Contacts of the helix formed by residues 2 - 35 (chain F) in PDB entry 5NC5
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 LEU 2 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 1.3 91.9 - - + +
3F GLU* 1.3 58.9 + - - +
5F LEU* 2.9 28.8 - - + +
6F LYS* 2.8 26.4 + - - +
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Residues in contact with GLU 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C HIS* 6.1 0.5 - - - -
339C GLU* 4.2 7.1 - - - +
342C LYS* 3.3 32.8 - - - +
1F MET 3.3 5.8 - - - +
2F LEU* 1.3 76.1 - - - +
4F LEU* 1.3 62.7 + - + +
6F LYS* 3.0 14.9 + - + +
7F SER* 2.9 26.4 + - - -
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Residues in contact with LEU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LYS* 3.6 42.8 - - + +
345C VAL* 4.4 23.6 - - + -
346C GLU* 4.7 11.9 - - + -
349C ILE* 4.9 11.4 - - + -
1F MET* 4.3 9.0 + - - +
3F GLU* 1.3 75.5 - - + +
5F LEU* 1.3 53.1 + - - +
7F SER* 2.9 6.8 + - - +
8F LEU* 2.4 44.8 + - + +
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Residues in contact with LEU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET 3.3 15.5 + - - +
2F LEU* 2.9 40.4 - - + +
3F GLU 3.2 0.2 - - - -
4F LEU* 1.3 79.4 - - - +
6F LYS* 1.3 68.8 + - + +
8F LEU* 3.5 22.4 + - + +
9F VAL* 3.6 21.9 - - + +
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Residues in contact with LYS 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU 2.8 17.1 + - - +
3F GLU* 3.0 19.9 + - + +
5F LEU* 1.3 79.5 - - + +
7F SER* 1.4 62.7 + - - +
9F VAL* 3.3 20.0 - - - +
10F PHE* 4.4 9.3 + - - +
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Residues in contact with SER 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LYS* 3.9 18.0 + - - -
346C GLU* 3.9 20.6 + - - +
3F GLU 2.9 12.3 + - - -
4F LEU* 2.9 20.6 + - - +
6F LYS* 1.4 79.9 - - - +
8F LEU* 1.3 70.3 + - - +
9F VAL 3.2 0.4 - - - -
10F PHE* 2.8 17.7 + - - +
11F ALA* 2.9 13.1 + - - +
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Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLU* 5.5 0.7 - - - -
349C ILE* 6.5 0.7 - - + -
4F LEU* 2.4 34.3 + - + +
5F LEU* 3.6 18.6 - - + +
6F LYS 3.5 0.4 - - - -
7F SER* 1.3 67.8 + - - +
9F VAL* 1.3 73.8 + - + +
11F ALA* 3.0 6.7 + - - +
12F VAL* 2.9 50.9 + - + +
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 3.6 14.8 - - + +
6F LYS* 3.3 20.0 - - - +
8F LEU* 1.3 87.8 - - + +
10F PHE* 1.3 77.2 + - + +
12F VAL* 4.0 1.2 - - - +
13F ILE* 2.9 35.9 + - + +
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Residues in contact with PHE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987C MET* 5.5 0.2 - - + -
991C ILE* 4.5 25.1 - - + -
6F LYS* 4.9 7.0 - - - +
7F SER* 2.8 13.2 + - - +
9F VAL* 1.3 88.1 - - + +
11F ALA* 1.3 63.9 + - - +
13F ILE* 3.4 9.7 + - + +
14F MET* 3.0 56.9 + - + +
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Residues in contact with ALA 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLU* 3.7 23.6 - - + +
350C LEU* 3.7 26.8 - - + +
987C MET* 5.0 4.0 - - + -
