Contacts of the helix formed by residues 9 - 33 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ASP* 1.3 73.1 - - - +
10K LYS* 1.3 57.4 + - - +
12K PHE* 2.8 4.0 + - + +
13K LEU* 2.7 56.5 + - + +
67K ILE* 4.0 7.6 - - + -
119K LEU* 3.6 8.1 - - - +
120K THR* 3.8 29.5 + - - +
123K GLU* 2.5 30.8 + - - +
125K ASP* 3.9 17.5 - - - +
128K THR* 3.9 9.2 - - + -
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Residues in contact with LYS 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 6.0 0.2 - - - +
8K ASP* 3.2 15.1 + - - +
9K THR* 1.3 78.4 - - - +
11K GLU* 1.3 72.6 + - - +
13K LEU 3.5 0.2 + - - -
14K ASN* 3.0 24.4 + - - +
64K LEU* 3.7 19.4 - - + +
67K ILE* 3.4 39.8 + - + -
68K GLY* 3.7 16.3 + - - -
69K GLY* 4.1 15.5 - - - -
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Residues in contact with GLU 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 3.0 35.9 - - + +
8K ASP* 2.7 33.9 + - - +
10K LYS* 1.3 79.2 - - - +
12K PHE* 1.3 60.5 - - - +
14K ASN* 3.4 5.2 + - - +
15K HIS* 2.9 29.7 + - - +
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Residues in contact with PHE 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 4.8 8.5 - - + +
8K ASP 2.8 5.4 + - - +
9K THR* 3.2 7.0 - - - +
11K GLU* 1.3 74.4 - - - +
13K LEU* 1.3 81.1 + - + +
15K HIS* 2.9 18.5 + - - +
16K GLN* 3.0 51.0 + - + +
112K GLU* 3.3 26.5 - - + -
113K TYR* 3.8 11.0 - + - -
115K GLN* 4.7 4.7 - - + -
116K GLY* 3.5 20.9 - - - -
119K LEU* 3.4 27.8 - - + -
120K THR* 5.5 1.3 - - - -
132K LEU* 3.8 30.3 - - + -
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Residues in contact with LEU 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K THR* 2.7 34.7 + - + +
10K LYS 3.7 4.3 - - - +
12K PHE* 1.3 95.7 - - + +
14K ASN* 1.3 62.5 + - - +
16K GLN* 2.9 16.0 + - + +
17K VAL* 3.0 10.3 + - - +
60K VAL* 3.5 26.3 - - + +
63K ARG* 4.2 8.5 - - + -
64K LEU* 4.1 20.4 - - + -
67K ILE* 3.9 18.8 - - + -
128K THR* 3.7 26.0 - - + -
131K MET* 4.3 11.2 - - + -
132K LEU* 4.4 3.1 - - + -
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Residues in contact with ASN 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K LYS 3.0 17.9 + - - +
11K GLU* 4.0 4.9 - - - +
13K LEU* 1.3 77.0 - - - +
15K HIS* 1.3 64.4 + - - +
17K VAL* 3.2 14.0 + - - +
18K ALA 3.2 9.0 + - - -
64K LEU* 3.7 13.7 - - + +
70K SER 3.1 20.6 + - - -
71K PRO* 3.1 6.8 - - - +
72K PHE* 2.6 72.4 + - + +
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Residues in contact with HIS 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K GLU 2.9 13.8 + - - +
12K PHE* 2.9 14.6 + - - +
14K ASN* 1.3 78.3 - - - +
16K GLN* 1.3 62.3 + - - +
18K ALA* 3.2 5.5 + - - +
19K ASN* 2.9 29.7 + - - -
72K PHE* 4.3 5.8 - - - -
81K ASN* 2.8 31.6 + - + -
82K ALA 3.9 0.2 - - - -
83K SER* 2.9 39.5 + - - -
