Contacts of the helix formed by residues 29 - 54 (chain I) in PDB entry 6KW5
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 ASN 29 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D GLN* 4.0 26.2 - - - +
429D ILE* 4.7 13.9 - - + +
430D GLN* 4.6 5.9 + - - +
426H GLN* 4.7 7.9 - - - +
429H ILE* 3.8 21.3 - - + +
430H GLN* 4.2 22.2 - - - +
433H VAL* 5.1 5.1 - - + +
24I ASP* 5.8 0.2 + - - -
27I VAL* 2.9 25.0 + - + +
28I SER* 1.3 84.8 - - - +
30I LEU* 1.3 63.6 + - - +
31I ALA 3.2 2.7 - - - -
32I ASP* 3.0 24.5 + - + +
33I LEU* 3.1 13.5 + - - +
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Residues in contact with LEU 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429H ILE* 3.8 33.7 - - + -
18I ILE* 3.8 24.7 - - + +
19I PRO* 3.6 23.1 - - + +
20I THR* 5.4 2.0 - - - -
22I LEU* 4.2 29.6 - - + +
24I ASP* 5.2 12.5 + - - +
27I VAL* 4.0 9.6 - - + +
29I ASN* 1.3 74.0 - - - +
31I ALA* 1.3 60.2 + - - +
33I LEU* 3.9 11.5 - - + +
34I LYS* 2.9 33.0 + - - +
409I LEU* 4.5 4.7 - - + -
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Residues in contact with ALA 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I SER 5.2 3.3 - - - +
29I ASN 4.5 2.2 - - - +
30I LEU* 1.3 79.3 - - - +
32I ASP* 1.3 55.6 + - - +
34I LYS* 3.3 16.4 - - + +
35I LYS* 2.9 39.5 + - - +
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Residues in contact with ASP 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D ILE* 3.3 34.3 - - + +
430D GLN* 3.8 14.3 - - + +
433D VAL* 3.2 36.8 - - - +
433H VAL* 5.7 1.1 - - + -
28I SER 5.3 2.0 - - - +
29I ASN* 3.0 17.8 + - - +
31I ALA* 1.3 76.3 - - - +
33I LEU* 1.3 61.1 + - - +
35I LYS* 3.2 17.1 + - - +
36I LEU* 3.0 31.2 + - - +
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429H ILE* 4.7 8.1 - - + -
432H LEU* 3.7 46.2 - - + -
433H VAL* 4.3 12.4 - - + +
436H THR* 3.9 21.5 - - - +
18I ILE* 4.7 12.6 - - + -
29I ASN 3.1 13.4 + - - +
30I LEU* 3.9 24.0 - - + +
32I ASP* 1.3 72.7 - - - +
34I LYS* 1.3 59.6 + - - +
36I LEU* 3.2 12.1 + - + +
37I ILE* 2.9 49.0 + - + +
409I LEU* 5.4 1.8 - - + -
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Residues in contact with LYS 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I LEU* 2.9 22.3 + - - +
31I ALA* 3.3 15.2 - - - +
33I LEU* 1.3 77.0 - - - +
35I LYS* 1.3 58.1 + - + +
37I ILE* 3.1 10.8 + - - +
38I GLU* 2.8 46.4 + - - +
200M THR 5.8 2.4 + - - -
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Residues in contact with LYS 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D VAL* 4.7 7.9 - - + -
437D MET* 5.4 17.6 - - + +
31I ALA* 2.9 26.7 + - - +
32I ASP* 3.2 21.4 + - - +
34I LYS* 1.3 75.0 - - + +
36I LEU* 1.3 58.1 + - - +
38I GLU* 3.3 21.4 + - - +
39I MET* 2.9 31.8 + - - +
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Residues in contact with LEU 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D VAL* 3.7 30.1 - - + -
436D THR* 5.4 0.7 - - + -
433H VAL* 3.8 41.1 - - + +
436H THR* 4.3 18.7 - - + +
437H MET* 3.9 25.8 - - - -
440H LEU* 4.0 14.2 - - + +
32I ASP 3.0 17.6 + - - +
33I LEU* 3.5 14.1 - - + +
35I LYS* 1.3 75.7 - - - +
37I ILE* 1.3 58.3 + - - +
39I MET* 3.3 16.0 - - + +
40I ASP* 3.0 27.9 + - - +
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Residues in contact with ILE 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432H LEU* 6.1 1.1 - - + -
436H THR* 5.6 5.4 - - + +
