Contacts of the helix formed by residues 18 - 40 (chain K) in PDB entry 6CP3
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 GLY 18 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K THR 2.9 3.2 + - - -
17K ILE* 1.3 73.5 - - - +
19K LEU* 1.3 54.7 + - - +
20K LEU* 3.1 5.6 - - - -
21K GLY* 2.9 21.5 + - - -
22K ALA 4.0 1.0 + - - -
65K CYS* 3.5 14.9 - - - -
17L ILE* 3.6 23.2 - - - +
19L LEU* 3.7 23.1 - - - +
20L LEU* 4.1 8.4 - - - -
23L GLY* 5.3 0.2 - - - -
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Residues in contact with LEU 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K THR* 3.3 28.6 + - + +
18K GLY* 1.3 71.2 - - - +
20K LEU* 1.3 53.8 + - - +
21K GLY 3.1 0.7 - - - -
22K ALA* 2.9 16.7 + - + +
23K GLY* 2.5 32.4 + - - -
59K GLU* 5.6 0.7 - - - +
62K GLY* 4.4 17.9 - - - +
65K CYS* 4.2 3.4 - - - +
66K LEU* 4.6 13.7 - - + -
18T GLY* 3.3 28.9 - - - +
61T THR* 3.2 31.7 - - - +
62T GLY* 4.0 0.4 - - - -
64T PHE* 5.0 3.1 - - + -
65T CYS* 3.7 31.6 - - + +
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Residues in contact with LEU 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ILE* 2.6 36.5 + - + +
19K LEU* 1.3 78.4 - - - +
21K GLY* 1.3 56.6 + - - +
23K GLY* 3.0 3.9 + - - +
24K ILE* 2.9 35.8 + - + +
20L LEU* 3.8 26.5 - - + -
17T ILE* 4.7 3.8 - - + +
18T GLY* 4.3 10.8 - - - +
20T LEU* 3.8 26.2 - - + -
21T GLY* 3.3 30.5 - - - +
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Residues in contact with GLY 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLY 2.9 12.1 + - - -
20K LEU* 1.3 75.4 - - - +
22K ALA* 1.3 51.2 + - - +
24K ILE* 3.0 5.0 + - - +
25K GLY* 2.6 31.0 + - - -
20L LEU* 3.5 21.4 - - - +
23L GLY* 3.1 26.4 - - - +
24L ILE* 3.6 7.6 + - - -
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Residues in contact with ALA 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLY 4.0 1.6 + - - -
19K LEU* 2.9 19.0 + - + +
21K GLY* 1.3 74.2 - - - +
23K GLY* 1.3 58.5 + - - +
24K ILE 3.7 0.2 - - - -
25K GLY* 3.0 14.8 + - - +
26K ILE* 3.4 21.3 - - - +
58K SER 4.7 3.4 - - - +
59K GLU* 3.3 42.8 - - - +
62K GLY* 4.6 6.9 - - - +
23L GLY* 3.9 11.3 - - - -
61T THR* 3.4 5.2 - - + +
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Residues in contact with GLY 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K LEU 2.5 17.2 + - - -
20K LEU* 3.0 7.8 + - - -
22K ALA* 1.3 73.8 - - - +
24K ILE* 1.3 57.2 + - - +
26K ILE* 6.1 0.2 - - - +
27K ALA* 4.3 2.4 - - - +
18T GLY 5.6 0.9 - - - -
21T GLY 2.9 20.7 - - - +
22T ALA* 3.7 12.1 + - - -
25T GLY* 3.3 15.1 - - - -
58T SER* 5.4 1.7 - - - +
61T THR* 3.5 20.3 + - - -
62T GLY 5.3 0.2 - - - -
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Residues in contact with ILE 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 2.9 22.1 + - + +
21K GLY 3.7 4.5 - - - +
22K ALA 3.7 0.2 - - - -
23K GLY* 1.3 77.9 - - - +
25K GLY* 1.3 66.6 + - - +
26K ILE 3.8 0.2 - - - -
27K ALA* 3.3 15.3 - - - +
28K ILE* 3.7 10.7 + - + +
20L LEU* 5.5 0.2 - - + -
24L ILE* 3.9 35.7 - - + -
21T GLY* 3.8 21.8 - - - +
24T ILE* 4.7 23.6 - - + -
25T GLY* 5.0 1.8 - - - -
28T ILE* 4.1 8.5 - - + +
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Residues in contact with GLY 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K GLY 2.6 21.8 + - - -
22K ALA* 3.0 5.3 + - - -
24K ILE* 1.3 73.2 - - - +
26K ILE* 1.3 60.8 + - - -
