Contacts of the helix formed by residues 46 - 73 (chain K) in PDB entry 2F8N
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 46 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288D SER* 3.8 14.0 - - - +
1315D VAL* 4.0 21.5 - - - +
1318D TYR* 5.3 2.0 - - - -
256J T 4.7 0.6 + - - -
44K GLY* 2.7 7.7 + - - -
45K ALA* 1.3 77.0 - - - +
47K ALA* 1.3 62.4 + - - -
48K PRO* 3.4 0.9 - - - -
49K VAL* 2.9 9.2 + - - +
50K TYR* 2.9 22.9 + - - +
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Residues in contact with ALA 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286D ILE* 3.8 21.3 - - + +
1287D THR 3.8 9.0 - - - -
1288D SER* 3.6 16.6 - - - +
1291D VAL* 3.9 14.0 - - + +
34K LEU* 4.2 6.5 - - + -
43K VAL* 4.0 8.3 - - + -
44K GLY 3.0 8.7 + - - +
46K GLY* 1.3 74.5 - - - +
48K PRO* 1.3 64.2 - - + +
50K TYR* 3.4 1.8 + - - +
51K LEU* 2.9 31.5 + - - +
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Residues in contact with PRO 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ARG* 5.0 1.1 - - - +
27K VAL* 3.6 14.3 - - + +
30K VAL* 3.7 11.5 - - + +
31K HIS* 3.4 55.0 - - + +
34K LEU* 4.0 4.5 - - + -
43K VAL* 4.1 7.6 - - + -
44K GLY 3.1 13.7 - - - +
45K ALA 3.9 9.0 - - - +
46K GLY 3.5 2.0 - - - -
47K ALA* 1.3 92.8 - - + +
49K VAL* 1.3 60.2 + - - +
52K ALA* 2.9 31.6 + - - +
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Residues in contact with VAL 49 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1314D ALA* 3.8 22.0 - - + +
1315D VAL* 3.9 6.1 - - - +
1318D TYR* 3.9 24.9 - - + -
17K ARG* 5.5 0.2 - - - -
21K ALA* 3.4 30.7 - - + -
23K LEU* 3.8 1.6 - - - +
27K VAL* 3.6 24.5 - - + -
45K ALA 3.5 21.3 - - - +
46K GLY* 2.9 8.0 + - - +
48K PRO* 1.3 75.1 - - - +
50K TYR* 1.3 60.2 + - - +
52K ALA* 3.5 1.7 - - - +
53K ALA* 2.8 30.3 + - - +
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Residues in contact with TYR 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288D SER* 4.0 24.2 - - - -
1291D VAL* 3.4 20.6 - - + -
1292D GLN* 2.7 60.0 + - + +
1295D VAL* 4.2 5.6 - - + -
1308D VAL* 3.1 18.8 - - - +
1311D GLY* 3.6 37.0 - - - -
1312D THR* 3.6 5.4 - - - -
1315D VAL* 4.6 7.5 - - + +
46K GLY 2.9 14.7 + - - +
47K ALA 3.6 3.8 - - - +
49K VAL* 1.3 76.8 - - - +
51K LEU* 1.3 64.8 + - - +
53K ALA* 2.9 9.9 + - - +
54K VAL* 2.8 38.2 + - + +
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Residues in contact with LEU 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267D PHE* 4.1 28.3 - - + +
1270D ILE* 3.9 39.7 - - + -
1271D ALA* 4.8 4.5 - - + -
1291D VAL* 4.0 15.2 - - + +
30K VAL* 4.0 21.5 - - + -
34K LEU* 4.4 17.7 - - + -
47K ALA 2.9 19.7 + - - +
50K TYR* 1.3 70.9 - - - +
52K ALA* 1.3 67.1 + - - +
54K VAL* 2.8 15.9 + - + +
55K LEU* 2.8 37.5 + - + +
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Residues in contact with ALA 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K LEU* 4.3 3.6 - - + -
25K PHE* 3.8 14.2 - - + +
27K VAL* 4.0 22.4 - - + +
