Contacts of the helix formed by residues 24 - 51 (chain A) in PDB entry 4NFT
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 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 1.3 78.3 - - - +
25A SER* 1.3 64.7 + - - +
26A LYS* 3.3 5.7 + - - +
27A ALA* 3.1 18.4 + - - +
28A MET* 3.1 18.4 + - - +
160A ARG* 3.8 33.1 - - - +
161A ILE 2.8 14.6 + - - -
162A THR* 4.3 6.3 - - - -
163A PRO* 3.6 14.2 - - - +
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 5.8 2.7 - - - -
23A ILE 3.7 1.0 + - - -
24A SER* 1.3 73.6 - - - +
26A LYS* 1.3 61.9 + - - +
28A MET* 3.5 8.3 + - - +
29A GLY* 3.3 17.5 + - - -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER* 3.1 5.9 + - - +
25A SER* 1.3 77.0 - - - +
27A ALA* 1.3 65.4 + - - +
29A GLY* 3.4 2.9 + - - -
30A ILE* 3.3 25.3 + - + +
163A PRO* 3.8 21.5 - - + -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.5 23.8 - - + -
24A SER* 3.1 9.6 + - - +
26A LYS* 1.3 77.3 - - - +
28A MET* 1.3 57.7 + - - +
30A ILE* 3.1 5.5 + - - +
31A MET* 2.9 30.3 + - - +
161A ILE* 3.6 16.6 - - + +
162A THR 3.7 11.2 - - - +
163A PRO* 3.7 4.6 - - - +
166A LEU* 3.5 22.5 - - + +
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Residues in contact with MET 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 3.4 44.9 - - - +
10A VAL* 3.7 35.0 - - + -
11A TYR* 3.4 43.5 - - + +
23A ILE* 3.8 17.2 - - + +
24A SER 3.1 12.4 + - - +
25A SER* 3.7 12.6 - - - +
26A LYS 3.2 0.4 - - - -
27A ALA* 1.3 77.0 - - - +
29A GLY* 1.3 56.6 + - - +
31A MET* 3.2 3.8 + - - +
32A ASN* 2.8 27.6 + - - +
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER 3.3 10.6 + - - -
26A LYS* 3.4 3.8 + - - -
27A ALA 3.3 0.6 - - - -
28A MET* 1.3 78.4 - - - +
30A ILE* 1.3 57.5 + - - +
32A ASN* 3.3 7.5 + - - +
33A SER* 3.0 31.5 + - - -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS 3.3 15.1 + - - +
27A ALA 3.1 8.4 + - - +
29A GLY* 1.3 77.5 - - - +
31A MET* 1.3 57.4 + - - +
33A SER* 3.3 7.7 + - - -
34A PHE* 3.0 28.1 + - + +
163A PRO* 3.9 32.5 - - + +
166A LEU* 3.6 20.6 - - + -
167A GLN* 6.2 0.7 - - + +
170A ILE* 5.8 5.6 - - + -
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.3 13.7 - - + -
23A ILE* 4.0 19.5 - - + -
27A ALA 2.9 16.3 + - - +
28A MET* 3.2 10.1 + - - +
30A ILE* 1.3 78.4 - - - +
32A ASN* 1.3 56.2 + - - +
34A PHE* 3.3 15.5 + - + +
35A VAL* 3.0 34.7 + - + +
142A THR* 3.8 36.6 - - + +
145A VAL* 3.7 28.3 - - + -
146A LEU* 4.0 17.7 - - + -
166A LEU* 4.0 15.3 - - + -
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 4.9 9.1 - - - +
4A GLU 3.2 20.1 + - - +
5A SER* 4.2 2.9 - - - +
6A TYR* 2.7 37.8 + - - +
7A SER* 3.5 16.2 + - - +
10A VAL* 5.4 2.7 - - - -
28A MET* 2.8 20.7 + - + +
29A GLY* 3.7 8.5 + - - +
30A ILE 3.3 0.2 - - - -
31A MET* 1.3 71.3 - - - +
33A SER* 1.3 64.0 + - - +
35A VAL* 3.6 5.8 + - - +
36A ASN* 3.0 33.9 + - - +
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 3.5 31.0 + - - +
29A GLY 3.0 14.7 + - - -
30A ILE* 3.5 9.9 - - - -
31A MET 3.2 0.2 - - - -
32A ASN* 1.3 75.2 - - - +
34A PHE* 1.3 59.4 + - - +
36A ASN 3.3 0.9 + - - -
37A ASP* 2.8 42.6 + - - -
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.0 15.1 + - + +
31A MET* 3.3 24.0 + - + +
33A SER* 1.3 75.5 - - - +
35A VAL* 1.3 75.8 + - + +
37A ASP* 4.0 4.2 - - - +
38A ILE* 3.0 35.2 + - + +
141A LEU* 4.1 35.2 - - + -
142A THR* 4.5 6.1 - - - -
145A VAL* 4.1 24.9 - - + -
170A ILE* 5.9 2.0 - - + -
176A LEU* 5.3 1.1 - - + -
179A LEU* 4.2 18.4 - - + -
180A ILE* 3.6 34.5 - - + -
183A THR* 6.5 0.7 - - + -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.6 30.5 - - + -
10A VAL* 4.6 10.8 - - + -