112K GLU* 3.1 20.1 + - - -
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Residues in contact with GLN 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K PHE* 3.0 49.5 + - + +
13K LEU* 2.9 8.3 + - + +
15K HIS* 1.3 80.7 + - - +
17K VAL* 1.3 56.1 + - - +
18K ALA 3.0 1.6 - - - -
19K ASN* 2.9 24.7 + - - +
20K LEU* 2.7 46.4 + - + +
60K VAL* 4.4 12.1 - - + -
109K LEU* 3.6 5.4 - - - +
112K GLU* 3.0 27.7 + - - +
113K TYR* 3.6 27.2 - - + +
132K LEU* 5.9 0.4 - - + -
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Residues in contact with VAL 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I TRP* 4.4 12.1 - - + -
13K LEU 3.0 18.6 + - - +
14K ASN* 3.2 19.9 + - - +
16K GLN* 1.3 75.9 - - - +
18K ALA* 1.3 62.5 + - - +
20K LEU* 3.9 4.4 - - - +
21K ASN* 2.8 37.9 + - - +
57K MET* 4.5 6.3 - - - +
60K VAL* 3.8 17.9 - - + +
61K ALA* 3.9 21.5 - - + +
64K LEU* 4.9 2.0 - - + -
71K PRO* 4.6 3.4 - - + -
72K PHE* 3.8 12.8 - - + +
78K PHE* 3.8 23.1 - - + -
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Residues in contact with ALA 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ASN 3.2 8.4 + - - +
15K HIS 3.4 9.0 - - - +
16K GLN 3.0 0.2 - - - -
17K VAL* 1.3 82.7 - - - +
19K ASN* 1.3 64.5 + - - +
21K ASN* 3.3 3.3 + - - +
22K VAL* 3.3 23.4 + - - +
72K PHE* 4.3 3.8 - - + -
78K PHE* 3.7 25.5 - - - +
81K ASN* 3.9 13.7 - - + -
82K ALA* 3.7 25.8 - - - +
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Residues in contact with ASN 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K HIS* 2.9 17.2 + - - +
16K GLN* 2.9 29.9 + - - +
18K ALA* 1.3 75.9 - - - +
20K LEU* 1.3 58.5 + - - +
22K VAL* 2.9 4.7 + - - +
23K PHE* 2.8 30.6 + - - +
82K ALA* 3.4 4.5 - - - -
83K SER* 2.7 35.5 + - - -
84K VAL* 3.0 25.8 + - + +
109K LEU* 4.0 8.0 - - + +
112K GLU* 2.9 24.0 + - - -
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Residues in contact with LEU 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K GLN* 2.7 25.5 + - + +
19K ASN* 1.3 72.8 - - - +
21K ASN* 1.3 62.8 + - - +
23K PHE* 3.2 6.7 + - + +
24K THR* 2.9 27.5 + - - -
53K PHE* 4.2 23.0 - - + +
56K GLN* 4.1 4.0 - - + -
57K MET* 3.6 46.0 - - + +
60K VAL* 4.1 16.8 - - + -
109K LEU* 4.2 26.5 - - + -
113K TYR* 3.4 27.6 - - - +
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Residues in contact with ASN 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I VAL* 4.6 8.1 - - - +
28I HIS* 5.4 0.9 - - - -
50I TYR* 5.3 1.6 + - - -
75I LEU* 4.1 3.3 - - + +
17K VAL* 2.8 31.0 + - - +
18K ALA 3.8 0.9 - - - +
19K ASN 3.2 0.2 - - - -
20K LEU* 1.3 78.4 - - - +
22K VAL* 1.3 61.9 + - - +
24K THR* 3.2 24.3 - - - +
25K VAL* 3.4 13.7 - - - +
57K MET* 3.4 36.5 - - - +
78K PHE* 3.2 54.2 - - + -
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Residues in contact with VAL 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I LEU* 4.1 24.2 - - + -
