Contacts of the helix formed by residues 3 - 34 (chain 0) in PDB entry 2X17
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 SER 3 (chain 0).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10 MET 3.8 1.8 + - - -
20 LEU* 1.3 75.1 - - - +
40 GLU* 1.3 65.8 + - - +
50 ARG* 4.1 3.3 + - - -
60 MET* 2.9 23.7 + - - +
70 LEU* 2.9 12.4 + - - +
1110 GLU* 2.6 34.2 + - - -
1130 ASP* 5.6 0.8 + - - -
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Residues in contact with GLU 4 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 LEU 3.8 1.0 + - - -
30 SER* 1.3 71.3 - - - +
50 ARG* 1.3 60.5 + - - +
70 LEU* 3.8 10.6 + - + +
80 LYS* 3.4 22.5 + - - +
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Residues in contact with ARG 5 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30 SER* 3.1 3.2 - - - +
40 GLU* 1.3 78.9 - - - +
60 MET* 1.3 56.7 + - - +
80 LYS* 3.5 9.0 + - + +
90 ALA* 3.1 26.9 + - - +
1070 LEU* 4.6 19.1 - - + +
1110 GLU* 3.8 20.2 - - - +
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Residues in contact with MET 6 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 LEU* 3.9 15.5 - - + -
30 SER* 2.9 25.0 + - - +
50 ARG* 1.3 77.5 - - - +
70 LEU* 1.3 59.3 + - - +
90 ALA* 3.1 4.9 + - - +
100 LEU* 2.9 32.8 + - + +
1040 LEU* 4.3 17.7 - - - +
1070 LEU* 3.9 20.9 - - + -
1080 ALA* 3.7 38.6 - - + +
1110 GLU* 3.9 10.3 + - - +
1130 ASP* 3.8 21.1 - - + +
1160 THR* 3.8 17.7 - - - +
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Residues in contact with LEU 7 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 LEU* 3.9 21.9 - - + +
30 SER 2.9 14.4 + - - +
40 GLU* 4.0 9.9 - - + +
60 MET* 1.3 76.4 - - - +
80 LYS* 1.3 54.1 + - - +
100 LEU* 3.6 3.2 + - - +
110 ASN* 2.7 48.1 + - - +
610 ILE* 3.8 16.2 - - + -
660 GLY* 3.9 9.2 - - - -
670 ARG* 3.6 42.6 - - + +
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Residues in contact with LYS 8 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40 GLU 3.4 17.4 + - - +
50 ARG* 3.6 8.5 - - + +
60 MET 3.2 0.2 - - - -
70 LEU* 1.3 79.7 - - - +
90 ALA* 1.3 57.7 + - - +
110 ASN* 3.3 6.3 + - - +
120 ASP* 2.9 58.3 + - - +
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Residues in contact with ALA 9 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50 ARG 3.1 15.8 + - - +
60 MET 3.1 6.8 + - - +
80 LYS* 1.3 76.1 - - - +
100 LEU* 1.3 60.3 + - - +
120 ASP* 3.7 8.7 + - - +
130 GLN* 3.3 22.2 + - - +
160 ARG* 4.6 2.3 + - - -
1040 LEU* 3.8 24.7 - - + +
1070 LEU* 3.9 18.4 - - + -
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Residues in contact with LEU 10 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 LEU* 3.8 38.6 - - + -
60 MET* 2.9 27.7 + - + +
70 LEU* 3.9 3.6 - - - +
90 ALA* 1.3 76.1 - - - +
110 ASN* 1.3 59.9 + - - +
130 GLN* 3.4 2.9 + - - +
140 LEU* 3.0 27.2 + - - +
570 PHE* 3.8 33.4 - - + -
600 TYR* 4.1 15.3 - - + -
610 ILE* 3.9 17.6 - - + +
1040 LEU* 4.3 9.9 - - + -
1160 THR* 4.0 18.6 - - + -
1190 PHE* 4.2 8.1 - - + -
1200 LEU* 5.1 1.3 - - + -
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Residues in contact with ASN 11 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70 LEU* 2.7 37.8 + - - +
80 LYS* 3.6 8.1 - - + +
100 LEU* 1.3 75.6 - - - +
120 ASP* 1.3 66.0 + - - +
140 LEU* 3.4 8.4 - - - +
150 ASN* 3.2 20.4 + - - +
610 ILE* 3.9 8.5 - - - +
670 ARG 3.3 18.2 + - - -
680 VAL* 3.3 12.1 - - - +
690 GLU* 3.0 41.4 + - + +
710 ASP* 4.7 5.1 - - - +
