Contacts of the helix formed by residues 49 - 76 (chain L) in PDB entry 5OXV
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 LEU 49 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K PRO* 3.2 32.1 - - + +
47L SER* 3.2 6.0 + - - +
48L GLY* 1.3 77.8 - - - +
50L ILE* 1.3 62.3 + - - +
51L TYR 3.5 0.2 - - - -
52L GLU* 4.0 6.8 + - + +
53L GLU* 3.7 12.1 + - - +
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Residues in contact with ILE 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K PHE* 4.5 8.5 - - + -
119K ILE* 3.3 39.0 - - + +
120K MET* 3.2 38.1 - - - +
121K PRO* 3.4 2.9 - - + -
124K ILE* 3.8 21.1 - - + -
34L ILE* 5.1 1.6 - - + +
46L ILE* 3.9 16.2 - - + -
47L SER 2.9 16.3 + - - +
49L LEU* 1.3 77.1 - - - +
51L TYR* 1.3 70.8 + - + +
53L GLU* 3.0 5.3 + - - +
54L THR* 2.9 37.5 + - - +
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Residues in contact with TYR 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-227J G 4.4 1.9 + - - -
31L LYS* 3.5 49.5 - - + -
34L ILE* 3.9 31.3 - - + +
35L ARG* 2.8 28.1 + - + -
46L ILE* 3.3 36.3 + - + +
47L SER 4.1 3.6 - - - -
48L GLY* 3.3 32.7 + - - +
49L LEU 3.5 0.8 - - - -
50L ILE* 1.3 74.3 - - + +
52L GLU* 1.3 60.3 + - - +
54L THR* 3.5 6.4 + - - -
55L ARG* 3.0 42.7 + - - +
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Residues in contact with GLU 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ILE* 6.1 0.3 - - - +
27L GLN* 2.6 32.2 + - - +
48L GLY 5.0 1.2 + - - -
49L LEU* 4.0 8.5 + - + +
50L ILE 3.2 0.8 - - - -
51L TYR* 1.3 75.1 - - - +
53L GLU* 1.3 67.8 + - - +
55L ARG* 3.0 23.4 + - - +
56L GLY* 2.9 19.2 + - - -
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Residues in contact with GLU 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K PRO* 3.6 22.1 - - + +
124K ILE* 4.6 21.7 - - + +
125K GLN* 2.6 39.9 + - - +
49L LEU 3.7 10.9 + - - +
50L ILE* 3.0 9.2 + - - +
52L GLU* 1.3 78.4 - - - +
54L THR* 1.3 63.5 + - - +
56L GLY* 3.1 3.5 + - - -
57L VAL* 2.9 26.9 + - + +
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Residues in contact with THR 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K LEU* 3.7 25.8 - - + -
103K LEU* 5.8 1.1 - - + -
104K PHE* 3.7 22.0 - - + -
124K ILE* 4.1 7.0 - - + +
29L ILE* 6.0 2.5 - - + -
34L ILE* 3.5 34.4 - - + +
37L LEU* 5.8 0.4 - - + -
50L ILE* 2.9 25.9 + - - +
51L TYR 3.8 1.3 - - - -
52L GLU 3.1 0.2 - - - -
53L GLU* 1.3 76.0 - - - +
55L ARG* 1.3 53.0 + - - +
57L VAL* 3.1 7.9 + - + +
58L LEU* 2.7 35.2 + - + +
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Residues in contact with ARG 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ILE* 3.3 49.4 + - + +
27L GLN* 3.9 25.6 + - - +
29L ILE* 3.2 27.1 + - + -
30L THR* 4.6 1.2 - - - +
31L LYS* 4.5 10.9 - - - +
34L ILE* 3.8 15.8 - - + +
51L TYR* 3.0 38.3 + - - +
52L GLU* 3.0 38.0 + - - +
54L THR* 1.3 73.6 - - - +
56L GLY* 1.3 66.8 + - - +
58L LEU* 4.3 4.5 - - - -
59L LYS* 3.0 26.0 + - - +
