Contacts of the helix formed by residues 13 - 42 (chain L) in PDB entry 5JKL
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 HIS 13 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ARG* 3.8 0.4 - - - -
11L ASN 3.9 3.0 + - - -
12L TYR* 1.3 77.7 - - - +
14L GLN* 1.3 74.3 + - + +
15L ASP* 3.0 46.5 + - - +
16L SER* 3.0 28.8 + - - +
17L GLU* 3.1 12.3 + - - +
124L LYS* 3.7 40.3 + - + -
126L ASP* 4.8 1.0 + - - +
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Residues in contact with GLN 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L ARG* 3.7 14.1 - - - +
12L TYR 3.7 0.4 + - - -
13L HIS* 1.3 81.6 + - + +
15L ASP* 1.3 66.2 + - - +
17L GLU* 3.3 10.5 + - - +
18L GLU* 2.9 48.9 + - + +
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Residues in contact with ASP 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L HIS* 3.0 23.4 + - - +
14L GLN* 1.3 80.3 + - - +
16L SER* 1.3 57.8 + - - +
18L GLU* 3.5 14.2 + - - +
19L ALA* 2.9 29.3 + - - +
22L ARG* 4.8 2.1 + - - -
120L LEU* 3.5 24.1 - - + +
124L LYS* 3.5 19.9 + - - -
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Residues in contact with SER 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L TYR* 4.1 10.1 - - - -
13L HIS* 3.0 24.2 + - - +
15L ASP* 1.3 76.1 - - - +
17L GLU* 1.3 60.8 + - - +
19L ALA* 3.2 2.5 + - - +
20L ILE* 2.8 36.5 + - - +
117L LEU* 4.7 0.8 - - - +
120L LEU* 4.0 19.6 - - - +
121L ALA* 4.8 3.1 - - - -
124L LYS* 4.3 7.8 - - - +
126L ASP* 4.7 3.0 + - - +
129L LEU* 3.9 26.9 - - - +
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Residues in contact with GLU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L ARG* 2.8 33.5 + - - +
12L TYR* 3.7 22.8 - - + -
13L HIS 3.1 6.0 + - - +
14L GLN* 3.6 15.5 - - - +
16L SER* 1.3 78.5 - - - +
18L GLU* 1.4 64.1 + - + +
20L ILE 3.4 0.2 + - - -
21L ASN* 3.1 13.9 + - - +
73L GLN* 3.0 36.9 + - - +
78L GLY* 3.5 4.2 - - - -
79L ARG* 2.9 33.3 + - - +
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Residues in contact with GLU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L GLN* 2.9 48.4 + - + +
15L ASP* 3.6 13.9 - - - +
16L SER 3.2 0.2 - - - -
17L GLU* 1.4 77.2 - - + +
19L ALA* 1.3 65.7 + - - +
21L ASN* 3.2 12.7 + - - +
22L ARG* 3.2 41.4 + - - +
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Residues in contact with ALA 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L ASP 2.9 18.2 + - - +
16L SER 3.6 2.9 - - - +
18L GLU* 1.3 77.8 - - - +
20L ILE* 1.3 57.0 + - - +
22L ARG* 3.2 23.6 + - - +
23L GLN* 2.9 27.9 + - - +
117L LEU* 3.4 27.5 - - + +
120L LEU* 3.7 13.0 - - + -
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Residues in contact with ILE 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L TYR* 3.6 14.8 - - - +
16L SER 2.8 23.2 + - - +
17L GLU 3.7 4.5 - - - +
19L ALA* 1.3 69.9 - - - +
21L ASN* 1.3 66.3 + - - +
23L GLN* 3.1 4.9 + - - +
24L ILE* 2.9 26.8 + - + +
69L LEU* 3.8 40.8 - - + +
72L LEU* 4.3 6.7 - - + -
73L GLN* 3.7 20.6 - - + +
117L LEU* 3.6 29.2 - - + -
129L LEU* 3.9 24.7 - - + -
132L PHE* 5.2 0.4 - - + -
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Residues in contact with ASN 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L GLU* 3.1 15.4 + - - +
