Contacts of the helix formed by residues 9 - 33 (chain L) in PDB entry 1QGH
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 THR 9 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ASP* 1.3 75.0 - - - +
10L LYS* 1.3 57.4 + - - +
12L PHE* 2.9 8.2 + - + +
13L LEU* 2.7 55.0 + - + +
67L ILE* 3.8 8.3 - - + -
119L LEU* 4.6 2.7 - - - -
120L THR* 4.1 14.7 + - - +
123L GLU* 1.9 37.8 + - - +
125L ASP* 3.7 24.6 - - - +
128L THR* 4.0 10.5 - - + -
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Residues in contact with LYS 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ASP* 3.3 14.4 + - - +
9L THR* 1.3 77.7 - - - +
11L GLU* 1.3 71.7 + - - +
13L LEU* 3.2 2.3 + - - +
14L ASN* 2.9 24.7 + - - +
64L LEU* 3.7 17.6 - - + +
67L ILE* 3.4 39.4 + - + -
68L GLY* 3.8 15.5 + - - -
69L GLY* 4.0 15.2 - - - -
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Residues in contact with GLU 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 3.2 33.1 - - + +
8L ASP* 2.8 35.6 + - - +
10L LYS* 1.3 79.3 - - - +
12L PHE* 1.3 67.8 + - - +
14L ASN* 4.0 5.4 - - - +
15L HIS* 3.0 24.1 + - - +
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Residues in contact with PHE 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 5.3 7.9 - - + -
8L ASP 2.6 21.9 + - - +
9L THR* 3.4 4.7 - - + +
11L GLU* 1.3 73.6 - - - +
13L LEU* 1.3 82.6 + - + +
15L HIS* 3.1 8.3 + - - +
16L GLN* 3.1 54.1 + - + +
112L GLU* 3.1 30.1 - - + -
113L TYR* 3.9 10.8 - + - -
115L GLN* 4.7 4.3 - - + -
116L GLY* 3.5 27.8 - - - -
119L LEU* 4.0 14.6 - - + -
132L LEU* 4.0 21.3 - - + -
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Residues in contact with LEU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L THR* 2.7 34.7 + - + +
10L LYS 3.6 4.0 - - - +
12L PHE* 1.3 98.2 - - + +
14L ASN* 1.3 58.7 + - - +
16L GLN* 2.8 21.8 + - + +
17L VAL* 2.9 10.9 + - - +
60L VAL* 3.5 27.5 - - + +
63L ARG* 4.2 7.9 - - + -
64L LEU* 4.2 19.5 - - + -
67L ILE* 3.9 16.2 - - + -
128L THR* 3.7 26.5 - - + -
131L MET* 4.3 11.9 - - + -
132L LEU* 4.3 3.4 - - + -
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Residues in contact with ASN 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L LYS 2.9 15.9 + - - +
11L GLU* 4.0 6.7 - - - +
13L LEU* 1.3 77.0 - - - +
15L HIS* 1.3 64.6 + - - +
17L VAL* 3.0 15.2 + - - +
18L ALA 3.1 9.0 + - - -
64L LEU* 3.7 13.6 - - + +
70L SER 3.1 21.0 + - - -
71L PRO* 3.1 7.6 - - - +
72L PHE* 2.7 70.8 + - + +
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Residues in contact with HIS 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L GLU 3.0 17.9 + - - +
12L PHE* 3.4 9.3 - - + +
14L ASN* 1.3 79.0 - - - +
16L GLN* 1.3 66.6 + - - +
18L ALA* 3.3 5.9 + - - +
19L ASN* 3.0 29.7 + - - -
72L PHE* 4.3 6.5 - - - -
81L ASN* 2.9 32.9 + - + -
83L SER* 2.8 40.2 + - - -
112L GLU* 3.0 19.9 + - - -
