Contacts of the helix formed by residues 18 - 39 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L THR 3.2 3.2 + - - -
17L ILE* 1.3 77.6 - - - +
19L LEU* 1.3 55.5 + - - +
20L LEU 3.1 2.7 - - - -
21L GLY* 2.9 21.2 + - - -
22L ALA 3.7 1.6 + - - -
62L GLY* 3.7 4.8 - - - -
65L CYS* 3.5 24.4 - - - -
17M ILE* 4.1 11.3 - - - +
19M LEU* 3.7 22.9 - - - +
20M LEU* 4.8 3.0 - - - -
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Residues in contact with LEU 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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18K GLY* 3.7 15.5 - - - +
61K THR* 3.3 33.2 + - - +
62K GLY* 3.7 11.9 - - - +
64K PHE* 4.2 8.3 - - + -
65K CYS* 3.7 32.8 - - + +
68K VAL* 5.7 0.9 - - + -
16L THR* 3.7 21.6 + - + +
18L GLY* 1.3 72.0 - - - +
20L LEU* 1.3 56.1 + - - +
21L GLY 3.1 0.7 - - - -
22L ALA* 2.9 17.8 + - + +
23L GLY* 2.4 33.8 + - - -
62L GLY* 4.3 13.1 + - - +
65L CYS* 4.6 0.8 - - - +
66L LEU* 4.6 18.8 - - + -
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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
----------------------------------------------------------
17K ILE* 5.4 0.7 - - + +
18K GLY* 4.1 10.7 + - - +
20K LEU* 3.8 27.6 - - + -
21K GLY* 3.5 28.5 - - - +
24K ILE* 5.5 0.4 - - + -
17L ILE* 2.6 39.1 + - + +
19L LEU* 1.3 78.1 - - - +
21L GLY* 1.3 54.8 + - - +
23L GLY 4.0 1.1 - - - +
24L ILE* 2.9 46.2 + - + +
20M LEU* 3.7 33.4 - - + -
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Residues in contact with GLY 21 (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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18L GLY 2.9 13.1 + - - -
20L LEU* 1.3 73.8 - - - +
22L ALA* 1.3 63.9 + - - +
25L GLY* 3.3 8.8 + - - -
26L ILE* 4.5 0.7 + - - +
58L SER 6.1 0.4 - - - -
61L THR* 5.5 0.7 - - - -
62L GLY* 5.4 1.1 - - - -
20M LEU* 3.6 22.4 - - - +
23M GLY* 2.9 42.3 - - - +
24M ILE* 4.3 2.0 - - - -
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Residues in contact with ALA 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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61K THR* 3.9 27.1 - - + +
18L GLY 3.7 3.2 + - - -
19L LEU* 2.9 23.4 + - + +
21L GLY* 1.3 75.1 - - - +
23L GLY* 1.3 61.4 + - - +
25L GLY 3.0 12.8 + - - -
26L ILE* 3.3 28.3 - - + +
58L SER 5.9 0.2 - - - -
59L GLU* 4.5 21.3 - - - +
62L GLY* 4.6 5.8 - - - +
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Residues in contact with GLY 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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18K GLY 5.3 0.7 - - - -
21K GLY* 3.1 28.7 - - - +
22K ALA* 3.9 6.0 + - - -
25K GLY* 3.3 12.5 - - - -
58K SER 4.2 9.4 - - - +
61K THR* 4.2 10.8 - - - -
62K GLY 5.7 0.7 - - - -
19L LEU* 2.4 24.4 + - - -
20L LEU 3.0 3.0 + - - -
22L ALA* 1.3 65.7 - - - +
24L ILE* 1.3 60.0 + - - +
27L ALA* 3.7 5.0 - - - +
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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
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21K GLY* 3.8 15.7 - - - +
24K ILE* 3.9 36.1 - - + -
25K GLY* 4.3 4.2 - - - -
28K ILE* 5.8 0.7 - - + -
20L LEU* 2.9 29.5 + - + +
22L ALA 3.4 0.4 - - - -
23L GLY* 1.3 74.8 - - - +
25L GLY* 1.3 62.7 + - - +
27L ALA* 2.9 30.1 + - - +
28L ILE* 3.2 23.2 + - + +
24M ILE* 4.0 35.4 - - + -
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Residues in contact with GLY 25 (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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21L GLY 3.3 6.1 + - - -
22L ALA 3.0 6.5 + - - -
24L ILE* 1.3 79.7 - - - +
26L ILE* 1.3 62.1 + - - -
28L ILE* 3.0 27.6 + - - +
29L VAL 3.4 1.0 + - - -
23M GLY 3.4 23.1 - - - -
24M ILE* 4.4 4.5 - - - -
27M ALA* 3.4 15.8 - - - +