15I ASP* 5.8 7.0 - - - +
18I ILE* 4.7 19.1 - - + -
33I LEU* 2.9 41.5 + - + +
34I LYS* 3.1 9.2 + - - +
36I LEU* 1.3 78.8 - - + +
38I GLU* 1.3 60.1 + - - +
40I ASP* 3.2 8.4 + - - +
41I SER* 2.9 34.8 + - - +
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Residues in contact with GLU 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I LYS* 2.8 43.6 + - - +
35I LYS* 3.3 26.7 - - - +
37I ILE* 1.3 76.0 - - - +
39I MET* 1.3 62.3 + - - +
41I SER* 3.8 8.3 - - - -
42I ARG* 2.9 30.0 + - - +
287M LYS* 6.5 0.7 - - - -
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Residues in contact with MET 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D VAL* 4.5 2.9 - - + +
436D THR* 3.7 25.6 - - + +
437D MET* 3.6 51.1 - - + +
440D LEU* 3.7 31.8 - - + +
440H LEU* 4.0 19.7 - - + -
444H PHE* 5.3 0.2 - - - -
35I LYS 2.9 22.7 + - - +
36I LEU* 3.3 16.8 - - + +
38I GLU* 1.3 77.8 - - - +
40I ASP* 1.3 57.5 + - - +
42I ARG* 3.4 7.4 + - - +
43I LEU* 3.0 29.5 + - - +
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Residues in contact with ASP 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 4.5 7.6 + - - -
436H THR* 5.2 3.5 - - + +
439H LYS* 2.3 33.6 + - - -
440H LEU* 3.9 20.3 - - + +
443H LYS* 2.5 37.6 + - - +
36I LEU 3.0 13.8 + - - +
37I ILE* 3.2 11.0 + - - +
39I MET* 1.3 75.5 - - - +
41I SER* 1.3 57.3 + - - +
43I LEU* 3.4 1.8 + - - +
44I ASP* 2.9 27.3 + - - +
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Residues in contact with SER 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 3.6 26.3 + - - -
290A TRP* 4.5 20.9 - - - +
37I ILE* 2.9 22.6 + - - +
38I GLU* 3.8 9.7 - - - -
39I MET 3.3 0.2 - - - -
40I ASP* 1.3 77.3 - - - +
42I ARG* 1.3 56.1 + - - +
44I ASP* 3.5 1.7 + - - +
45I LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D LEU* 5.2 17.3 - - + +
444D PHE* 4.6 24.3 - - + +
38I GLU 2.9 18.1 + - - +
39I MET* 3.7 6.7 - - - +
41I SER* 1.3 78.1 - - - +
43I LEU* 1.3 61.4 + - - +
45I LEU* 3.2 13.9 + - + +
46I TYR* 3.0 22.7 + - - +
330M LYS* 5.9 2.8 - - - +
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D LEU* 4.2 16.6 - - + +
444D PHE* 3.6 31.2 - - + -
440H LEU* 4.2 22.7 - - + +
443H LYS* 3.7 39.5 - - + +
444H PHE* 4.9 8.3 - - + -
447H LEU* 3.7 24.0 - - + -
39I MET 3.0 17.0 + - - +
40I ASP* 3.8 4.5 - - - +
42I ARG* 1.3 76.9 - - - +
44I ASP* 1.3 57.7 + - - +
46I TYR* 3.3 3.5 + - - +
47I LEU* 3.0 35.1 + - + +
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Residues in contact with ASP 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 3.0 53.7 - - - +
288A ASN 3.5 0.2 + - - -
289A SER* 2.8 31.4 + - - +
290A TRP* 4.3 4.3 - - + -
443H LYS* 4.0 16.0 + - - +
40I ASP* 2.9 18.4 + - - +
41I SER 3.8 2.5 - - - +
43I LEU* 1.3 73.0 - - - +
45I LEU* 1.3 60.5 + - - +
47I LEU* 3.4 7.2 + - - +
48I THR* 2.8 34.9 + - - -
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Residues in contact with LEU 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A TRP* 4.1 23.7 - - + -
41I SER 2.9 15.5 + - - +
42I ARG* 3.2 17.7 + - + +
44I ASP* 1.3 76.1 - - - +
46I TYR* 1.3 61.8 + - - +
48I THR* 3.9 1.0 - - - -
49I ARG* 3.0 25.9 + - + +
290M SER* 5.4 4.9 - - - +
294M SER* 3.9 30.3 - - - +
297M LEU* 3.7 25.0 - - + +
331M GLU* 5.8 8.1 - - + -
335M ILE* 4.4 14.6 - - + -
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Residues in contact with TYR 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D PHE* 3.5 31.6 - + + -