30K VAL* 4.0 24.0 - - + +
48K PRO 2.9 23.3 + - - +
49K VAL 3.5 3.4 - - - +
51K LEU* 1.3 76.6 - - - +
53K ALA* 1.3 64.3 + - - +
55K LEU* 3.4 5.7 + - - +
56K GLU* 3.0 24.1 + - - +
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Residues in contact with ALA 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310D GLU* 3.9 17.3 - - + +
1311D GLY* 4.1 4.5 - - - -
1314D ALA* 3.6 25.4 - - + -
23K LEU* 3.9 18.6 - - + +
49K VAL 2.8 13.8 + - - +
50K TYR 3.0 10.1 - - - +
52K ALA* 1.3 77.2 - - - +
54K VAL* 1.3 57.8 + - - +
56K GLU* 3.3 3.7 + - - +
57K TYR* 3.0 27.5 + - - +
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Residues in contact with VAL 54 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270D ILE* 4.3 15.5 - - + -
1295D VAL* 4.2 25.4 - - + -
1299D LEU* 4.5 0.7 - - + -
1307D ALA* 4.1 24.7 - - + +
1311D GLY* 4.6 1.3 - - - -
50K TYR* 2.8 44.7 + - + +
51K LEU* 2.8 13.5 + - - +
53K ALA* 1.3 67.0 - - - +
55K LEU* 1.3 67.9 + - - +
57K TYR* 2.9 17.5 + - + +
58K LEU* 2.9 31.4 + - + +
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Residues in contact with LEU 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234D TYR* 4.8 0.7 - - - +
1262D PHE* 5.0 2.0 - - + -
1263D VAL* 3.9 19.9 - - + +
1266D ILE* 3.7 38.4 - - + -
1267D PHE* 3.7 40.4 - - + +
1270D ILE* 4.7 1.1 - - + -
25K PHE* 4.1 14.4 - - + -
30K VAL* 4.8 10.8 - - + -
51K LEU* 2.8 37.0 + - + +
52K ALA 3.8 3.6 - - - +
54K VAL* 1.3 71.4 - - - +
56K GLU* 1.3 53.4 + - - +
58K LEU* 3.4 5.8 + - + +
59K THR* 2.6 39.4 + - - -
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Residues in contact with GLU 56 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241D VAL* 3.6 13.5 - - + +
1244D GLN* 5.0 2.9 - - - +
22K GLY 5.2 0.7 - - - +
23K LEU* 3.5 20.8 - - - +
24K GLN* 2.6 44.1 + - - +
25K PHE* 2.7 38.3 + - + +
52K ALA 3.0 10.1 + - - +
53K ALA 3.5 9.0 - - - +
55K LEU* 1.3 76.6 - - - +
57K TYR* 1.3 58.6 + - - +
59K THR* 3.4 2.1 + - - -
60K ALA* 2.9 28.3 + - + +
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Residues in contact with TYR 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303D LEU* 3.4 30.8 + - + +
1306D HIS* 2.8 35.1 + - + +
1307D ALA* 3.2 39.5 - - + -
1310D GLU* 3.8 29.2 - - + +
53K ALA 3.0 13.0 + - - +
54K VAL* 2.9 11.7 + - - +
56K GLU* 1.3 73.6 - - - +
58K LEU* 1.3 75.1 + - + +
60K ALA* 2.8 22.7 + - + +
61K GLU* 3.0 37.9 + - - -
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Residues in contact with LEU 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262D PHE* 3.8 21.8 - - + -
1266D ILE* 3.9 28.5 - - + -
1299D LEU* 3.9 32.1 - - + -
1303D LEU* 3.8 39.7 - - + -
54K VAL* 2.9 25.8 + - + +
55K LEU* 3.9 3.6 - - - +
57K TYR* 1.3 77.3 - - + +
59K THR* 1.3 63.2 + - - +
61K GLU* 3.3 6.7 + - - +
62K ILE* 3.2 26.3 + - - +
93K LEU* 4.8 4.5 - - + -
96K LEU* 4.4 8.3 - - + -
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Residues in contact with THR 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238D VAL* 4.1 16.4 - - + -
