Contacts of the helix formed by residues 54 - 80 (chain K) in PDB entry 6MZL
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 GLU 54 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K ALA* 1.3 73.7 - - - +
55K LYS* 1.3 59.2 + - - +
56K ALA 3.4 1.6 - - - +
57K SER* 2.3 38.2 + - - +
58K VAL* 2.9 15.1 + - - +
194O THR* 5.4 1.6 - - + -
195O LEU* 3.2 12.9 + - - +
196O THR* 3.3 16.0 - - - +
197O MET* 3.0 52.4 + - - +
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Residues in contact with LYS 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K ALA* 4.0 3.0 + - - -
54K GLU* 1.3 71.8 - - - +
56K ALA* 1.3 61.6 + - - +
58K VAL* 3.1 10.1 + - + +
59K GLU* 3.0 48.5 + - + +
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Residues in contact with ALA 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K GLU 3.4 0.4 - - - -
55K LYS* 1.3 82.7 - - - +
57K SER* 1.3 55.2 + - - +
59K GLU* 3.4 8.6 + - - +
60K THR* 2.5 39.4 + - - +
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Residues in contact with SER 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K GLU* 2.3 50.9 + - - +
56K ALA* 1.3 76.3 - - - +
58K VAL* 1.3 57.3 + - - +
60K THR* 3.3 6.9 + - - -
61K LEU* 2.9 36.3 + - - +
195O LEU* 3.3 17.5 - - - +
196O THR 5.5 0.2 - - - -
197O MET* 4.8 4.5 - - - -
200O LEU* 4.3 24.5 - - - +
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Residues in contact with VAL 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K GLN* 5.6 6.1 - - + +
41K VAL* 3.8 24.2 - - + +
45K LEU* 4.5 9.6 - - + -
53K ALA* 3.8 19.1 - - + -
54K GLU 2.9 14.4 + - - +
55K LYS* 3.1 11.6 + - - +
57K SER* 1.3 81.9 + - - +
59K GLU* 1.3 60.8 + - + +
61K LEU* 3.2 9.6 + - - +
62K THR* 2.8 31.1 + - - +
195O LEU* 3.8 19.5 - - + -
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Residues in contact with GLU 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K ARG* 4.6 12.1 + - - +
38K GLN* 3.5 34.4 + - + +
55K LYS* 3.0 39.2 + - + +
56K ALA* 3.9 7.8 - - - +
58K VAL* 1.3 80.2 - - + +
60K THR* 1.3 57.5 + - - +
62K THR* 3.2 10.4 + - - -
63K GLU* 2.9 32.5 + - + +
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Residues in contact with THR 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K ALA* 2.5 25.3 + - - +
57K SER* 3.6 8.0 - - - -
58K VAL 3.2 0.2 - - - -
59K GLU* 1.3 74.5 - - - +
61K LEU* 1.3 59.6 + - + +
63K GLU* 3.2 11.9 + - + +
64K MET* 2.9 41.8 + - + +
42M PHE* 6.2 3.6 - - + -
45M ARG* 5.5 9.2 - - - +
200O LEU* 6.2 5.8 - - + -
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Residues in contact with LEU 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K VAL* 5.4 7.2 - - + -
57K SER 2.9 18.6 + - - +
58K VAL* 3.5 9.0 - - + +
60K THR* 1.3 73.0 - - - +
62K THR* 1.3 60.2 + - - +
64K MET* 3.2 29.8 + - + +
65K LEU* 2.8 27.7 + - - +
163O ILE* 4.7 9.4 - - + +
166O ILE* 4.5 32.8 - - + -
195O LEU* 3.9 27.6 - - + -
200O LEU* 3.9 25.1 - - + -
203O ALA* 5.2 3.6 - - + -
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Residues in contact with THR 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K ARG* 4.1 10.5 - - + +
37K LEU* 3.7 34.2 - - + +
38K GLN* 3.9 24.3 - - + +
41K VAL* 3.3 19.7 - - + +
58K VAL* 2.8 18.0 + - - +
59K GLU* 3.3 12.7 - - - -
61K LEU* 1.3 74.3 - - - +
63K GLU* 1.3 60.2 + - - +
65K LEU* 3.1 8.6 + - + +
66K GLN* 3.0 29.0 + - - +
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Residues in contact with GLU 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K ARG* 3.3 36.6 + - - +
59K GLU 2.9 19.7 + - - +
60K THR* 3.3 12.8 - - + +
62K THR* 1.3 77.6 - - - +
64K MET* 1.3 57.5 + - + +
66K GLN* 2.4 35.0 + - - +
67K SER* 2.9 31.1 + - - -
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Residues in contact with MET 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K THR* 2.9 26.4 + - + +