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Residues in contact with GLY 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLU 2.9 13.9 + - - -
53L GLU* 3.1 5.8 + - - -
55L ARG* 1.3 80.1 - - - +
57L VAL* 1.3 56.1 + - - +
59L LYS* 3.3 7.0 - - - +
60L VAL* 3.1 29.7 + - - +
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Residues in contact with VAL 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K TYR* 3.6 32.5 + - + +
100K LEU* 4.0 13.2 - - + -
103K LEU* 4.0 8.7 - - + -
124K ILE* 4.4 13.2 - - + -
128K ARG* 3.6 35.4 - - - +
53L GLU* 2.9 18.2 + - + +
54L THR* 3.3 7.9 - - - +
56L GLY* 1.3 72.2 - - - +
58L LEU* 1.3 61.5 + - - +
59L LYS 3.1 1.6 - - - -
60L VAL* 3.2 9.4 + - - +
61L PHE* 2.8 28.2 + - - +
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Residues in contact with LEU 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ILE* 4.7 4.3 - - + -
67K PHE* 5.1 2.5 - - + -
70K LEU* 4.4 3.6 - - + -
96K SER* 4.1 19.1 - - - +
99K TYR* 6.0 0.2 - - + -
100K LEU* 3.9 31.9 - - + -
26L ILE* 4.6 1.6 - - + -
29L ILE* 3.5 47.8 - - + -
54L THR* 2.7 20.4 + - + +
55L ARG* 3.8 4.9 - - - +
57L VAL* 1.3 74.9 - - - +
59L LYS* 1.3 53.2 + - - +
61L PHE* 3.2 11.4 + - + +
62L LEU* 2.7 58.2 + - + +
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Residues in contact with LYS 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K LEU* 5.7 2.5 - - + -
73K GLU* 5.1 9.9 - - - -
74K ILE* 5.0 17.0 - - + -
26L ILE* 4.7 23.1 - - + +
55L ARG 3.0 13.5 + - - +
56L GLY* 3.3 11.9 - - - +
58L LEU* 1.3 73.3 - - - +
60L VAL* 1.4 57.2 + - + +
61L PHE 3.0 0.9 - - - -
62L LEU* 3.1 6.5 + - - +
63L GLU* 2.7 71.4 + - + +
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Residues in contact with VAL 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128K ARG* 4.5 15.5 - - - +
134K ARG 3.9 20.9 - - - +
56L GLY 3.1 15.1 + - - +
57L VAL* 3.2 8.0 + - - +
59L LYS* 1.4 76.4 - - + +
61L PHE* 1.3 63.9 + - - +
63L GLU* 3.6 13.7 + - - +
64L ASN* 3.1 37.9 + - - +
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Residues in contact with PHE 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K LEU* 4.6 2.7 - - + -
95K ALA* 3.7 18.4 - - + -
96K SER* 3.4 38.4 - - - -
99K TYR* 4.0 33.4 - + + -
57L VAL 2.8 14.7 + - - +
58L LEU* 3.3 13.5 - - + +
59L LYS 3.0 0.2 - - - -
60L VAL* 1.3 76.7 - - - +
62L LEU* 1.3 64.8 + - + +
64L ASN* 2.9 22.2 + - + +
65L VAL* 3.1 39.3 + - + +
90L LEU* 4.2 9.0 - - + -
93L GLN* 6.4 0.9 - - + -
95L ARG* 3.9 28.3 - - - -
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Residues in contact with LEU 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K PHE* 4.0 9.4 - - + -
70K LEU* 3.8 24.2 - - + -
71K VAL* 3.8 24.5 - - + -
74K ILE* 4.3 11.4 - - + -
92K LEU* 4.1 12.3 - - + -
96K SER* 3.7 21.1 - - - +
58L LEU* 2.7 49.1 + - + +
59L LYS* 4.0 3.1 - - - +
61L PHE* 1.3 71.9 - - + +
63L GLU* 1.3 65.2 + - - +
65L VAL* 4.5 2.2 - - - +
66L ILE* 2.9 46.0 + - + +