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Residues in contact with GLN 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 3.1 49.2 + - + +
13L LEU* 2.8 9.3 + - + +
15L HIS* 1.3 84.3 + - - +
17L VAL* 1.3 59.6 + - - +
18L ALA 3.1 1.3 - - - -
19L ASN* 3.0 22.7 + - - +
20L LEU* 2.8 48.0 + - + +
60L VAL* 4.4 9.4 - - + -
109L LEU* 3.7 4.5 - - - +
112L GLU* 3.0 26.3 + - - +
113L TYR* 3.5 26.0 + - + +
132L LEU* 6.0 0.7 - - + -
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Residues in contact with VAL 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J TRP* 4.4 6.1 - - + -
13L LEU 2.9 17.0 + - - +
14L ASN* 3.0 21.0 + - - +
16L GLN* 1.3 74.9 - - - +
18L ALA* 1.3 62.8 + - - +
20L LEU* 3.9 4.1 - - - +
21L ASN* 2.8 43.5 + - - +
57L MET* 4.3 12.3 - - - +
60L VAL* 3.9 17.0 - - + +
61L ALA* 4.0 22.2 - - + +
64L LEU* 5.0 1.6 - - + -
71L PRO* 4.5 2.9 - - + -
72L PHE* 3.9 12.3 - - + +
78L PHE* 3.8 15.3 - - + -
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Residues in contact with ALA 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L ASN 3.1 10.0 + - - +
15L HIS 3.4 9.0 - - - +
16L GLN 3.1 0.4 - - - -
17L VAL* 1.3 78.3 - - - +
19L ASN* 1.3 63.9 + - - +
21L ASN* 3.1 12.0 + - - +
22L VAL* 3.1 16.5 + - - +
72L PHE* 4.3 4.0 - - + -
78L PHE* 3.7 39.5 - - - +
81L ASN* 4.0 12.8 - - + -
82L ALA* 3.7 14.1 - - - +
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Residues in contact with ASN 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L HIS* 3.0 15.8 + - - -
16L GLN* 3.0 25.7 + - - +
18L ALA* 1.3 76.5 - - - +
20L LEU* 1.3 58.9 + - - +
22L VAL* 3.0 3.6 + - - +
23L PHE* 2.7 31.5 + - - +
82L ALA* 3.5 4.3 - - - -
83L SER* 2.7 36.1 + - - -
84L VAL* 3.0 22.8 + - + +
108L LEU* 4.2 0.4 - - - +
109L LEU* 4.1 10.2 - - + +
112L GLU* 2.9 29.5 + - - -
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Residues in contact with LEU 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L GLN* 2.8 31.2 + - + +
19L ASN* 1.3 73.3 - - - +
21L ASN* 1.3 63.6 + - - +
23L PHE* 3.2 5.4 + - + +
24L THR* 2.9 27.6 + - - -
53L PHE* 4.2 29.7 - - + +
56L GLN* 4.3 3.4 - - + +
57L MET* 3.5 45.3 - - + +
60L VAL* 4.1 13.9 - - + -
109L LEU* 4.3 20.4 - - + -
113L TYR* 3.5 27.1 - - - +
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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
----------------------------------------------------------
25J VAL* 4.6 8.7 - - - +
28J HIS* 5.5 0.9 - - - -
50J TYR* 5.5 1.0 + - - -
75J LEU* 4.0 3.8 - - + +
17L VAL* 2.8 30.0 + - - +
18L ALA 3.1 2.9 + - - +
20L LEU* 1.3 78.5 - - - +
22L VAL* 1.3 63.0 + - - +
24L THR* 3.3 23.8 - - - +
25L VAL* 3.5 13.3 - - - +
57L MET* 3.4 37.2 - - - +
78L PHE* 3.2 50.2 - - + -
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Residues in contact with VAL 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75J LEU* 4.1 23.5 - - + +