447D LEU* 3.3 44.4 - - + +
448D CYS* 5.1 9.9 - - - -
451D GLU* 3.0 22.1 + - - +
447H LEU* 3.7 22.9 - - + -
450H LEU* 5.0 12.1 - - + -
454H LEU* 4.9 4.3 - - - +
42I ARG 3.0 9.8 + - - +
43I LEU 3.5 7.6 - - - +
45I LEU* 1.3 76.3 - - - +
47I LEU* 1.3 65.5 + - + +
49I ARG* 3.3 35.0 + - - +
50I ARG* 3.0 27.7 + - + +
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 4.5 21.3 - - + -
443H LYS* 4.3 36.3 - - + +
446H LYS* 4.6 21.8 - - + -
447H LEU* 4.5 28.7 - - + +
450H LEU* 4.6 16.6 - - + -
43I LEU* 3.0 21.0 + - + +
44I ASP* 3.8 8.1 - - - +
46I TYR* 1.3 77.8 - - + +
48I THR* 1.3 56.8 + - - +
50I ARG* 3.3 3.6 + - - +
51I ARG* 2.9 39.8 + - + +
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Residues in contact with THR 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 2.7 30.2 + - + +
288A ASN* 4.2 9.0 - - - +
290A TRP* 4.0 18.3 - - + -
44I ASP* 2.8 18.2 + - - -
45I LEU 3.9 2.7 - - - -
47I LEU* 1.3 72.9 - - - +
49I ARG* 1.3 60.6 + - - +
51I ARG* 3.4 7.2 + - + +
52I LEU* 3.0 29.8 + - + +
297M LEU* 4.7 20.1 - - + +
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Residues in contact with ARG 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D GLU* 3.2 34.4 + - - -
45I LEU* 3.0 18.3 + - + +
46I TYR* 3.3 32.5 + - - +
48I THR* 1.3 77.8 - - - +
50I ARG* 1.3 65.2 + - - +
52I LEU* 3.3 3.3 + - - +
53I ASP* 2.9 44.0 + - - +
297M LEU* 4.2 20.7 - - + +
334M LEU* 3.4 34.9 - - - +
335M ILE* 4.0 27.6 - - + +
338M ALA* 4.7 13.8 - - + +
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Residues in contact with ARG 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D GLU* 3.8 26.2 + - - +
454D LEU* 4.9 4.6 - - - +
458D LYS* 5.0 7.7 - - - +
450H LEU* 3.7 32.5 - - + -
454H LEU* 3.8 38.7 - - + +
46I TYR* 3.0 24.5 + - + +
47I LEU* 3.9 3.8 - - - +
48I THR 3.3 0.4 - - - -
49I ARG* 1.3 82.8 - - - +
51I ARG* 1.3 60.8 + - + +
53I ASP* 3.0 48.4 + - - +
54I THR* 2.9 37.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 4.2 23.1 - - + -
446H LYS* 3.1 43.0 - - - +
47I LEU* 2.9 27.3 + - + +
48I THR* 3.7 8.7 - - + +
50I ARG* 1.3 77.5 - - - +
52I LEU* 1.3 60.2 + - - +
54I THR* 3.3 22.9 - - - +
55I SER* 5.9 0.2 - - - -
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Residues in contact with LEU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I THR* 3.0 18.5 + - + +
49I ARG* 3.7 5.6 - - - +
50I ARG 3.2 0.2 - - - -
51I ARG* 1.3 75.8 - - - +
53I ASP* 1.3 61.9 + - - +
54I THR 3.4 0.9 + - - -
55I SER* 3.9 5.5 + - - -
56I ILE* 3.3 24.0 - - + +
297M LEU* 4.1 20.2 - - + +
299M GLU* 3.5 35.4 - - + +
338M ALA* 3.4 37.9 - - + +
339M THR* 4.5 5.8 - - + +
342M ASN* 3.7 21.1 - - + +
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Residues in contact with ASP 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D LYS* 4.8 8.9 + - - -
49I ARG* 2.9 30.2 + - - +
50I ARG* 3.0 32.6 + - - +
52I LEU* 1.3 75.1 - - - +
54I THR* 1.3 62.9 + - - +
55I SER 3.2 2.7 - - - -
56I ILE* 3.2 38.6 + - - +
337M GLU 5.8 0.2 - - - -
338M ALA* 4.0 21.3 - - + +
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454H LEU* 6.1 1.3 - - - +
457H GLU* 5.4 3.3 - - - +
50I ARG* 2.9 22.2 + - - +
51I ARG* 3.3 26.7 - - - +
53I ASP* 1.3 78.1 - - - +
55I SER* 1.3 62.7 + - - +
56I ILE 3.4 0.2 - - - -
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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