1.3 77.1 - - - +
64X ALA* 1.3 58.4 + - - +
66X TYR* 3.3 6.4 + - - +
67X ASP* 3.0 35.0 + - - +
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Residues in contact with ALA 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707 LEU* 3.7 27.1 - - + +
1717 ASN* 3.9 6.7 - - - +
1727 VAL* 5.6 5.8 - - + +
60X ILE* 2.9 20.5 + - + +
61X SER* 3.7 4.7 - - - +
63X GLU* 1.3 73.7 - - - +
65X ILE* 1.3 59.4 + - + +
67X ASP* 3.4 3.0 + - - +
68X THR* 2.9 32.4 + - - +
80Z PHE* 5.9 3.8 - - + -
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Residues in contact with ILE 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X SER* 3.0 28.7 + - - +
62X GLN* 3.5 32.5 - - - +
64X ALA* 1.3 75.2 - - + +
66X TYR* 1.3 64.7 + - - +
68X THR* 3.3 8.7 - - + +
69X ILE* 3.0 44.9 + - + +
90X PHE* 3.9 13.2 - - + -
93X PHE* 4.4 8.3 - - + -
94X MET* 4.0 14.6 - - + -
97X PHE* 4.7 20.9 - - + -
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Residues in contact with TYR 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587 TRP* 3.2 42.7 + + - +
1607 VAL* 6.4 0.7 - - + -
328 LEU* 4.5 20.6 - - + -
358 ILE* 4.9 16.2 - - + -
368 LEU* 4.1 8.1 - - + +
398 TYR* 3.3 41.7 - + - +
62X GLN 2.8 19.3 + - - +
63X GLU* 3.4 6.1 - - - +
65X ILE* 1.3 76.9 - - - +
67X ASP* 1.3 59.9 + - - +
69X ILE* 3.4 3.0 + - - +
70X MET* 2.9 48.6 + - + +
86X PHE* 3.4 31.2 - + - -
90X PHE* 4.7 13.9 - + + -
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Residues in contact with ASP 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637 TYR* 5.4 2.5 - - - -
1687 GLY 4.6 0.9 - - - +
1697 ASN* 2.9 35.1 - - - +
1707 LEU* 3.8 10.0 - - - +
1717 ASN* 3.2 13.2 + - + +
398 TYR* 2.6 33.6 + - - -
63X GLU* 3.0 19.4 + - - +
64X ALA* 4.0 4.0 - - - +
65X ILE 3.3 0.2 - - - -
66X TYR* 1.3 80.9 - - - +
68X THR* 1.3 58.7 + - - +
70X MET* 3.8 13.2 - - - +
71X ASN* 2.9 31.0 + - - +
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Residues in contact with THR 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1717 ASN* 3.4 19.1 - - - +
1727 VAL* 4.5 9.6 + - + +
1737 MET* 3.3 38.2 + - - +
64X ALA 2.9 18.2 + - - +
65X ILE* 3.3 21.3 - - + +
67X ASP* 1.3 76.5 - - - +
69X ILE* 1.3 64.0 + - + +
72X MET* 3.3 7.3 - - - +
93X PHE* 6.1 3.8 - - + -
232X TYR* 4.3 13.2 - - + -
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Residues in contact with ILE 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X ILE* 3.0 24.4 + - + +
66X TYR 4.1 2.7 - - - +
68X THR* 1.3 84.6 - - + +
70X MET* 1.3 60.5 + - - +
72X MET* 3.3 19.8 - - + +
73X THR* 2.9 30.7 + - - +
86X PHE* 3.8 18.8 - - + -
89X ILE* 4.5 16.8 - - + +
90X PHE* 3.6 29.4 - - + -
93X PHE* 3.7 38.8 - - + -
232X TYR* 5.7 3.8 - - + -
235X ALA* 6.3 0.4 - - + -
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Residues in contact with MET 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1587 TRP* 4.0 5.4 - - + +
1597 ASP* 3.4 41.3 - - - +
1607 VAL* 3.9 10.3 - - + +
1637 TYR* 6.1 4.3 - - + -
398 TYR* 5.4 3.8 - - + -
66X TYR* 2.9 35.4 + - + +
67X ASP* 3.3 22.0 + - - +
69X ILE* 1.3 77.1 - - - +
71X ASN* 1.3 66.4 + - - +
73X THR 3.9 0.2 - - - -
74X LYS* 3.0 35.8 + - + +
82X TRP* 4.0 15.1 - - + -
86X PHE* 3.8 17.9 - - + -