18K ALA 3.5 13.2 - - - +
19K ASN 2.9 7.0 + - - +
21K ASN* 1.3 75.3 - - - +
23K PHE* 1.3 67.9 + - - +
25K VAL* 3.1 5.4 + - - +
26K LYS* 3.0 20.4 + - - +
78K PHE* 4.6 4.3 - - + +
79K LEU* 5.0 7.0 - - + -
82K ALA* 3.5 20.0 - - + -
84K VAL* 3.7 28.9 - - + +
85K GLU 4.5 0.2 - - - +
86K GLU* 3.9 33.2 - - + +
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Residues in contact with PHE 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K ASN 2.8 16.0 + - - +
20K LEU* 3.5 8.5 - - + +
22K VAL* 1.3 78.3 - - - +
24K THR* 1.3 63.0 + - - +
26K LYS* 2.9 17.4 + - + +
27K ILE* 2.8 39.4 + - + +
49K LEU* 5.2 0.9 - - + -
53K PHE* 3.8 35.9 - + + -
84K VAL* 4.4 5.3 - - + +
102K LEU* 3.4 34.8 - - + -
105K THR* 3.3 31.4 - - + -
106K LEU* 3.8 17.9 - - + -
109K LEU* 3.5 26.2 - - + -
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Residues in contact with THR 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I TYR* 5.8 3.4 - - - +
20K LEU 2.9 13.9 + - - +
21K ASN* 3.2 24.0 - - - +
22K VAL 3.2 0.2 - - - -
23K PHE* 1.3 78.1 - - - +
25K VAL* 1.3 73.1 + - + +
27K ILE* 3.3 13.5 + - - +
28K HIS 3.1 15.6 + - - -
50K TYR* 3.4 49.3 + - + +
53K PHE* 4.7 5.2 - - - +
54K GLY* 4.3 12.9 + - - -
57K MET* 5.9 3.8 - - + -
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Residues in contact with VAL 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN* 4.4 8.1 - - - +
73I SER* 3.5 23.7 - - - +
74I THR* 3.9 6.5 - - - +
75I LEU* 3.7 17.5 - - + -
78I PHE* 3.5 33.4 - - + -
21K ASN 3.4 14.6 - - - +
22K VAL 3.1 7.6 + - - +
24K THR* 1.3 83.8 - - + +
26K LYS* 1.3 63.7 + - - +
28K HIS* 3.0 14.1 + - + +
29K GLN* 2.9 19.6 + - - +
32K TRP* 6.0 0.2 - - + -
50K TYR* 6.1 0.4 - - + +
86K GLU* 4.9 0.9 - - - +
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Residues in contact with LYS 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I SER 5.2 2.0 - - - -
22K VAL* 3.0 11.5 + - + +
23K PHE* 2.9 21.0 + - + +
25K VAL* 1.3 78.4 - - - +
27K ILE* 1.3 61.8 + - - +
29K GLN* 2.9 26.4 + - - +
30K ILE* 3.0 24.8 + - + +
84K VAL* 4.2 9.9 - - - -
85K GLU 2.7 30.9 + - - -
86K GLU* 3.9 12.9 - - + +
87K ALA 4.9 1.8 - - - +
101K ASP* 3.2 37.5 + - - +
102K LEU* 5.2 0.4 - - - -
105K THR* 3.4 27.6 - - - +
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Residues in contact with ILE 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K PHE* 2.8 53.2 + - + +
24K THR* 3.4 16.2 - - - +
26K LYS* 1.3 76.5 - - - +
28K HIS* 1.3 62.9 + - - +
29K GLN 3.2 0.2 + - - -
30K ILE* 3.3 9.4 + - + +
31K HIS* 3.0 23.5 + - + +
46K MET* 3.4 38.7 - - + +
49K LEU* 4.0 33.7 - - + +
50K TYR* 3.8 12.6 - - + +
53K PHE* 4.4 3.6 - - + -
102K LEU* 4.9 3.6 - - + -