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Residues in contact with GLU 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K ILE* 3.7 25.7 - - + +
78K PHE* 3.7 12.3 - - + -
59L LYS* 2.7 60.4 + - + +
60L VAL* 3.9 14.5 - - - +
62L LEU* 1.3 74.0 - - - +
64L ASN* 1.3 63.0 + - - +
67L ARG* 3.0 42.0 + - - +
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Residues in contact with ASN 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134K ARG 5.2 2.4 + - - -
60L VAL* 3.1 34.0 + - - +
61L PHE* 2.9 10.3 + - + +
63L GLU* 1.3 79.8 - - - +
65L VAL* 1.3 65.9 + - + +
67L ARG* 2.8 24.4 + - - +
68L ASP* 3.4 15.8 + - - +
93L GLN* 3.6 29.2 + - - +
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Residues in contact with VAL 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K LEU* 3.5 26.0 - - + -
61L PHE* 3.1 46.5 + - + +
62L LEU* 3.5 1.5 + - - +
64L ASN* 1.3 77.4 - - + +
66L ILE* 1.3 53.1 + - - +
68L ASP* 3.3 5.1 + - - +
69L ALA* 2.7 32.9 + - + +
86L VAL* 4.3 4.0 - - + +
89L ALA* 3.6 14.7 - - + +
90L LEU* 3.7 30.5 - - + +
93L GLN* 4.9 11.2 - - + +
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Residues in contact with ILE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K VAL* 3.7 30.5 - - + +
74K ILE* 4.3 17.3 - - + -
75K ALA* 4.1 17.0 - - + -
78K PHE* 4.8 3.1 - - + -
84K PHE* 4.8 11.2 - - + -
92K LEU* 3.8 18.8 - - + -
62L LEU* 2.9 38.1 + - + +
63L GLU 4.8 0.2 - - - +
65L VAL* 1.3 74.9 - - - +
67L ARG* 1.3 67.0 + - - +
68L ASP 3.1 0.9 - - - -
69L ALA* 3.9 10.1 - - + -
70L VAL* 2.8 47.2 + - + +
81L VAL* 5.8 0.9 - - + -
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Residues in contact with ARG 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K PHE* 3.4 45.7 - - + -
63L GLU* 3.0 35.6 + - - +
64L ASN* 2.8 32.1 + - - +
66L ILE* 1.3 78.3 - - - +
68L ASP* 1.3 67.1 + - - +
70L VAL* 3.7 3.4 - - - +
71L THR* 2.8 31.8 + - - +
96N ARG 5.5 6.5 - - - +
101N GLY* 6.4 0.6 - - - +
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Residues in contact with ASP 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L ASN 3.4 5.2 + - - +
65L VAL 3.3 8.3 + - - +
66L ILE 3.1 0.2 - - - -
67L ARG* 1.3 84.7 - - - +
69L ALA* 1.3 70.1 + - - +
70L VAL 3.1 1.5 + - - -
71L THR* 3.2 3.2 + - - -
72L TYR* 3.1 24.7 + - + -
89L ALA* 3.8 15.0 - - + -
92L ARG* 2.9 28.9 + - - +
93L GLN* 2.6 29.5 + - - +
96N ARG 5.3 1.0 - - - +
97N LEU* 3.7 26.5 - - + +
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Residues in contact with ALA 69 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K LEU* 5.8 0.7 - - + -
65L VAL* 2.7 22.8 + - + +
66L ILE* 3.3 16.4 + - + +
68L ASP* 1.3 74.4 - - - +
70L VAL* 1.3 60.9 + - - +
72L TYR* 3.1 7.5 + - - +
73L THR* 2.9 22.0 + - - -
81L VAL* 4.5 7.4 - - + -
85L ASP* 3.6 24.1 - - - +
86L VAL* 4.2 22.2 - - + +
89L ALA* 3.7 1.5 - - + +
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Residues in contact with VAL 70 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K ALA* 4.8 3.6 - - + -