61K LEU* 3.4 34.5 - - + +
63K GLU* 1.3 76.1 - - + +
65K LEU* 1.3 57.4 + - - +
67K SER* 2.6 22.0 + - - +
68K TYR* 2.9 16.3 + - - +
162O PHE* 4.7 15.7 - - + -
166O ILE* 5.9 3.8 - - + -
200O LEU* 5.6 1.8 - - - -
203O ALA* 4.8 13.7 - - + +
204O LEU* 5.3 14.1 - - + -
206O GLU* 6.3 2.7 - - + -
207O TYR* 5.5 12.6 - - + +
208O GLY* 5.8 0.9 - - - +
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Residues in contact with LEU 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LEU* 5.3 14.8 - - + +
40K VAL* 5.4 11.2 - - + -
41K VAL* 4.7 13.9 - - + -
44K LEU* 5.9 0.9 - - + -
61K LEU 2.8 13.2 + - - +
62K THR* 3.1 10.1 + - - +
64K MET* 1.3 78.3 - - - +
66K GLN* 1.3 57.8 + - - +
68K TYR* 3.0 8.2 + - + +
69K ILE* 2.9 40.4 + - + +
130O ILE* 5.9 2.9 - - + -
159O ALA* 3.7 27.8 - - + +
162O PHE* 3.7 17.2 - - + -
163O ILE* 3.7 35.4 - - + -
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Residues in contact with GLN 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K HIS* 5.5 1.0 - - - -
34K ARG* 4.5 11.2 - - - +
37K LEU* 4.0 18.0 - - + +
62K THR 3.0 13.3 + - - +
63K GLU* 2.4 47.4 + - - +
65K LEU* 1.3 77.3 - - - +
67K SER* 1.3 58.3 + - - +
69K ILE* 3.3 13.2 + - - +
70K SER* 2.9 31.3 + - - -
138O TYR* 3.0 40.4 + - + -
141O ARG* 4.8 5.1 + - - +
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Residues in contact with SER 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K GLU 2.9 13.0 + - - -
64K MET* 2.6 28.5 + - - +
66K GLN* 1.3 78.9 - - - +
68K TYR* 1.3 55.3 + - - +
70K SER* 3.6 8.0 - - - +
71K GLU* 2.8 32.5 + - - +
74K ARG* 4.6 4.2 + - - +
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Residues in contact with TYR 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K MET 2.9 15.1 + - - +
65K LEU* 3.0 14.5 + - + +
67K SER* 1.3 75.4 + - - +
69K ILE* 1.3 58.8 + - - +
71K GLU* 3.2 17.8 + - - +
72K ILE* 2.9 54.3 + - + +
97K LEU* 4.0 18.0 - - + +
100K MET* 3.6 37.7 + - + +
101K GLY 5.4 0.5 + - - -
102K PHE* 5.2 5.9 - - - +
158O ALA* 5.0 4.6 - - + +
159O ALA* 4.9 8.7 - - + -
162O PHE* 4.2 52.8 - + + -
206O GLU* 6.5 1.3 - - + -
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Residues in contact with ILE 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LEU* 5.0 15.7 - - + -
65K LEU* 2.9 31.0 + - + +
66K GLN* 3.4 18.2 - - + +
68K TYR* 1.3 76.5 - - - +
70K SER* 1.3 57.2 + - - +
72K ILE* 3.2 15.4 + - + +
73K GLY* 2.9 23.4 + - - -
130O ILE* 6.4 1.6 - - + -
135O THR* 5.0 11.0 - - + +
138O TYR* 4.0 29.6 - - + -
139O LEU* 4.0 22.3 - - + +
155O ILE* 5.1 8.1 - - + -
159O ALA* 4.8 15.0 - - + -
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Residues in contact with SER 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K GLN 2.9 17.8 + - - -
67K SER* 3.8 7.4 - - - -
69K ILE* 1.3 76.1 - - - +
71K GLU* 1.3 57.4 + - - +
73K GLY* 3.2 0.5 + - - -
74K ARG* 2.8 45.8 + - - +
138O TYR* 4.4 18.0 + - - -
141O ARG* 4.8 13.7 + - - +
142O ALA* 3.9 16.0 + - - +
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Residues in contact with GLU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K SER* 2.8 21.8 + - - +
68K TYR* 3.4 19.7 - - - +
69K ILE 3.2 0.2 - - - -
70K SER* 1.3 74.6 - - - +
72K ILE* 1.3 58.5 + - - +
74K ARG* 3.4 25.9 + - - +
75K SER* 2.7 36.9 + - - +
100K MET* 3.7 18.2 - - + +
207O TYR* 4.3 23.2 + - - -
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Residues in contact with ILE 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K TYR* 2.9 43.9 + - + +
69K ILE* 3.3 11.2 - - + +
71K GLU* 1.3 75.7 - - - +
73K GLY* 1.3 58.3 + - - +
75K SER* 3.3 2.1 + - - -
76K ALA* 2.9 32.4 + - + +
93K ILE* 4.9 8.1 - - + -
96K THR* 4.4 9.5 - - + +
97K LEU* 4.4 12.8 - - + -