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Residues in contact with ASP 12 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80 LYS* 2.9 50.6 + - - +
90 ALA* 3.9 7.2 - - - +
100 LEU 3.3 0.2 - - - -
110 ASN* 1.3 76.9 - - - +
130 GLN* 1.3 58.7 + - - +
150 ASN* 3.3 10.2 + - - +
160 ARG* 3.0 49.7 + - - +
710 ASP* 3.8 15.8 - - - +
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Residues in contact with GLN 13 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90 ALA 3.3 8.1 + - - +
100 LEU 3.8 4.9 - - - +
110 ASN 3.3 0.4 - - - -
120 ASP* 1.3 76.3 - - - +
140 LEU* 1.3 60.2 + - - +
160 ARG* 3.1 21.9 + - - +
170 GLU* 2.9 54.1 + - - +
570 PHE* 3.4 28.9 - - + -
970 ILE* 3.9 15.2 - - - +
1000 SER* 2.9 32.3 + - - -
1010 ILE* 3.9 9.4 - - + +
1040 LEU* 3.7 22.0 - - + +
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Residues in contact with LEU 14 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100 LEU 3.0 12.0 + - - +
110 ASN* 3.4 12.8 - - - +
130 GLN* 1.3 75.9 - - - +
150 ASN* 1.3 62.4 + - - +
170 GLU* 3.5 4.6 + - - +
180 LEU* 3.2 41.6 + - + +
540 ALA* 3.5 20.8 - - + +
570 PHE* 4.0 12.0 - - + -
580 TYR* 3.6 31.9 - - + +
610 ILE* 3.9 17.9 - - + -
680 VAL* 4.0 15.9 - - + -
700 LEU* 3.9 17.5 - - + -
25I PHE* 4.4 7.0 - - + -
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Residues in contact with ASN 15 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110 ASN 3.2 9.4 + - - +
120 ASP* 3.4 12.8 - - - +
130 GLN 3.2 0.4 - - - -
140 LEU* 1.3 79.5 - - - +
160 ARG* 1.3 60.5 + - - +
180 LEU* 3.3 8.1 + - - +
190 TYR* 2.9 28.6 + - - +
700 LEU* 6.4 0.2 - - - -
710 ASP* 3.5 33.0 + - + +
720 GLU 3.0 29.2 + - - +
730 ILE* 4.2 7.1 - - - +
740 PRO* 4.8 7.1 - - - +
22I TYR* 3.9 7.5 + - - -
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Residues in contact with ARG 16 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90 ALA 4.6 2.2 + - - -
120 ASP* 3.0 30.2 + - - +
130 GLN* 3.1 53.9 + - - +
150 ASN* 1.3 77.7 - - - +
170 GLU* 1.3 59.2 + - - +
190 TYR* 3.4 8.3 + - - +
200 SER* 2.9 32.1 + - - -
960 PHE* 4.0 28.5 - - + -
970 ILE* 4.0 9.6 - - + +
1000 SER* 3.8 23.8 + - - -
1040 LEU* 5.6 1.2 - - - +
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Residues in contact with GLU 17 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130 GLN* 2.9 40.3 + - - +
140 LEU 3.9 4.5 - - - +
160 ARG* 1.3 75.3 - - - +
180 LEU* 1.3 58.0 + - - +
200 SER* 3.4 3.5 + - - -
210 ALA* 3.1 21.0 + - - +
500 GLU* 2.9 50.5 - - - +
530 HIS* 3.2 28.0 + - + +
540 ALA* 4.0 8.1 - - + +
570 PHE* 4.1 19.4 - - + -
970 ILE* 3.8 15.2 - - - +
1010 ILE* 4.5 2.3 - - - +
1230 PHE* 4.2 7.4 - - - -
1270 GLN* 4.6 2.6 + - - -
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Residues in contact with LEU 18 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140 LEU* 3.2 41.5 + - + +
150 ASN* 3.6 6.7 - - - +
160 ARG 3.3 0.2 - - - -
170 GLU* 1.3 74.8 - - - +
190 TYR* 1.3 62.9 + - - +
210 ALA* 3.4 7.2 + - + +
220 TYR* 3.1 20.3 + - - +
510 ILE* 5.0 20.6 - - + -
540 ALA* 3.8 15.9 - - + -
700 LEU* 4.0 2.9 - - + -
730 ILE* 4.5 16.5 - - + +
22I TYR* 3.6 38.1 - - + +
25I PHE* 4.4 10.1 - - + -
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Residues in contact with TYR 19 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150 ASN* 2.9 19.4 + - - +
160 ARG* 3.8 7.2 - - - +
170 GLU 3.4 0.2 - - - -
180 LEU* 1.3 73.6 - - - +
200 SER* 1.3 56.1 + - - +
220 TYR* 3.0 3.9 + - + +
230 LEU* 2.7 46.3 + - + +
730 ILE* 4.0 14.5 - - + +
740 PRO* 3.7 49.6 - - + -
750 LYS 4.5 2.2 + - - -
760 PRO* 4.0 13.5 - - + +