1241D VAL* 4.5 1.8 - - + -
1259D MET* 4.5 9.0 - - + -
1262D PHE* 4.1 8.5 - - - -
1263D VAL* 3.7 12.1 - - + +
25K PHE* 3.1 31.2 - - + -
55K LEU 2.6 25.6 + - - -
56K GLU 3.4 6.3 - - - +
57K TYR 3.0 0.2 - - - -
58K LEU* 1.3 78.0 - - - +
60K ALA* 1.3 64.4 - - - +
62K ILE* 3.3 2.3 + - - +
63K LEU* 2.9 48.7 + - + +
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Residues in contact with ALA 60 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241D VAL* 3.5 22.6 - - + +
1245D VAL* 3.7 12.2 - - + +
56K GLU* 2.9 12.6 + - + +
57K TYR* 2.8 21.4 + - + +
59K THR* 1.3 71.9 - - - +
61K GLU* 1.3 51.0 + - - +
63K LEU* 3.2 3.5 + - - +
64K GLU* 2.7 37.6 + - - +
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Residues in contact with GLU 61 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1303D LEU* 4.1 19.9 - - + +
1306D HIS* 5.3 1.0 + - - -
57K TYR* 3.0 39.3 + - + +
58K LEU* 3.4 13.2 - - - +
60K ALA* 1.3 73.2 - - - +
62K ILE* 1.3 67.0 + - + +
64K GLU* 3.0 23.7 + - - +
65K LEU* 3.1 25.8 + - + +
90K ASP* 5.8 0.7 - - - +
93K LEU* 4.5 15.5 - - + -
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Residues in contact with ILE 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259D MET* 3.7 13.9 - - + -
1262D PHE* 3.5 49.4 - - + -
58K LEU 3.2 8.3 + - - +
59K THR 3.9 1.6 - - - +
61K GLU* 1.3 80.0 - - - +
63K LEU* 1.3 53.9 + - - +
65K LEU* 3.3 2.8 + - - +
66K ALA* 2.8 33.5 + - + +
83K LEU* 3.5 27.8 - - + -
86K ALA* 4.5 1.7 - - + +
87K ILE* 4.6 16.8 - - + -
93K LEU* 3.7 28.9 - - + -
97K LEU* 4.2 13.2 - - + -
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Residues in contact with LEU 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238D VAL* 3.7 19.5 - - + +
1241D VAL* 3.6 18.8 - - + -
1242D LEU* 3.6 34.3 - - + +
1245D VAL* 4.0 17.1 - - + +
1251D ILE* 4.8 8.1 - - + -
1259D MET* 4.5 15.0 - - + -
59K THR* 2.9 41.7 + - + +
60K ALA 3.4 4.5 - - - +
62K ILE* 1.3 78.6 - - - +
64K GLU* 1.3 56.5 + - - +
66K ALA* 4.0 2.9 - - - +
67K GLY* 2.9 28.2 + - - -
78K ILE* 4.2 10.6 - - + +
83K LEU* 5.5 2.0 - - + -
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Residues in contact with GLU 64 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245D VAL* 3.9 33.4 - - + +
60K ALA 2.7 16.8 + - - +
61K GLU* 3.0 20.2 + - - +
63K LEU* 1.3 74.6 - - - +
65K LEU* 1.3 66.6 + - + +
67K GLY* 3.9 0.9 - - - -
68K ASN* 3.1 45.0 + - - +
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Residues in contact with LEU 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K GLU* 3.1 20.8 + - + +
62K ILE* 4.0 1.3 - - - +
64K GLU* 1.3 77.5 - - + +
66K ALA* 1.3 61.7 + - - +
68K ASN* 3.4 16.9 + - + +
69K ALA* 2.9 28.4 + - - +
86K ALA* 3.6 21.5 - - + +
90K ASP* 4.1 22.7 - - + -
93K LEU* 4.0 26.0 - - + -
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Residues in contact with ALA 66 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ILE 2.8 22.5 + - - +