78K PHE* 5.0 13.7 - - + +
79K LYS* 4.5 9.4 - - + -
82K LEU* 3.7 31.6 - - + -
66L ILE* 2.8 36.9 + - + +
67L ARG* 3.7 4.5 - - - +
69L ALA* 1.3 75.3 - - + +
71L THR* 1.3 54.2 + - - +
73L THR* 2.6 30.9 + - - +
74L GLU* 2.7 38.6 + - + +
81L VAL* 4.7 4.7 - - + -
----------------------------------------------------------
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Residues in contact with THR 71 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L ARG* 2.8 21.7 + - - +
68L ASP* 3.6 8.3 + - - -
70L VAL* 1.3 75.6 - - - +
72L TYR* 1.3 61.2 + - - +
74L GLU* 3.8 11.6 + - - +
75L HIS* 3.0 22.7 + - - +
93N THR* 3.5 25.0 + - - +
96N ARG* 3.9 31.1 + - + +
97N LEU* 3.7 23.0 - - + +
----------------------------------------------------------
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Residues in contact with TYR 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L ASP 3.1 25.1 + - - -
69L ALA 3.3 6.1 - - - +
71L THR* 1.3 75.5 - - - +
73L THR* 1.3 57.5 + - - +
75L HIS* 3.0 4.9 + - - +
76L ALA* 2.8 30.7 + - - +
85L ASP* 3.5 34.1 - - + +
88L TYR* 3.9 25.5 + + + -
89L ALA* 4.2 4.9 - - - -
92L ARG* 3.6 16.2 - - - +
73N GLU* 3.1 22.3 + - - -
76N ARG* 5.1 1.0 + - - -
77N LEU* 3.4 31.9 - - + -
80N TYR* 3.8 32.0 - + + -
81N ASN* 5.6 2.2 + - - -
97N LEU* 3.8 22.7 - - + -
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Residues in contact with THR 73 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82K LEU* 5.0 6.3 - - + -
69L ALA 2.9 17.0 + - - -
70L VAL* 2.6 21.2 + - - -
72L TYR* 1.3 72.2 - - - +
74L GLU* 1.3 57.9 + - - -
76L ALA 3.5 1.6 + - - -
77L LYS 3.3 3.8 + - - -
78L ARG* 3.0 43.4 + - + +
80L THR 3.1 36.3 - - - +
81L VAL* 3.6 17.4 - - + +
85L ASP* 3.6 17.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 74 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K PHE 5.1 1.7 - - - +
79K LYS* 3.2 39.2 - - + +
82K LEU* 6.2 0.9 - - + -
70L VAL* 2.7 30.2 + - + +
71L THR* 3.8 10.7 + - - +
73L THR* 1.3 70.5 - - - +
75L HIS* 1.3 61.0 + - - +
77L LYS* 3.0 18.0 + - - +
78L ARG 4.9 3.4 - - - +
89N ARG* 3.4 11.5 + - - -
96N ARG* 3.4 31.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 75 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L THR 3.0 17.6 + - - +
72L TYR 3.0 5.6 + - - +
74L GLU* 1.3 72.7 - - - +
76L ALA* 1.3 58.0 + - - +
77L LYS* 2.8 11.7 + - - +
77N LEU* 3.8 18.8 - - + +
81N ASN* 3.7 23.3 + - + +
83N ARG* 6.4 0.9 - - - -
89N ARG* 3.3 36.4 + - + +
90N GLU* 2.9 43.3 + - + +
93N THR* 2.4 47.6 - - + +
96N ARG* 6.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L TYR 2.8 16.3 + - - +
73L THR 3.9 1.6 - - - +
74L GLU 3.4 0.2 - - - -
75L HIS* 1.3 70.8 + - - +
77L LYS* 1.3 67.2 + - - +
78L ARG* 3.2 47.9 - - - +
81N ASN* 3.4 24.8 + - - +
----------------------------------------------------------
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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