770 PRO* 3.8 23.4 - - - +
930 HIS* 3.7 30.5 - + - -
960 PHE* 6.1 1.1 - + - -
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Residues in contact with SER 20 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160 ARG 2.9 18.5 + - - -
170 GLU* 3.4 8.8 + - - -
190 TYR* 1.3 77.4 - - - +
210 ALA* 1.3 59.6 + - - +
230 LEU* 3.5 3.0 + - - +
240 TYR* 3.0 36.2 + - - -
500 GLU* 3.5 22.0 - - - -
930 HIS* 2.8 32.6 + - - -
940 GLU* 5.4 0.6 + - - -
970 ILE* 3.4 14.9 - - - +
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Residues in contact with ALA 21 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170 GLU 3.1 9.5 + - - +
180 LEU* 3.4 12.8 - - + +
190 TYR 3.2 0.2 - - - -
200 SER* 1.3 76.9 - - - +
220 TYR* 1.3 56.0 + - - +
250 PHE* 3.1 25.1 + - - +
470 ALA* 3.3 35.8 - - + +
500 GLU* 3.6 14.3 - - + +
510 ILE* 3.8 19.1 - - + +
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Residues in contact with TYR 22 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180 LEU 3.1 12.3 + - - +
190 TYR* 3.0 11.5 + + + +
210 ALA* 1.3 74.8 - - - +
230 LEU* 1.3 58.6 + - - +
250 PHE* 3.4 8.9 + + + +
260 ALA* 2.9 28.2 + - - +
730 ILE* 3.9 22.9 - - + -
740 PRO 4.0 4.5 - - - -
760 PRO* 3.6 31.3 - - + +
15I ASN* 3.6 10.9 + - - -
18I LEU* 3.6 29.2 - - + +
70I LEU* 3.5 30.6 - - + +
71I ASP 2.7 29.7 + - - -
72I GLU* 4.8 0.7 - - - -
73I ILE* 3.7 20.7 - - + +
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Residues in contact with LEU 23 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190 TYR* 2.7 31.8 + - + +
200 SER* 3.8 4.5 - - - +
220 TYR* 1.3 73.2 - - - +
240 TYR* 1.3 61.3 + - + +
260 ALA* 3.2 7.2 + - - +
270 MET* 2.8 46.7 + - + +
760 PRO* 4.2 5.5 - - + +
770 PRO* 3.8 29.6 - - + -
800 TRP* 4.0 19.7 - - + -
890 ALA 5.1 0.9 - - - +
930 HIS* 3.6 46.0 - - + +
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Residues in contact with TYR 24 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200 SER* 3.0 25.7 + - - +
230 LEU* 1.3 77.7 - - + +
250 PHE* 1.3 61.1 + - - +
270 MET* 3.3 12.7 + - + +
280 ALA* 2.8 23.6 + - - +
420 TRP* 5.9 0.7 - + - -
430 MET* 3.4 48.5 - - + +
460 GLN* 3.7 23.6 - - + -
470 ALA* 4.0 5.6 - - + -
500 GLU* 3.8 31.4 - - + -
900 ALA* 3.9 27.2 + - + +
930 HIS* 4.4 9.6 - + - -
940 GLU* 2.6 35.3 + - - +
1340 VAL* 4.8 5.8 - - + +
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Residues in contact with PHE 25 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210 ALA 3.1 18.3 + - - +
220 TYR* 3.6 16.2 - + - +
240 TYR* 1.3 75.9 - - - +
260 ALA* 1.3 59.4 + - - +
280 ALA* 3.5 8.6 - - + +
290 ALA* 3.2 23.9 + - - +
440 LYS* 4.6 10.8 - - + -
470 ALA* 4.1 8.4 - - + +
14I LEU* 4.3 10.3 - - + -
18I LEU* 4.4 13.5 - - + -
54I ALA* 5.0 3.8 - - + -
55I LEU* 3.8 29.8 - - + -
58I TYR* 3.7 38.5 - + + -
70I LEU* 3.6 37.2 - - + +
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Residues in contact with ALA 26 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220 TYR 2.9 14.5 + - - +
230 LEU 3.2 9.2 + - - +
250 PHE* 1.3 74.6 - - - +
270 MET* 1.3 58.9 + - - +
290 ALA* 3.4 7.8 + - - +
300 TYR* 3.1 24.6 + - - +
760 PRO* 3.8 24.0 - - + -
770 PRO 3.8 16.2 - - - +
780 LYS* 4.7 3.4 - - - +
800 TRP* 4.2 5.5 - - + -
67I ARG* 5.2 0.2 + - - -
70I LEU* 3.6 12.1 - - + +
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Residues in contact with MET 27 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230 LEU* 2.8 36.3 + - + +
240 TYR* 3.6 15.3 - - + +
250 PHE 3.3 0.2 - - - -
260 ALA* 1.3 73.8 - - - +
280 ALA* 1.3 61.5 + - - +