28K ILE* 3.0 27.1 + - - +
29K VAL* 3.4 5.2 + - - +
23L GLY 3.3 16.6 - - - -
24L ILE* 4.3 4.7 - - - -
27L ALA* 3.6 12.7 - - - +
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Residues in contact with ILE 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ALA* 3.4 12.3 + - - +
25K GLY* 1.3 71.8 - - - +
27K ALA* 1.3 57.7 + - + +
29K VAL* 3.0 12.2 + - + +
30K PHE* 2.9 34.3 + - + -
55K PHE* 3.6 56.3 - - + +
58K SER* 4.2 8.5 - - - +
59K GLU* 3.3 34.1 - - + +
57T LEU 4.0 4.5 - - - +
58T SER* 3.3 43.3 - - - +
61T THR* 3.9 2.2 - - + -
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLY 4.3 1.8 - - - +
24K ILE 3.3 15.5 - - - +
26K ILE* 1.3 80.9 - - - +
28K ILE* 1.3 58.4 + - - +
30K PHE* 3.0 9.5 + - - +
31K ALA* 2.8 23.9 + - - +
25T GLY* 3.3 39.5 - - - +
28T ILE* 3.8 7.2 - - + -
29T VAL* 3.6 12.2 - - + +
58T SER* 4.1 8.3 - - - +
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Residues in contact with ILE 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 4.2 9.6 - - + +
25K GLY* 3.0 16.5 + - - +
27K ALA* 1.3 76.7 - - - +
29K VAL* 1.3 59.3 + - - +
31K ALA* 3.6 12.1 - - + -
32K ALA* 2.8 34.3 + - + +
24L ILE* 5.8 0.7 - - + -
27L ALA* 4.8 0.7 - - + -
28L ILE* 3.6 43.3 - - + +
31L ALA* 4.2 12.5 - - + +
28T ILE* 3.6 25.8 - - + -
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Residues in contact with VAL 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K GLY 3.6 13.5 - - - +
26K ILE* 3.0 17.2 + - + +
28K ILE* 1.3 78.7 - - - +
30K PHE* 1.3 58.9 + - + +
33K LEU* 3.2 19.9 + - - +
51K ALA* 3.9 9.4 - - + +
54K GLY* 3.9 10.1 - - - +
55K PHE* 3.7 31.2 - - + +
27L ALA* 3.5 35.9 - - + +
30L PHE* 4.5 9.2 - - + -
31L ALA 5.2 3.1 - - - +
34L ILE* 3.5 14.8 - - + +
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Residues in contact with PHE 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K ILE* 2.9 29.2 + - + -
27K ALA 3.4 6.3 - - - +
29K VAL* 1.3 80.2 - - - +
31K ALA* 1.3 52.4 + - - +
33K LEU* 2.9 23.9 - - + +
34K ILE* 2.6 40.9 + - + +
48K PHE* 6.1 3.1 - + - -
51K ALA* 6.4 0.2 - - + -
52K ILE* 6.3 1.6 - - + -
55K PHE* 3.5 41.1 - + + -
29T VAL* 4.4 15.7 - - + -
50T MET* 4.3 13.0 - - + -
51T ALA* 5.6 1.6 - - - -
53T LEU* 4.1 19.1 - - + -
54T GLY* 3.6 41.7 - - - -
57T LEU* 4.7 2.9 - - + -
58T SER* 4.7 0.9 - - - -
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Residues in contact with ALA 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K ALA 2.8 15.9 + - - +
28K ILE* 2.9 18.3 + - + -
30K PHE* 1.3 76.3 - - - +
32K ALA* 1.3 52.7 + - - +
34K ILE* 2.9 5.2 + - - -
35K ASN* 2.6 39.3 + - - +
28T ILE* 3.9 14.4 - - + +
29T VAL* 4.4 2.9 - - - +
32T ALA* 3.3 28.1 - - + +
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Residues in contact with ALA 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K ILE* 2.8 17.5 + - + +
31K ALA* 1.3 71.0 - - - +
33K LEU* 1.3 60.0 + - - +
35K ASN* 4.2 9.2 - - - +
36K GLY* 2.9 20.1 + - - -
31L ALA* 3.3 38.6 - - + +
34L ILE* 3.3 16.5 - - + +
35L ASN* 3.6 14.5 - - - +
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Residues in contact with LEU 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K VAL 3.2 16.5 + - - +
30K PHE* 2.9 34.7 + - + +
32K ALA* 1.3 76.8 - - - +
34K ILE* 1.3 55.7 + - - +
36K GLY* 3.9 0.2 - - - -
37K VAL* 2.8 37.1 + - + +
44K LYS* 6.3 1.3 - - + -
47K VAL* 3.9 26.9 - - + +