18L ALA 3.1 13.2 + - - +
19L ASN 3.0 6.8 + - - +
21L ASN* 1.3 78.0 - - - +
23L PHE* 1.3 64.9 + - - +
25L VAL* 3.4 4.7 + - - +
26L LYS* 3.0 20.1 + - - +
78L PHE 4.7 3.8 - - - +
79L LEU* 5.0 6.5 - - + -
82L ALA* 3.5 21.1 - - + -
84L VAL* 3.7 31.9 - - + +
85L GLU 4.5 0.4 - - - +
86L GLU* 3.9 31.4 - - + +
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Residues in contact with PHE 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L ASN 2.7 20.8 + - - +
20L LEU* 3.7 7.6 - - + +
22L VAL* 1.3 73.4 - - - +
24L THR* 1.3 57.3 + - - +
26L LYS* 2.9 14.9 + - + +
27L ILE* 2.8 50.0 + - + +
49L LEU* 5.2 0.9 - - + -
53L PHE* 3.7 45.1 - + + -
84L VAL* 4.3 4.9 - - + +
102L LEU* 3.4 35.7 - - + -
105L THR* 3.4 31.6 - - + -
106L LEU* 3.8 14.6 - - + -
109L LEU* 3.6 20.0 - - + -
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Residues in contact with THR 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J TYR* 5.8 3.1 - - - +
20L LEU 2.9 14.5 + - - +
21L ASN* 3.3 23.1 - - - +
22L VAL 3.2 0.2 - - - -
23L PHE* 1.3 77.6 - - - +
25L VAL* 1.3 70.2 + - + +
27L ILE* 3.2 10.9 + - - +
28L HIS 3.2 16.3 + - - -
50L TYR* 3.4 53.1 + - + +
53L PHE* 4.8 3.4 - - - -
54L GLY* 4.3 12.6 + - - -
57L MET* 6.0 5.2 - - + -
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Residues in contact with VAL 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN* 4.5 7.6 - - - +
73J SER* 3.6 22.8 - - - +
74J THR* 3.8 7.4 - - - +
75J LEU* 3.5 21.8 - - + -
78J PHE* 3.5 34.3 - - + -
21L ASN 3.5 14.1 - - - +
22L VAL 3.4 3.7 + - - +
24L THR* 1.3 82.1 - - + +
26L LYS* 1.3 55.8 + - - +
28L HIS* 3.1 12.3 + - + +
29L GLN* 2.9 26.0 + - - +
32L TRP* 5.9 0.2 - - + -
50L TYR* 6.1 0.4 - - + +
86L GLU* 4.9 0.7 - - - +
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Residues in contact with LYS 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J SER 5.3 1.3 - - - -
22L VAL* 3.0 12.2 + - + +
23L PHE* 2.9 20.5 + - + +
25L VAL* 1.3 76.6 - - - +
27L ILE* 1.3 64.0 + - - +
29L GLN* 3.1 26.4 + - - +
30L ILE* 3.1 25.2 + - + +
84L VAL* 4.3 9.6 - - - -
85L GLU 2.8 29.6 + - - -
86L GLU* 4.1 13.1 - - + +
87L ALA 4.9 1.8 - - - +
101L ASP* 3.2 38.2 + - - +
102L LEU* 5.2 0.2 - - - -
105L THR* 3.4 25.5 + - - +
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Residues in contact with ILE 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L PHE* 2.8 56.0 + - + +
24L THR* 3.2 14.6 + - - +
26L LYS* 1.3 76.1 - - - +
28L HIS* 1.3 63.1 + - - +
30L ILE* 3.4 9.6 + - - +
31L HIS* 3.0 24.4 + - + +
46L MET* 3.3 38.8 - - + +
49L LEU* 3.9 32.1 - - + +
50L TYR* 3.9 11.9 - - + +
53L PHE* 4.4 3.8 - - + -
102L LEU* 4.9 5.2 - - + -
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Residues in contact with HIS 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN* 5.3 2.0 - - - -