300 TYR* 3.3 2.6 + - - +
310 PHE* 3.0 40.6 + - + -
430 MET* 3.8 30.3 - - + -
800 TRP* 3.5 39.3 - - + -
860 ALA* 3.4 30.5 - - + +
890 ALA* 4.3 4.0 - - + -
900 ALA* 3.8 22.2 - - + +
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Residues in contact with ALA 28 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240 TYR 2.8 18.0 + - - +
250 PHE* 3.5 11.4 - - + +
270 MET* 1.3 76.3 - - - +
290 ALA* 1.3 56.7 + - - +
310 PHE 3.4 0.2 + - - -
320 GLU* 2.9 24.8 + - - +
400 ALA* 3.4 30.4 - - - +
430 MET* 3.8 9.6 - - + +
440 LYS* 3.8 17.5 - - + +
58I TYR* 2.9 14.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 29 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250 PHE 3.2 10.6 + - - +
260 ALA* 3.4 13.2 - - - +
270 MET 3.3 0.2 - - - -
280 ALA* 1.3 78.9 - - - +
300 TYR* 1.3 61.7 + - - +
320 GLU 3.3 0.5 + - - -
330 ASP* 3.1 15.9 + - - +
58I TYR* 3.4 19.7 + - + -
62I TYR* 2.6 30.7 + - - +
67I ARG* 4.1 3.1 - - - +
68I VAL* 4.1 21.1 - - + +
70I LEU* 5.6 2.0 - - + -
----------------------------------------------------------
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Residues in contact with TYR 30 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260 ALA 3.1 13.8 + - - +
270 MET* 3.3 10.3 + - - +
290 ALA* 1.3 77.3 - - - +
310 PHE* 1.3 74.7 + + - +
330 ASP* 3.5 5.9 + - - +
340 LEU* 3.5 48.5 + - + +
780 LYS 4.1 5.4 - - - +
790 GLU* 4.4 4.5 - - + -
800 TRP* 3.0 60.7 + + + -
810 GLU 3.9 1.9 + - - -
820 SER* 3.2 23.6 - - - -
830 PRO* 3.5 1.8 - - - +
860 ALA* 3.9 23.1 - - + -
67I ARG* 4.0 21.9 - - - +
----------------------------------------------------------
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Residues in contact with PHE 31 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270 MET* 3.0 29.5 + - + +
280 ALA 3.9 2.0 - - - +
300 TYR* 1.3 82.4 - + - +
320 GLU* 1.3 62.7 + - - +
340 LEU* 3.4 5.0 + - + +
350 GLY 3.4 3.1 + - - -
360 LEU* 2.9 46.3 + - + +
390 PHE* 3.5 24.9 - + + -
400 ALA* 3.8 17.5 - - - +
430 MET* 4.1 20.9 - - + -
830 PRO* 3.6 34.8 - - + -
860 ALA* 4.1 15.7 - - + -
870 PHE* 3.6 35.7 - + - -
----------------------------------------------------------
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Residues in contact with GLU 32 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280 ALA 2.9 7.4 + - - +
290 ALA 3.6 4.7 - - - +
300 TYR 3.3 0.2 - - - -
310 PHE* 1.3 75.2 - - - +
330 ASP* 1.3 60.0 + - - +
350 GLY* 3.0 18.6 + - - +
360 LEU 4.4 2.0 - - - +
370 GLU* 3.5 30.3 - - - +
400 ALA* 3.5 13.8 - - - +
410 ASN* 5.1 0.3 - - - +
440 LYS* 3.1 27.9 + - - -
58I TYR* 3.1 25.8 + - - +
62I TYR* 3.7 34.6 - - + +
----------------------------------------------------------
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Residues in contact with ASP 33 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290 ALA 3.1 9.0 + - - +
300 TYR* 3.6 10.9 - - - +
320 GLU* 1.3 73.9 - - - +
340 LEU* 1.3 60.1 + - - +
350 GLY* 3.0 9.0 + - - -
790 GLU* 5.5 1.2 - - - +
62I TYR* 3.7 8.2 - - + -
66I GLY 4.4 8.5 - - - +
67I ARG* 3.2 43.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300 TYR* 3.5 50.8 + - + +
310 PHE* 3.4 10.0 + - + +
320 GLU 3.3 0.6 - - - -
330 ASP* 1.3 79.1 - - + +
350 GLY* 1.3 60.9 + - - +
360 LEU* 3.3 18.9 + - + +
830 PRO* 4.2 19.1 - - + -
139G ASP* 6.2 0.2 - - - +
143G PHE* 5.2 11.9 - - + -
----------------------------------------------------------
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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