991C ILE* 6.3 2.2 - - + -
7F SER 2.9 8.5 + - - +
8F LEU* 3.0 9.4 + - - +
10F PHE* 1.3 79.2 - - - +
12F VAL* 1.3 56.8 + - + +
14F MET* 2.7 29.4 + - - +
15F VAL* 3.1 12.3 + - - +
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ILE* 5.7 3.1 - - + -
350C LEU* 5.4 1.8 - - + -
353C LEU* 3.7 35.4 - - + -
8F LEU* 2.9 41.9 + - + +
9F VAL* 4.2 2.5 - - - +
11F ALA* 1.3 74.4 - - + +
13F ILE* 1.3 61.6 + - + +
15F VAL* 3.4 10.1 + - + +
16F PRO* 2.8 26.4 - - + +
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Residues in contact with ILE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 2.9 38.1 + - + +
10F PHE* 3.5 10.3 - - + +
12F VAL* 1.3 83.0 - - + +
14F MET* 1.3 64.1 + - + +
16F PRO* 3.0 14.5 - - - +
17F VAL* 2.9 33.9 - - + +
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Residues in contact with MET 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987C MET* 3.4 43.7 - - + +
991C ILE* 5.1 8.1 - - + -
10F PHE* 3.0 48.7 + - + +
11F ALA 2.7 17.2 + - - +
13F ILE* 1.3 74.4 - - + +
15F VAL* 1.3 51.5 + - - +
17F VAL* 2.8 17.9 + - - -
18F VAL* 2.6 45.1 + - - +
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Residues in contact with VAL 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LEU* 3.6 23.8 - - + +
353C LEU* 4.0 29.6 - - + -
354C VAL* 3.8 26.4 - - + +
357C LEU* 4.2 18.5 - - + +
980C LEU* 6.0 0.2 - - - +
984C LEU* 3.8 12.9 - - + +
11F ALA 3.1 14.2 + - - +
12F VAL* 3.6 10.1 - - - +
13F ILE 3.2 0.6 - - - -
14F MET* 1.3 76.1 - - - +
16F PRO* 1.3 70.4 - - + +
18F VAL* 3.9 2.0 - - - +
19F MET* 3.5 18.2 + - - +
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Residues in contact with PRO 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 6.0 0.7 - - + -
357C LEU* 5.0 11.9 - - + -
512C PHE* 6.5 1.1 - - + -
12F VAL* 2.8 29.2 - - + +
13F ILE* 3.0 12.1 - - - +
15F VAL* 1.3 77.9 - - + +
17F VAL* 1.3 68.3 + - + +
19F MET* 3.1 8.2 + - + +
20F ALA* 2.9 22.8 + - - +
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Residues in contact with VAL 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ILE* 2.9 34.3 - - + +
14F MET* 2.8 23.4 + - - +
16F PRO* 1.3 75.5 - - + +
18F VAL* 1.3 58.6 + - - +
20F ALA* 3.2 8.2 - - + +
21F ILE* 3.0 45.5 + - + +
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Residues in contact with VAL 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980C LEU* 3.5 20.6 - - + -
983C ILE* 4.3 16.4 - - + -
984C LEU* 3.3 31.4 - - + -
987C MET* 5.1 7.2 - - - -
14F MET* 2.6 48.7 + - + +
15F VAL 3.9 2.2 - - - +
17F VAL* 1.3 70.1 - - - +
19F MET* 1.3 69.9 + - - +
20F ALA 3.1 1.1 - - - -
21F ILE* 3.2 9.4 + - + +
22F ILE* 3.2 25.0 + - + +
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Residues in contact with MET 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C VAL* 5.3 3.4 - - + +
357C LEU* 3.1 37.5 - - + -
358C PHE* 3.3 40.2 - - + -
516C PHE* 3.8 17.0 - - + -
519C MET* 5.8 0.4 - - + -
976C LEU* 6.5 0.2 - - - -
980C LEU* 4.1 22.8 - - + +
15F VAL 3.5 12.3 + - - +
16F PRO* 3.1 12.3 + - + +