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Residues in contact with ILE 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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57K LEU 3.6 11.0 - - - +
58K SER* 3.3 26.0 - - - +
61K THR* 4.7 9.0 - - + -
21L GLY 4.5 0.6 + - - +
22L ALA* 3.3 21.0 + - + +
25L GLY* 1.3 70.5 - - - +
27L ALA* 1.3 64.4 + - - +
29L VAL* 3.0 22.6 + - - +
30L PHE* 3.2 16.5 + - - -
54L GLY 4.9 0.4 - - - +
55L PHE* 3.6 46.2 - - + +
58L SER* 4.0 9.2 - - - -
59L GLU* 3.7 35.2 - - + +
23M GLY 4.7 0.4 + - - +
27M ALA* 4.8 0.2 - - - -
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Residues in contact with ALA 27 (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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25K GLY* 3.6 35.7 - - - +
28K ILE* 4.6 1.3 - - - -
29K VAL* 3.5 16.5 - - + +
58K SER* 3.9 14.8 - - - -
23L GLY 3.7 5.4 - - - +
24L ILE 2.9 15.8 + - - +
26L ILE* 1.3 81.8 - - - +
28L ILE* 1.3 60.5 + - + +
30L PHE* 3.0 9.8 + - - +
31L ALA* 3.0 16.8 + - - +
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Residues in contact with ILE 28 (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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28K ILE* 3.6 23.1 - - + -
24L ILE* 3.3 33.7 - - + +
25L GLY* 3.0 11.1 + - - +
27L ALA* 1.3 74.5 - - - +
29L VAL* 1.3 65.5 + - + +
31L ALA* 2.9 27.5 - - + +
32L ALA* 3.0 9.5 + - - +
24M ILE* 5.2 2.7 - - + +
27M ALA* 4.7 1.3 - - + -
28M ILE* 3.6 39.0 - - + +
31M ALA* 4.3 8.5 - - + +
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Residues in contact with VAL 29 (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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25L GLY 3.7 12.8 - - - +
26L ILE* 3.0 13.2 + - - +
28L ILE* 1.3 76.7 - - - +
30L PHE* 1.3 59.3 + - + +
32L ALA 3.1 2.9 + - - -
33L LEU* 2.8 24.8 + - + +
51L ALA* 4.3 21.3 - - + +
54L GLY 4.6 10.5 - - - +
55L PHE* 5.1 1.8 - - - +
27M ALA* 3.3 35.9 - - + +
30M PHE* 4.5 13.2 - - + -
31M ALA* 4.5 6.5 - - - +
34M ILE* 3.3 21.1 - - + +
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Residues in contact with PHE 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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29K VAL* 4.5 12.8 - - + -
50K MET* 5.0 4.9 - - + -
51K ALA* 6.4 0.2 - - - -
53K LEU* 4.1 19.7 - - + -
54K GLY* 3.6 39.5 - - - -
57K LEU* 4.8 2.7 - - + -
58K SER* 3.6 16.6 - - - -
26L ILE 3.2 19.7 + - - -
27L ALA* 3.0 8.7 + - - +
29L VAL* 1.3 79.1 - - + +
31L ALA* 1.3 57.5 + - - +
33L LEU* 3.0 27.4 + - + +
34L ILE* 2.9 39.4 + - + +
48L PHE* 5.6 4.3 - + - -
51L ALA* 6.3 1.8 - - + -
52L ILE* 5.5 8.5 - - + -
55L PHE* 3.8 33.7 - + + -
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Residues in contact with ALA 31 (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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28K ILE* 4.2 23.6 - - + +
29K VAL* 5.0 0.8 - - - +
32K ALA* 3.3 33.7 - - + +
27L ALA 3.0 7.5 + - - +
28L ILE* 2.9 24.9 + - + +
30L PHE* 1.3 73.7 - - - +
32L ALA* 1.3 59.7 + - - +
34L ILE* 3.1 13.7 + - - -
35L ASN* 3.4 7.5 + - - -
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Residues in contact with ALA 32 (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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28L ILE 3.0 7.4 + - - +
29L VAL 3.7 5.8 - - - +
31L ALA* 1.3 75.2 - - - +
33L LEU* 1.3 57.9 + - - +
35L ASN* 4.3 6.5 - - - +
36L GLY* 2.9 20.5 + - - -
31M ALA* 3.5 42.6 - - + +
34M ILE* 3.2 14.5 - - + +
35M ASN* 4.3 16.3 - - - +
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Residues in contact with LEU 33 (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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50K MET* 3.7 36.8 - - + -