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Residues in contact with ASN 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1647 LYS* 5.8 1.7 + - - -
1697 ASN* 3.7 27.5 - - - +
1717 ASN* 3.0 28.6 + - - +
1737 MET* 3.7 12.4 - - + +
67X ASP* 2.9 18.9 + - - +
70X MET* 1.3 81.0 - - - +
72X MET* 1.3 65.6 + - - +
74X LYS* 4.3 19.7 + - - +
75X GLY* 4.0 9.2 + - - -
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Residues in contact with MET 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1737 MET* 3.3 9.4 - - + +
68X THR 3.3 19.5 - - - +
69X ILE* 3.3 21.4 + - + +
70X MET 3.1 0.4 - - - -
71X ASN* 1.3 81.6 - - - +
73X THR* 1.3 77.3 + - - +
74X LYS 3.2 0.5 + - - -
75X GLY 3.3 1.2 + - - -
76X GLN* 2.9 42.3 + - + +
89X ILE* 3.9 28.5 - - + -
232X TYR* 3.3 29.6 - - + +
235X ALA* 4.2 18.6 - - + +
236X ILE* 3.7 19.7 - - + -
239X ALA* 4.0 7.4 - - - -
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Residues in contact with THR 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X ILE 2.9 23.2 + - - +
70X MET 4.0 0.2 - - - +
72X MET* 1.3 87.0 - - - +
74X LYS* 1.3 65.6 + - - +
76X GLN* 3.7 7.0 - - - +
77X ILE* 3.3 40.2 + - - +
82X TRP* 3.6 13.7 + - + -
85X TYR 5.9 0.3 - - - -
86X PHE* 3.5 29.3 + - + -
89X ILE* 4.5 15.0 - - + +
239X ALA* 4.7 4.0 - - - +
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Residues in contact with LYS 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597 ASP* 3.8 27.9 + - - +
70X MET* 3.0 21.6 + - + +
71X ASN* 4.7 17.3 + - - +
73X THR* 1.3 77.9 - - - +
75X GLY* 1.3 63.2 + - - +
77X ILE* 4.7 0.2 - - - +
78X GLY* 3.0 31.9 + - - -
82X TRP* 3.6 38.6 - - + +
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Residues in contact with GLY 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T ASP* 4.3 25.5 - - - +
71X ASN 4.0 6.9 + - - -
72X MET 3.3 5.9 + - - -
74X LYS* 1.3 80.5 - - - +
76X GLN* 1.3 71.9 + - - +
78X GLY* 4.5 2.8 + - - -
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Residues in contact with GLN 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T ASP* 5.3 2.3 - - - +
48T PHE* 3.4 34.6 - - - -
52T ILE* 5.6 2.0 - - - +
72X MET* 2.9 40.0 + - + +
73X THR* 3.8 8.3 - - - -
74X LYS 3.2 0.8 - - - -
75X GLY* 1.3 84.3 - - - +
77X ILE* 1.3 66.1 + - + +
236X ILE* 3.6 25.5 + - + +
239X ALA* 4.1 14.1 - - + -
240X SER* 4.7 12.9 - - - +
243X LYS* 3.2 30.1 + - - +
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Residues in contact with ILE 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73X THR* 3.3 29.8 + - - +
76X GLN* 1.3 78.2 - - + +
78X GLY* 1.3 64.3 + - - +
79X GLY* 3.1 4.6 + - - +
81X ASN 5.1 0.9 - - - +
82X TRP* 3.3 40.4 - - + +
85X TYR* 5.1 13.2 - - + -
86X PHE 5.8 0.2 - - - +
239X ALA* 3.4 29.4 - - - +
242X LEU* 4.7 9.0 - - + -
243X LYS* 3.7 33.9 - - + +
247X TYR* 4.3 10.7 - - + -
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Residues in contact with GLY 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X LYS 3.0 21.2 + - - -
75X GLY* 5.1 2.2 - - - -
76X GLN 3.5 1.5 - - - -
77X ILE* 1.3 78.9 - - - +
79X GLY* 1.3 64.1 + - - +
80X LYS 3.8 0.9 + - - -
82X TRP* 5.0 1.6 - - - -
247X TYR* 4.9 1.4 - - - -
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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