18L GLU* 3.2 11.9 + - - +
20L ILE* 1.3 78.0 - - - +
22L ARG* 1.3 60.6 + - + +
24L ILE* 3.5 15.7 + - - +
25L ASN* 3.2 19.9 + - - +
73L GLN* 3.1 18.8 + - - +
79L ARG 3.1 20.6 + - - -
80L ILE* 3.4 6.2 - - - +
81L PHE* 3.2 46.2 + - + +
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Residues in contact with ARG 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L ASP 4.8 2.6 + - - -
18L GLU* 3.2 29.4 + - - +
19L ALA* 3.5 32.5 - - - +
21L ASN* 1.3 76.6 - - + +
23L GLN* 1.3 62.3 - - - +
25L ASN* 3.3 9.2 + - - +
26L LEU* 3.1 21.5 + - - +
83L GLN* 6.3 2.0 - - - +
113L SER* 5.9 0.7 - - - -
120L LEU* 5.6 1.4 - - - +
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Residues in contact with GLN 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ALA 2.9 14.5 + - - +
20L ILE* 3.5 10.1 - - - +
22L ARG* 1.3 74.1 - - - +
24L ILE* 1.3 66.6 + - - +
26L LEU* 3.1 13.6 + - - +
27L GLU* 2.9 45.3 + - - +
69L LEU* 3.6 21.5 - - + -
110L VAL* 3.8 11.9 + - - +
113L SER* 2.6 35.9 + - - +
114L LEU* 3.6 29.0 - - + +
117L LEU* 4.3 12.7 - - + +
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Residues in contact with ILE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L ILE* 2.9 24.7 + - + +
21L ASN* 3.6 25.1 - - - +
22L ARG 3.3 0.2 - - - -
23L GLN* 1.3 75.0 - - - +
25L ASN* 1.3 63.7 + - - +
27L GLU* 3.2 5.4 + - - +
28L LEU* 3.1 40.0 + - + +
66L ALA* 4.1 4.6 - - + +
69L LEU* 3.6 29.4 - - + +
70L MET* 3.7 41.5 - - + +
73L GLN* 4.8 0.4 - - + -
80L ILE* 4.7 8.3 - - + -
82L LEU* 4.1 15.0 - - + -
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Residues in contact with ASN 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K TYR* 4.2 4.2 + - - -
21L ASN 3.2 10.1 + - - +
22L ARG* 3.3 10.7 + - - +
24L ILE* 1.3 79.7 - - - +
26L LEU* 1.3 59.1 + - - +
28L LEU* 3.3 7.8 + - - +
29L TYR* 2.9 30.7 + - - +
83L GLN* 3.3 32.4 + - + +
84L ASP 2.9 28.0 + - - +
85L ILE* 4.4 6.2 - - - +
86L GLN* 5.3 6.1 + - - +
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Residues in contact with LEU 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ARG 3.1 11.8 + - - +
23L GLN* 3.1 21.3 + - - +
25L ASN* 1.3 75.1 - - - +
27L GLU* 1.3 61.5 + - - +
29L TYR* 3.4 23.2 + - + +
30L ALA* 2.9 27.9 + - - +
106L LEU* 5.4 1.8 - - + -
109L ASN* 4.7 4.7 - - + +
110L VAL* 4.0 27.1 - - + +
113L SER* 3.5 35.7 - - - +
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Residues in contact with GLU 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLN* 2.9 41.2 + - - +
24L ILE 3.2 6.0 + - - +
26L LEU* 1.3 78.3 - - - +
28L LEU* 1.3 56.6 + - - +
30L ALA* 3.2 5.4 + - - +
31L SER* 2.9 28.6 + - - -
62L GLU* 2.7 17.4 - - - +
65L HIS* 3.3 12.8 - - + +
66L ALA* 3.9 18.2 - - + +
69L LEU* 3.7 17.9 - - + -
110L VAL* 3.6 10.6 - - - +
114L LEU* 4.4 0.9 - - - +
137L TYR* 4.2 14.3 - - - -
201L FE 2.0 33.4 - - - -
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Residues in contact with LEU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K TYR* 3.6 37.2 - - + +
35K LEU* 4.1 13.9 - - + -
24L ILE* 3.1 34.1 + - + +
25L ASN* 3.6 8.7 - - - +
27L GLU* 1.3 77.6 - - - +
29L TYR* 1.3 57.0 + - - +
31L SER* 3.3 8.9 + - - -
32L TYR* 3.0 25.8 + - - +