18F VAL* 1.3 80.9 - - - +
20F ALA* 1.3 62.5 + - - +
22F ILE* 3.3 4.4 - - - +
23F LEU* 3.0 46.1 + - + +
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Residues in contact with ALA 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F PRO 2.9 12.0 + - - +
17F VAL* 3.2 14.1 - - + +
18F VAL 3.1 0.2 - - - -
19F MET* 1.3 75.5 - - - +
21F ILE* 1.3 60.9 + - + +
23F LEU* 4.0 5.6 - - - +
24F GLY* 2.8 30.0 + - - -
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Residues in contact with ILE 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 3.0 29.5 + - + +
18F VAL* 3.2 9.8 + - + +
20F ALA* 1.3 76.9 - - + +
22F ILE* 1.3 60.2 + - + +
24F GLY* 3.9 1.4 - - - -
25F LEU* 3.0 42.8 + - + +
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Residues in contact with ILE 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976C LEU* 4.0 22.4 - - + -
980C LEU* 3.5 34.1 - - + -
983C ILE* 4.4 12.3 - - + -
1012C VAL* 4.2 25.4 - - + -
1015C THR* 5.9 4.7 - - + -
1016C VAL* 4.5 12.1 - - + +
18F VAL* 3.2 14.8 + - + +
19F MET* 3.3 12.8 - - - +
21F ILE* 1.3 78.5 - - + +
23F LEU* 1.4 74.8 + - + +
25F LEU* 3.1 21.0 + - + +
26F ILE* 3.1 21.1 + - + +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C PHE* 4.6 3.4 - - + -
519C MET* 4.0 27.6 - - + -
520C PHE* 4.2 15.5 - - + -
523C SER* 4.5 18.4 + - - +
972C LEU* 6.2 0.4 - - + -
976C LEU* 4.0 17.7 - - + -
19F MET* 3.0 47.5 + - + +
20F ALA* 4.0 4.5 - - - +
22F ILE* 1.4 75.6 - - + +
24F GLY* 1.3 67.5 + - - +
26F ILE* 3.0 25.8 - - + +
27F TYR* 3.0 24.2 + - - +
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Residues in contact with GLY 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ALA 2.8 17.4 + - - -
21F ILE* 3.9 1.8 - - - -
23F LEU* 1.3 76.9 - - - +
25F LEU* 1.3 61.6 + - - +
27F TYR* 3.4 6.8 + - - +
28F GLY* 2.9 22.2 + - - -
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012C VAL* 5.3 11.0 - - + -
1016C VAL* 4.2 23.3 - - + -
21F ILE* 3.0 42.0 + - + +
22F ILE* 3.1 15.0 + - + +
24F GLY* 1.3 78.6 - - - +
26F ILE* 1.3 57.3 + - - +
28F GLY* 3.8 0.8 - - - -
29F LEU* 2.9 38.8 + - + +
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Residues in contact with ILE 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C SER* 5.1 9.6 - - - +
527C TYR* 5.2 12.6 - - + -
972C LEU* 5.0 9.9 - - + -
976C LEU* 4.3 17.7 - - + -
1015C THR* 5.9 0.2 - - + -
1016C VAL* 3.9 20.4 - - + +
1019C ILE* 3.5 32.3 - - + -
1020C PHE* 3.8 12.2 - - + -
22F ILE* 3.1 11.5 + - + +
23F LEU* 3.0 42.0 - - + +
25F LEU* 1.3 72.2 - - - +
27F TYR* 1.3 56.4 + - + +
29F LEU* 3.6 5.1 - - - -
30F GLY* 2.7 32.9 + - - -
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Residues in contact with TYR 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LYS* 6.5 0.7 - - + -
523C SER* 5.2 14.8 - - - +
526C HIS* 3.2 41.5 + + + -
23F LEU 3.0 16.8 + - - +
24F GLY* 3.7 7.2 - - - +
26F ILE* 1.3 78.3 - - + +
28F GLY* 1.3 64.9 + - - +
30F GLY 3.4 0.2 + - - -
31F GLU* 3.2 31.6 + - - +