29L VAL* 2.8 13.2 + - + +
30L PHE* 3.0 36.7 + - + +
32L ALA* 1.3 78.3 - - - +
34L ILE* 1.3 59.6 + - + +
36L GLY 2.9 4.2 + - - -
37L VAL* 2.9 29.9 + - + +
44L LYS* 5.7 1.8 - - - +
47L VAL* 3.8 31.6 - - + -
48L PHE* 4.5 13.5 - - + +
51L ALA* 4.1 14.8 - - + -
34M ILE* 3.5 7.1 - - + +
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Residues in contact with ILE 34 (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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29K VAL* 3.5 29.4 - - + +
32K ALA* 3.3 20.0 - - + +
33K LEU* 3.7 23.6 - - + +
36K GLY* 4.7 3.4 - - - -
37K VAL 5.4 0.7 - - - +
47K VAL* 4.8 11.9 - - + -
50K MET* 4.7 11.9 - - + -
51K ALA* 4.0 26.2 - - + +
30L PHE* 2.9 26.3 + - + +
31L ALA 3.1 3.1 + - - +
33L LEU* 1.3 75.1 - - + +
35L ASN* 1.3 54.6 + - - +
37L VAL* 3.0 13.0 + - + +
38L SER* 2.8 37.4 + - - -
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Residues in contact with ASN 35 (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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32K ALA* 3.6 24.0 - - - +
35K ASN* 3.5 11.0 - - - +
36K GLY* 3.2 26.3 + - - -
31L ALA 3.4 8.7 + - - +
32L ALA* 4.3 5.0 - - - +
34L ILE* 1.3 75.2 - - - +
36L GLY* 1.3 58.0 + - - +
37L VAL 3.0 5.9 + - - -
38L SER* 3.0 20.9 + - - +
39L ARG* 3.2 25.5 + - - +
35M ASN* 5.3 5.8 - - - +
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Residues in contact with GLY 36 (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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32L ALA 2.9 19.8 + - - -
33L LEU* 2.9 9.1 + - - -
35L ASN* 1.3 74.4 - - - +
37L VAL* 1.3 57.5 + - - +
39L ARG* 4.9 2.2 - - - -
40L ASN* 3.9 11.2 - - - +
43L ILE* 4.6 7.8 - - - +
47L VAL* 5.1 1.8 - - - +
34M ILE* 4.1 4.3 - - - -
35M ASN* 5.2 2.6 + - - -
38M SER* 3.3 37.9 - - - -
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Residues in contact with VAL 37 (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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43K ILE* 4.4 5.1 - - + +
47K VAL* 3.7 26.9 - - + -
50K MET* 3.8 16.6 - - + -
33L LEU* 2.9 14.3 + - + +
34L ILE* 3.0 14.1 + - - +
36L GLY* 1.3 78.9 - - - +
38L SER* 1.3 65.1 + - - +
39L ARG 3.5 0.7 - - - -
40L ASN 3.2 25.8 - - - +
41L PRO* 3.3 13.3 - - + +
43L ILE 5.3 0.4 - - - +
44L LYS* 3.7 46.2 - - + +
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Residues in contact with SER 38 (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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40H GLY 4.7 0.7 - - - +
45H HIS* 5.8 0.5 + - - -
36K GLY* 3.3 41.9 + - - -
39K ARG* 5.0 4.6 - - - +
40K ASN* 3.5 30.2 + - - +
43K ILE* 4.3 18.8 - - - -
47K VAL* 5.9 0.2 - - - -
34L ILE* 2.8 15.3 + - - -
35L ASN* 3.0 13.2 + - - -
37L VAL* 1.3 81.0 - - - +
39L ARG* 1.3 64.3 + - - +
40L ASN 3.1 0.9 + - - -
41L PRO* 4.0 2.1 - - - +
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Residues in contact with ARG 39 (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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36H SER* 2.4 52.9 + - - -
37H GLY* 5.0 0.4 - - - -
39H ILE* 3.4 42.0 - - + +
40H GLY 4.3 1.8 - - - -
45H HIS* 6.2 1.1 - - - -
39K ARG* 3.1 44.8 - - - +
35L ASN* 3.3 24.2 - - - +
36L GLY* 4.9 3.8 - - - -
38L SER* 1.3 79.8 + - - +
40L ASN* 1.3 62.5 + - + +
41L PRO* 4.0 2.9 - - - -
35M ASN* 5.2 8.2 + - - -
38M SER* 4.0 9.6 + - - +
39M ARG* 3.9 36.4 - - - +
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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
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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) + - + + + + + -
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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