63L ARG* 4.0 26.7 - - - +
66L ALA* 3.6 20.2 - - + -
82L LEU* 4.7 0.7 - - + -
85L ILE* 3.9 22.3 - - + +
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Residues in contact with TYR 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L ASN* 2.9 18.7 + - - +
26L LEU* 3.5 23.8 - - + +
28L LEU* 1.3 73.0 - - - +
30L ALA* 1.3 67.5 + - - +
32L TYR* 3.0 3.7 + - + +
33L VAL* 2.9 50.4 + - + +
85L ILE* 3.8 10.8 - - + +
86L GLN* 3.2 42.0 - - + +
87L LYS 3.8 12.1 + - - -
88L PRO* 4.1 4.5 - - - +
89L ASP* 3.7 23.2 + - - -
106L LEU* 4.0 18.4 - - + -
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Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L LEU 2.9 14.8 + - - +
27L GLU* 3.6 8.3 - - - +
29L TYR* 1.3 75.6 - - - +
31L SER* 1.3 63.4 + - - +
33L VAL* 3.6 1.3 - - - +
34L TYR* 3.1 28.1 + - + -
62L GLU* 3.9 23.8 - - + +
106L LEU* 4.0 32.3 - - + -
107L GLU* 5.7 0.7 - - - +
110L VAL* 4.4 9.6 - - + -
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Residues in contact with SER 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K ARG* 2.8 28.8 + - - -
27L GLU 2.9 13.9 + - - -
28L LEU* 3.4 14.1 - - - -
29L TYR 3.2 0.2 - - - -
30L ALA* 1.3 78.3 - - - +
32L TYR* 1.4 55.6 + - - +
35L LEU* 3.0 15.4 + - - +
59L SER* 2.7 48.2 + - - +
62L GLU* 3.6 12.7 - - - +
63L ARG* 3.8 12.4 + - - +
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Residues in contact with TYR 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K ASN* 4.2 2.1 + - - -
28K LEU* 3.6 30.8 - - + +
63K ARG* 4.8 2.8 - - - +
82K LEU* 3.6 32.0 - - + +
83K GLN 2.6 31.7 + - - -
85K ILE* 3.7 27.4 - - + +
28L LEU 3.0 12.8 + - - +
29L TYR* 3.4 8.7 - - - +
31L SER* 1.4 73.4 - - - +
33L VAL* 1.3 58.6 + - - +
35L LEU* 3.3 15.3 + - + +
36L SER* 2.9 29.3 + - - -
85L ILE* 3.9 10.5 - - + -
86L GLN 3.4 19.1 - - - +
87L LYS* 3.9 12.3 - - - -
88L PRO* 3.9 7.6 - - + -
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Residues in contact with VAL 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L TYR* 2.9 53.8 + - + +
30L ALA 3.6 6.5 - - - +
32L TYR* 1.3 76.0 - - - +
34L TYR* 1.3 60.9 + - - +
36L SER* 3.3 4.2 + - - -
37L MET* 2.9 51.0 + - + +
88L PRO* 3.7 15.5 - - + -
93L TRP* 4.2 12.1 - - + -
106L LEU* 3.8 24.2 - - + -
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Residues in contact with TYR 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ALA 3.1 18.6 + - - +
33L VAL* 1.3 77.8 - - - +
35L LEU* 1.3 61.1 + - - +
37L MET* 4.2 7.2 - - - -
38L SER* 2.8 30.5 + - - -
55L PHE* 3.5 46.0 - + - +
58L GLN* 3.7 29.1 + - + +
59L SER* 3.6 11.9 - - - +
62L GLU* 3.8 20.6 - - + -
103L ALA* 3.9 17.0 + - + +
106L LEU* 4.1 16.4 - - + -
107L GLU* 2.5 41.4 + - - +
148L LEU* 3.9 11.9 - - + +
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Residues in contact with LEU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K LEU* 4.2 13.2 - - + -
63K ARG* 4.0 28.0 - - - +
67K GLU* 4.1 6.1 - - + -
70K MET* 3.9 23.2 - - + +
82K LEU* 5.5 0.2 - - + -
31L SER 3.0 14.9 + - - +
32L TYR* 3.5 28.9 - - + +
33L VAL 3.3 0.2 - - - -
34L TYR* 1.3 76.8 - - - +
36L SER* 1.3 61.8 + - - +
38L SER* 3.3 6.1 + - - -
39L TYR* 3.3 48.9 + - + +
56L LEU* 3.8 16.2 - - + -