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Residues in contact with HIS 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN* 5.5 1.1 - - - -
54I GLY 5.3 1.2 + - - -
57I MET* 3.5 29.0 - - + +
58I ASP* 3.7 29.1 + - + +
24K THR 3.1 6.5 + - - +
25K VAL* 3.0 16.5 + - + +
27K ILE* 1.3 77.2 - - - +
29K GLN* 1.3 64.1 + - - +
31K HIS* 3.3 13.1 + + - +
32K TRP* 2.9 50.5 + + + -
47K ASP* 4.8 5.8 + - - -
50K TYR* 3.0 53.2 + + + +
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Residues in contact with GLN 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I SER* 3.0 46.2 + - - +
74I THR* 4.2 0.5 - - - +
25K VAL 2.9 11.7 + - - +
26K LYS* 2.9 21.5 + - - +
28K HIS* 1.3 78.3 - - - +
30K ILE* 1.3 68.7 + - - +
32K TRP* 3.1 2.2 + - - -
33K TYR* 2.9 38.9 + - + +
87K ALA 3.1 29.0 + - - +
89K TYR* 3.8 21.3 + - + +
93K LYS* 5.2 5.3 - - - +
98K LEU* 5.4 5.0 - - + +
101K ASP* 4.6 13.1 + - - -
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Residues in contact with ILE 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K LYS* 3.0 26.7 + - + +
27K ILE* 3.7 9.4 - - + +
29K GLN* 1.3 79.9 - - + +
31K HIS* 1.3 58.7 + - - +
33K TYR* 5.1 0.4 - - - -
34K MET* 2.8 48.6 + - + +
46K MET* 4.1 7.0 - - + -
98K LEU* 3.9 48.0 - - + +
99K MET* 3.5 24.5 - - + -
101K ASP* 5.2 3.6 - - + +
102K LEU* 4.0 27.4 - - + +
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Residues in contact with HIS 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E FE 2.2 29.6 - - - -
58I ASP* 3.7 3.6 - - - -
62I GLU* 3.0 3.0 + - - -
27K ILE* 3.0 18.7 + - + +
28K HIS* 3.3 15.0 - - - +
30K ILE* 1.3 77.7 - - - +
32K TRP* 1.3 87.9 + + - +
34K MET* 3.9 15.9 - - - +
39K PHE* 4.5 1.2 - - - -
43K HIS* 2.9 76.5 + + - -
46K MET* 3.8 12.3 - - + +
47K ASP* 3.3 21.9 + - - -
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Residues in contact with TRP 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 4.0 10.9 + - - -
17I VAL* 4.3 5.2 - - + -
57I MET* 3.7 28.3 - - + -
58I ASP* 2.6 28.5 + - - -
61I ALA* 3.4 24.7 - - + +
62I GLU* 3.9 16.9 + - + +
65I LEU* 3.5 32.8 - - + +
71I PRO* 3.7 18.6 - - + -
72I PHE 3.6 20.6 - - - -
73I SER* 4.1 15.5 - - - -
78I PHE* 4.9 4.9 - + - -
25K VAL* 6.0 0.4 - - + -
28K HIS* 2.9 43.4 + + + +
29K GLN* 3.7 2.9 - - - +
31K HIS* 1.3 98.8 - + - +
33K TYR* 1.3 68.3 + + + +
34K MET 3.5 3.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I LEU* 4.7 6.1 - - + -
70I SER* 3.1 24.0 - - - -
71I PRO* 2.4 48.3 + - + -
73I SER* 3.5 23.3 - - - -
29K GLN* 2.9 30.6 + - + +
30K ILE* 4.5 1.3 - - - +
32K TRP* 1.3 81.2 - - + +
34K MET* 1.3 67.3 + - - +
35K ARG* 3.5 12.1 + - - +
89K TYR* 3.4 69.1 + + + -
98K LEU* 4.7 2.4 - - + +
----------------------------------------------------------
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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