48K PHE* 4.7 12.1 - - + -
51K ALA* 3.8 29.6 - - + -
34L ILE* 3.7 12.0 - - + +
50T MET* 3.7 31.2 - - + -
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Residues in contact with ILE 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PHE* 2.6 22.5 + - + +
31K ALA 2.9 6.8 + - - +
33K LEU* 1.3 71.8 - - - +
35K ASN* 1.3 53.9 + - - +
37K VAL* 2.9 3.5 + - - -
38K SER* 2.6 36.8 + - - -
29T VAL* 3.7 37.5 - - + +
32T ALA* 3.4 28.3 - - + +
33T LEU* 3.9 15.9 - - + +
36T GLY* 4.5 8.3 - - - -
47T VAL* 4.8 9.6 - - + -
50T MET* 3.8 23.1 - - + -
51T ALA* 4.1 18.6 - - + -
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Residues in contact with ASN 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K ALA* 2.6 22.1 + - - +
32K ALA* 4.2 4.6 - - - +
34K ILE* 1.3 70.6 - - - +
36K GLY* 1.3 60.5 + - - +
38K SER* 3.2 13.5 + - - -
39K ARG* 3.9 8.5 + - - +
35L ASN* 3.5 15.0 - - - +
32T ALA* 3.4 25.7 - - - +
35T ASN* 3.4 31.7 - - - +
39T ARG* 3.9 13.6 + - - +
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Residues in contact with GLY 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ALA 2.9 22.9 + - - -
33K LEU 3.9 0.2 - - - -
35K ASN* 1.3 76.8 - - - +
37K VAL* 1.3 57.7 + - - +
39K ARG* 2.9 26.0 + - - +
40K ASN 3.5 3.5 + - - -
34L ILE* 4.7 2.0 - - - -
35L ASN* 3.2 7.7 + - - -
38L SER* 3.3 32.5 - - - -
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Residues in contact with VAL 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K LEU* 2.8 30.2 + - + +
34K ILE 2.9 1.5 + - - +
36K GLY* 1.3 68.6 - - - -
38K SER* 1.3 67.2 + - - +
39K ARG 3.2 0.2 - - - -
40K ASN 3.3 29.1 - - - +
41K PRO* 3.3 7.3 - - + +
43K ILE* 3.9 7.8 - - + +
44K LYS* 3.7 41.1 - - + +
47K VAL* 4.7 2.5 - - + -
34L ILE* 5.4 0.8 - - - +
43T ILE* 3.4 7.6 - - - +
47T VAL* 3.7 26.0 - - + -
50T MET* 3.7 13.2 - - + -
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Residues in contact with SER 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H VAL* 3.2 16.0 - - - +
34K ILE* 2.6 24.8 + - - -
35K ASN* 3.2 6.8 + - - -
37K VAL* 1.3 76.6 - - - +
39K ARG* 1.3 60.3 + - - +
40K ASN 3.5 0.3 + - - -
41K PRO* 4.0 0.7 - - - +
36T GLY* 3.6 32.9 - - - -
39T ARG* 2.8 27.5 + - - -
40T ASN* 3.6 14.4 + - - +
43T ILE* 3.7 13.0 - - - -
47T VAL* 5.2 1.3 - - - -
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Residues in contact with ARG 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G GLU* 4.6 22.6 + - - +
36H SER* 4.1 9.7 + - - -
39H ILE* 3.9 17.6 - - - +
45H HIS* 4.0 21.4 + - + +
46H VAL* 3.2 32.1 + - + +
48H THR* 5.3 6.6 + - - +
50H GLU* 3.8 19.8 + - - -
35K ASN 4.0 8.5 - - - +
36K GLY* 2.9 12.9 + - - +
38K SER* 1.3 81.8 + - - +
40K ASN* 1.3 60.9 + - + +
41K PRO* 3.9 0.7 - - - -
38L SER* 5.0 2.9 - - - +
39L ARG* 3.1 48.8 - - - +
39T ARG* 4.5 7.2 - - - +
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Residues in contact with ASN 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H GLY 4.2 7.9 + - - -
42H LEU* 3.9 16.6 - - - +
44H ASN 3.2 12.4 - - - +
45H HIS* 4.2 11.0 - - + +
36K GLY 3.5 3.2 + - - +
37K VAL* 3.3 7.9 - - - +
39K ARG* 1.3 81.4 - - + +
41K PRO* 1.3 64.4 - - - +
42K SER* 3.2 20.9 + - - -
43K ILE* 3.3 29.1 - - + +
38L SER 3.5 27.7 + - - +
41L PRO* 3.8 19.6 - - - +
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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