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Residues in contact with GLY 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLY 2.9 16.5 + - - -
25F LEU* 4.0 0.7 - - - -
27F TYR* 1.3 80.7 - - - +
29F LEU* 1.3 62.9 + - - +
30F GLY 3.1 0.2 - - - -
31F GLU* 3.2 7.3 + - - +
32F VAL* 2.8 29.7 + - - +
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Residues in contact with LEU 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016C VAL* 3.4 30.7 - - + +
1017C LEU* 4.2 13.0 - - + -
1020C PHE* 3.7 22.4 - - + -
25F LEU* 2.9 23.9 + - + +
26F ILE 3.9 0.2 - - - +
28F GLY* 1.3 75.8 - - - +
30F GLY* 1.3 61.0 + - - +
32F VAL* 3.7 13.5 - - + -
33F PHE* 3.1 62.8 + - + +
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Residues in contact with GLY 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C HIS* 3.8 7.4 - - - -
527C TYR* 5.9 1.1 - - - -
530C SER* 3.1 24.0 + - - -
1020C PHE* 4.1 4.9 - - - -
26F ILE 2.7 17.1 + - - -
27F TYR 3.4 3.1 + - - -
28F GLY 3.1 0.2 - - - -
29F LEU* 1.3 77.3 - - - +
31F GLU* 1.3 56.5 + - - +
32F VAL 3.3 0.3 + - - -
33F PHE 3.3 0.7 + - - -
34F ASN* 2.7 37.0 + - - -
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C HIS* 2.9 34.0 + - + -
27F TYR* 3.2 36.1 + - - +
28F GLY* 3.2 10.2 + - - +
30F GLY* 1.3 76.3 - - - +
32F VAL* 1.3 59.1 + - + +
34F ASN* 3.8 7.7 + - - +
35F ILE* 2.8 40.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLY 2.8 28.4 + - - +
29F LEU* 3.8 19.7 - - + +
30F GLY 3.2 0.2 - - - -
31F GLU* 1.3 78.3 - - + +
33F PHE* 1.3 70.4 + - + +
35F ILE* 3.5 12.5 + - + +
36F PHE* 3.2 22.7 + - + +
----------------------------------------------------------
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Residues in contact with PHE 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C SER* 4.0 5.2 - - - +
534C ILE* 3.2 28.9 - - + -
541C TYR* 3.0 18.0 + + - +
544C LEU* 4.1 17.9 - - + -
1017C LEU* 5.9 3.6 - - + -
1020C PHE* 3.5 39.9 - + + -
1021C PHE* 3.9 22.2 - + - -
29F LEU* 3.1 45.4 + - + +
30F GLY 3.3 3.1 + - - +
32F VAL* 1.3 83.0 - - + +
34F ASN* 1.3 57.6 + - - +
36F PHE* 3.6 5.2 - + + -
37F SER* 2.7 36.7 + - - -
----------------------------------------------------------
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Residues in contact with ASN 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C HIS* 4.0 12.1 + - - -
529C ASP* 6.3 0.2 - - - +
530C SER* 3.1 32.2 + - - +
533C GLY* 5.2 2.8 - - - -
30F GLY 2.7 21.9 + - - +
31F GLU* 3.9 10.3 - - - +
32F VAL 3.3 0.2 - - - -
33F PHE* 1.3 74.8 - - - +
35F ILE* 1.3 56.0 + - + +
36F PHE 2.7 14.4 + - - -
37F SER* 3.1 20.7 + - - -
----------------------------------------------------------
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Residues in contact with ILE 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F GLU* 2.8 32.9 + - + +
32F VAL* 3.6 13.0 - - + +
33F PHE 3.4 0.2 - - - -
34F ASN* 1.3 75.2 - - + +
36F PHE* 1.4 55.8 + - - +
----------------------------------------------------------
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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