59L SER* 3.6 8.9 - - - +
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Residues in contact with SER 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K MET* 5.0 3.1 - - - -
82K LEU* 3.6 28.1 - - - +
32L TYR 2.9 11.1 + - - -
33L VAL 3.3 8.9 + - - -
35L LEU* 1.3 75.8 - - - +
37L MET* 1.3 61.4 + - - +
39L TYR* 3.4 3.3 + - - +
40L TYR* 3.2 21.8 + - - +
88L PRO* 3.8 10.9 - - - +
90L GLU 3.8 9.2 + - - -
91L ASP* 4.7 5.7 + - - +
93L TRP* 3.0 18.6 + - - -
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Residues in contact with MET 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L VAL* 2.9 32.9 + - + +
34L TYR* 3.7 13.9 - - + +
35L LEU 3.3 0.2 - - - -
36L SER* 1.3 75.4 - - - +
38L SER* 1.3 65.0 + - - +
40L TYR* 3.3 8.5 + - - +
41L PHE* 3.0 24.8 + - + -
55L PHE* 3.9 33.9 - - + -
93L TRP* 3.7 39.5 - - + -
99L ALA* 3.5 28.3 - - + +
102L GLU* 3.8 15.3 - - + -
103L ALA* 3.7 16.6 - - - +
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Residues in contact with SER 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR 2.8 17.9 + - - -
35L LEU* 3.5 7.4 - - - -
36L SER 3.3 0.2 - - - -
37L MET* 1.3 75.4 - - - +
39L TYR* 1.3 72.5 + - - +
41L PHE 3.2 11.1 + - - -
42L ASP* 3.4 1.4 + - - +
52L ALA* 2.7 47.3 + - - +
55L PHE* 3.7 7.1 - - - +
56L LEU* 3.4 26.2 - - - +
----------------------------------------------------------
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Residues in contact with TYR 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K GLU* 3.4 28.8 + - + +
70K MET* 3.5 38.6 - - + -
71K LYS* 3.7 26.7 - - + +
74K ASN* 2.8 24.8 + - - +
80K ILE* 3.6 20.5 - - + +
35L LEU* 3.3 31.3 + - + +
36L SER 3.4 2.2 + - - +
38L SER* 1.3 84.7 - - - +
40L TYR* 1.3 64.0 + - - +
42L ASP* 3.3 26.9 + - + -
43L ARG* 3.4 3.5 + - - +
56L LEU* 4.2 16.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L SER 3.2 13.2 + - - +
37L MET 3.4 8.3 - - - +
39L TYR* 1.3 76.1 - - - +
41L PHE* 1.3 86.3 + + - +
43L ARG* 3.1 52.6 + - - +
46L VAL* 3.5 31.3 - - + +
91L ASP 4.4 4.9 - - - +
92L ASP* 3.5 25.9 + - - -
93L TRP* 3.6 32.5 - - + -
94L GLU* 3.2 39.7 + - - -
95L SER* 4.2 3.7 - - - -
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Residues in contact with PHE 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L MET* 3.0 25.3 + - + -
38L SER 3.2 5.3 + - - +
40L TYR* 1.3 94.2 - + - +
42L ASP* 1.3 55.2 + - - +
43L ARG 3.3 0.2 - - - -
46L VAL* 3.5 18.6 - - + -
47L ALA* 3.3 8.7 + - - -
48L LEU* 3.0 54.1 + - + +
49L LYS* 5.0 0.3 - - - -
51L PHE* 3.5 17.3 - + + -
52L ALA* 3.7 11.4 - - - +
55L PHE* 3.5 31.4 - + - -
93L TRP* 5.0 0.2 - - + -
95L SER 3.6 22.0 - - - -
96L GLY* 3.6 24.9 - - - -
99L ALA* 3.6 14.6 - - + -
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Residues in contact with ASP 42 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K LYS* 4.1 16.6 + - - +
74K ASN* 2.9 38.5 + - - +
38L SER 3.4 5.7 + - - +
39L TYR* 3.3 30.8 + - + +
40L TYR 3.2 0.6 - - - -
41L PHE* 1.3 73.5 - - - +
43L ARG* 1.4 66.6 + - - +
44L ASP* 3.6 1.7 + - - -
47L ALA* 5.2 1.1 - - - +
49L LYS* 6.1 1.1 - - - +
52L ALA* 4.1 9.8 - - + +
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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