100K MET* 3.6 24.2 - - + +
139O LEU* 5.2 1.8 - - + -
155O ILE* 3.8 48.9 - - + +
158O ALA* 5.6 1.1 - - + -
159O ALA* 5.8 1.1 - - + +
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Residues in contact with GLY 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K ILE 2.9 11.6 + - - -
70K SER 3.2 0.2 + - - -
71K GLU 3.2 0.4 - - - -
72K ILE* 1.3 75.4 - - - +
74K ARG* 1.3 58.6 + - - +
76K ALA* 4.1 4.3 - - - +
77K LYS* 2.8 31.4 + - - +
139O LEU* 4.3 9.2 - - - -
142O ALA* 3.1 32.2 - - - +
143O GLY 5.2 0.3 - - - -
144O PHE* 5.1 4.5 - - - +
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Residues in contact with ARG 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543G SER* 4.6 18.8 - - - +
67K SER* 4.6 3.6 + - - +
70K SER* 2.8 35.1 + - - +
71K GLU* 3.5 40.0 + - - +
73K GLY* 1.3 70.4 - - - +
75K SER* 1.3 60.4 + - - +
77K LYS* 3.3 10.0 - - + +
78K SER* 3.0 32.2 + - - -
142O ALA* 4.5 0.9 - - + +
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Residues in contact with SER 75 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K GLU* 2.7 25.1 + - - +
72K ILE 3.6 3.6 - - - -
74K ARG* 1.3 76.7 - - - +
76K ALA* 1.3 52.2 + - - +
78K SER* 3.8 1.7 - - - -
79K TYR* 2.8 39.4 + - - +
96K THR* 3.7 20.0 - - - -
99K GLU* 6.3 2.0 - - - -
100K MET* 3.6 14.7 - - - +
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Residues in contact with ALA 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K ILE* 2.9 18.6 + - + +
73K GLY* 4.2 4.0 - - - +
75K SER* 1.3 73.6 - - - +
77K LYS* 1.3 60.8 + - - +
79K TYR* 4.0 5.4 - - - -
80K CYS* 2.9 36.1 + - - +
88K PRO* 4.5 10.7 - - + +
93K ILE* 3.7 29.6 - - + -
96K THR* 4.3 9.1 - - + +
144O PHE* 5.0 8.5 - - + -
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Residues in contact with LYS 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G GLY 3.2 27.8 - - - +
542G HIS* 3.7 2.0 - - - +
543G SER* 3.3 35.7 - - - +
564G ASP* 4.1 11.9 + - - +
566G THR* 4.5 12.5 - - - +
568G ARG* 4.0 11.7 - - - +
582G LYS* 6.3 0.6 - - - +
73K GLY 2.8 20.4 + - - +
74K ARG* 3.3 11.2 - - + +
76K ALA* 1.3 79.6 - - - +
78K SER* 1.3 66.2 + - - +
79K TYR 3.2 0.3 + - - -
80K CYS* 4.1 0.7 - - - +
81K GLU* 3.3 36.6 + - - +
88K PRO* 6.0 1.3 - - - -
142O ALA 4.2 7.6 - - - +
143O GLY 4.6 8.3 - - - +
144O PHE* 6.1 1.2 - - - +
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Residues in contact with SER 78 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582G LYS* 5.0 11.2 + - - -
74K ARG 3.0 11.9 + - - -
75K SER* 4.4 1.6 - - - -
77K LYS* 1.3 84.9 - - - +
79K TYR* 1.3 57.6 + - - +
80K CYS 3.6 0.2 - - - -
81K GLU* 4.0 19.8 + - - +
82K HIS* 3.1 23.8 + - - -
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Residues in contact with TYR 79 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919E GLU* 4.4 10.0 + - + +
922E GLN* 5.4 2.3 - - - +
923E GLN* 3.3 44.2 + - + +
75K SER 2.8 23.3 + - - +
76K ALA* 3.9 4.3 - - - +
77K LYS 3.1 0.4 - - - -
78K SER* 1.3 80.2 - - - +
80K CYS* 1.3 69.2 + - - +
81K GLU 3.3 2.2 - - - -
82K HIS* 3.0 27.7 - + - +
83K THR* 4.7 0.3 + - - +
92K ASP* 4.6 13.5 - - + -
95K VAL* 3.3 32.8 - - + +
96K THR* 4.5 13.0 - - - +
99K GLU* 6.0 7.9 - - + -
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Residues in contact with CYS 80 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K ALA* 2.9 19.1 + - - +
77K LYS 4.1 0.7 - - - +
79K TYR* 1.3 82.9 - - - +
81K GLU* 1.3 56.7 + - - +
82K HIS 3.1 5.2 - - - +
83K THR* 2.7 30.0 + - + +
85K ARG 3.0 8.1 - - - +
86K THR* 3.4 22.0 - - - +
87K GLN 4.9 0.9 - - - +
88K PRO* 3.6 27.1 - - + -
92K ASP* 3.6 32.3 - - - -
----------------------------------------------------------
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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