63K LEU* 4.0 1.1 - - - +
65K LEU* 1.3 71.0 - - - +
67K GLY* 1.3 53.2 + - - +
69K ALA* 2.9 6.9 + - - +
70K ALA* 2.7 36.0 + - - +
78K ILE* 4.0 21.1 - - + -
82K HIS* 4.0 6.8 - - - +
83K LEU* 3.4 28.9 - - + -
86K ALA* 3.5 12.0 - - + +
----------------------------------------------------------
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Residues in contact with GLY 67 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242D LEU* 5.8 1.1 - - - -
1246D HIS* 5.7 7.0 - - - -
1249D THR* 4.7 9.4 - - - -
63K LEU 2.9 18.5 + - - -
64K GLU 3.9 1.1 - - - -
66K ALA* 1.3 75.8 - - - +
68K ASN* 1.3 65.3 + - - +
70K ALA* 2.9 5.5 + - - +
71K ARG* 2.9 27.3 + - - +
78K ILE* 3.6 17.6 - - - +
----------------------------------------------------------
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Residues in contact with ASN 68 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246D HIS* 5.8 3.3 - - - -
64K GLU* 3.1 36.6 + - - +
65K LEU* 3.5 21.2 - - - +
67K GLY* 1.3 76.3 - - - +
69K ALA* 1.3 54.1 + - - +
71K ARG* 2.9 14.4 + - - +
72K ASP* 2.6 46.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 69 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K LEU 2.9 14.3 + - - +
66K ALA* 3.2 12.6 - - - +
68K ASN* 1.3 75.0 - - - +
70K ALA* 1.3 62.5 + - - +
72K ASP* 3.3 14.1 + - - +
73K ASN* 3.1 22.5 + - - +
82K HIS* 3.9 24.6 - - + +
85K LEU* 4.6 16.9 - - + +
86K ALA* 4.7 3.1 - - - +
----------------------------------------------------------
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Residues in contact with ALA 70 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249D THR* 4.9 3.1 - - + -
66K ALA 2.7 14.6 + - - +
67K GLY* 3.2 9.2 - - - +
69K ALA* 1.3 71.5 - - - +
71K ARG* 1.3 59.0 + - + +
73K ASN* 2.9 19.8 + - - +
74K LYS 3.2 0.2 + - - -
75K LYS* 3.0 29.9 + - + +
77K ARG 4.6 0.2 - - - -
78K ILE* 4.0 18.4 - - + +
82K HIS* 3.5 33.3 - - + +
----------------------------------------------------------
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Residues in contact with ARG 71 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246D HIS* 2.5 50.2 + - - -
1249D THR* 4.2 13.2 - - + +
67K GLY 3.3 14.1 + - - +
68K ASN* 2.9 15.8 + - - +
70K ALA* 1.3 73.2 - - + +
72K ASP* 1.3 59.0 + - - +
74K LYS* 2.7 25.2 + - - +
75K LYS 3.7 14.8 - - - +
76K THR* 6.0 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K ASN* 2.6 35.0 + - - +
69K ALA* 3.4 13.5 + - - +
70K ALA 3.1 0.2 - - - -
71K ARG* 1.3 72.2 - - - +
73K ASN* 1.3 58.5 + - - +
74K LYS* 3.0 13.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 73 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K ALA 3.1 8.4 + - - +
70K ALA 2.9 10.1 + - - +
72K ASP* 1.3 77.1 - - - +
74K LYS* 1.3 73.3 + - - +
75K LYS* 3.2 31.2 - - + +
82K HIS* 4.2 11.8 + - + +
85K LEU* 6.0 4.1 - - + +
----------------------------------------------------------
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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