54J GLY 5.3 1.4 + - - -
57J MET* 3.5 30.0 - - + +
58J ASP* 3.6 29.7 + - + +
24L THR 3.2 6.3 + - - +
25L VAL* 3.1 14.6 + - + +
27L ILE* 1.3 77.1 - - - +
29L GLN* 1.3 59.0 + - - +
31L HIS* 3.3 12.8 - + - +
32L TRP* 2.8 55.3 + + + -
47L ASP* 4.8 5.1 + - - -
50L TYR* 3.0 52.9 + + - +
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Residues in contact with GLN 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J SER* 3.0 45.5 + - - +
74J THR* 4.1 0.7 - - - +
25L VAL 2.9 13.4 + - - +
26L LYS* 3.1 21.6 + - - +
28L HIS* 1.3 76.9 - - - +
30L ILE* 1.3 62.6 + - - +
32L TRP* 4.2 3.5 - - - -
33L TYR* 2.8 44.1 + - + +
87L ALA 3.0 28.5 + - - +
89L TYR* 3.9 17.7 + - + -
93L LYS* 4.4 16.8 - - - +
98L LEU* 5.4 1.1 - - + +
101L ASP* 4.6 8.5 + - - -
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Residues in contact with ILE 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LYS* 3.1 26.5 + - + +
27L ILE* 3.7 9.4 - - - +
29L GLN* 1.3 84.4 - - + +
31L HIS* 1.3 59.7 + - - +
33L TYR* 5.1 0.2 - - - -
34L MET* 2.9 50.7 + - + +
46L MET* 3.9 8.7 - - - -
98L LEU* 3.8 47.1 - - + +
99L MET* 3.7 17.9 - - + -
101L ASP* 5.1 3.1 - - + +
102L LEU* 4.1 27.1 - - + +
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Residues in contact with HIS 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP* 4.8 0.2 - - - -
157G FE 2.4 29.5 - - - -
58J ASP* 3.6 6.5 - - - -
62J GLU* 2.9 3.0 + - - -
27L ILE* 3.0 18.8 + - + +
28L HIS* 3.3 13.7 - - - +
30L ILE* 1.3 80.5 - - - +
32L TRP* 1.3 85.1 + + - +
34L MET* 3.8 9.9 - - - +
39L PHE* 4.6 1.2 - - - -
43L HIS* 2.9 71.1 + + - -
46L MET* 3.7 18.3 - - + +
47L ASP* 3.2 27.3 + - - -
----------------------------------------------------------
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Residues in contact with TRP 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP* 4.2 9.7 + - - -
17J VAL* 4.4 5.8 - - + -
21J ASN* 4.9 2.0 - - - -
57J MET* 3.8 25.6 - - + -
58J ASP* 2.7 25.2 + - - -
61J ALA* 3.5 24.4 - - + +
62J GLU* 4.0 16.5 + - + +
65J LEU* 3.7 33.2 - - + +
71J PRO* 3.8 22.0 - - + -
72J PHE 3.5 20.9 - - - -
73J SER* 4.0 16.2 - - - -
78J PHE* 4.9 3.8 - + - -
25L VAL* 5.5 0.7 - - + -
28L HIS* 2.8 46.4 + + + +
29L GLN* 3.8 2.2 - - - +
31L HIS* 1.3 93.3 - + - +
33L TYR* 1.3 64.5 + + + +
34L MET 3.5 3.5 + - - +
39L PHE* 5.3 0.2 - - - -
43L HIS* 5.4 0.4 - + - -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J LEU* 4.7 5.4 - - + -
70J SER* 3.1 25.0 + - - -
71J PRO* 2.5 48.7 + - + -
73J SER* 3.5 23.5 + - - -
29L GLN* 2.8 30.3 + - + +
30L ILE* 4.6 1.6 - - - +
32L TRP* 1.3 81.9 - - + +
34L MET* 1.3 68.2 + - - +
35L ARG* 3.5 13.0 + - - +
89L TYR* 3.3 70.3 + + + +
98L LEU* 4.7 2.6 - - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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