31A MET* 3.0 19.4 + - + +
32A ASN* 3.9 5.8 - - - +
33A SER 3.4 0.2 - - - -
34A PHE* 1.3 82.8 - - + +
36A ASN* 1.3 62.6 + - - +
38A ILE* 4.2 1.2 - - - +
39A PHE* 3.1 23.4 + - - +
107A PHE* 3.9 23.1 - - + -
138A LEU* 4.0 17.5 - - + +
142A THR* 3.6 24.5 - - + +
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Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 25.4 - - + +
3A LYS* 3.5 26.8 - - + +
4A GLU* 2.9 45.0 + - - +
6A TYR* 3.9 11.8 - - - -
32A ASN* 3.0 28.8 + - - +
33A SER 3.7 3.8 - - - +
35A VAL* 1.3 77.6 - - - +
37A ASP* 1.3 58.9 + - - +
39A PHE* 3.4 4.0 + - - +
40A GLU* 2.9 24.9 + - - +
115A HIS* 3.7 10.6 - - - -
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.9 0.5 - - - +
3A LYS* 2.7 24.9 + - - -
33A SER* 2.8 25.9 + - - +
34A PHE* 4.0 4.6 - - - +
36A ASN* 1.3 75.1 - - - +
38A ILE* 1.3 66.1 + - - +
40A GLU* 3.4 17.3 + - - +
41A ARG* 3.3 27.0 + - - +
183A THR* 3.6 23.2 - - + +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.0 24.6 + - + +
35A VAL* 4.2 3.8 - - - +
37A ASP* 1.3 77.5 - - - +
39A PHE* 1.3 61.0 + - - +
41A ARG* 3.0 12.4 + - + +
42A ILE* 2.9 41.1 + - + +
70A LEU* 5.1 3.8 - - + -
71A LEU* 4.0 16.2 - - + -
138A LEU* 3.8 21.5 - - + -
141A LEU* 3.9 20.2 - - + -
179A LEU* 3.8 33.2 - - + -
183A THR* 4.3 11.6 - - + +
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.3 0.2 - - - -
6A TYR* 4.8 4.5 - + + -
35A VAL* 3.1 18.2 + - + +
36A ASN* 3.8 4.3 - - - +
38A ILE* 1.3 81.2 - - - +
40A GLU* 1.3 61.0 + - - +
42A ILE* 4.4 9.6 - - + +
43A ALA* 2.8 45.1 + - + +
63A ILE* 6.1 0.2 - - + -
112A ILE* 4.2 12.1 - - + -
115A HIS* 3.3 53.6 - + + -
116A LEU* 3.7 33.7 - - + -
134A SER* 4.1 20.0 - - - -
138A LEU* 3.6 32.1 - - + -
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 53.4 + - + +
36A ASN 2.9 16.9 + - - +
37A ASP* 3.6 19.9 - - - +
38A ILE 3.3 0.2 - - - -
39A PHE* 1.3 76.9 - - - +
41A ARG* 1.3 60.1 + - + +
43A ALA* 4.2 2.4 - - - +
44A GLY* 2.9 25.8 + - - -
119A ARG* 4.6 9.1 + - - +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 3.3 6.9 + - - +
38A ILE* 3.0 13.3 + - + +
40A GLU* 1.3 80.1 - - + +
42A ILE* 1.3 64.1 + - - +
44A GLY* 3.8 1.0 - - - -
45A GLU* 3.0 19.9 + - - +
70A LEU* 3.4 49.6 + - + +
179A LEU* 4.3 6.9 + - - +
182A ALA* 3.6 32.5 + - - +
183A THR* 2.6 61.4 + - - +
185A ALA 5.2 4.0 + - - -
186A GLY* 5.7 4.7 - - - -
52B TYR* 4.9 8.2 + - - -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 2.9 42.3 + - + +
39A PHE* 4.0 13.7 - - + +
41A ARG* 1.3 74.7 - - - +
43A ALA* 1.3 59.9 + - - +
46A ALA* 2.8 30.8 + - - +
63A ILE* 4.0 29.8 - - + -
66A ALA* 3.6 11.3 - - + +
67A VAL* 3.8 24.2 - - + -
70A LEU* 3.8 19.3 - - + -
71A LEU* 5.3 2.7 - - + -
134A SER* 5.5 0.9 - - - +
137A ILE* 4.1 16.8 - - + -
138A LEU* 5.2 3.8 - - + -
141A LEU* 5.2 1.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 2.8 28.3 + - + +
40A GLU 4.2 1.8 - - - +
42A ILE* 1.3 75.7 - - - +
44A GLY* 1.3 62.7 + - - +
46A ALA* 3.7 6.5 - - - +
47A SER* 2.8 33.5 + - - -
58A ILE* 5.1 1.6 - - - +
63A ILE* 5.5 0.2 - - - -
116A LEU* 4.1 21.5 - - + -
119A ARG* 4.0 27.9 - - + +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU 2.9 20.3 + - - -
41A ARG* 3.8 1.3 - - - -
42A ILE 3.3 0.2 - - - -
43A ALA* 1.3 78.2 - - - +
45A GLU* 1.3 60.5 + - - +
47A SER* 3.4 10.1 + - - -
48A ARG* 3.4 14.7 + - - +
119A ARG* 5.3 3.9 - - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG 3.0 16.3 + - - +
44A GLY* 1.3 72.4 - - - +
46A ALA* 1.3 67.9 + - - +
48A ARG* 3.4 36.6 + - - +
49A LEU* 3.2 55.4 + - + +
66A ALA* 3.9 20.0 - - + -
69A LEU* 4.0 14.9 - - + +
70A LEU* 4.2 4.9 - - + -
49B LEU* 4.4 0.2 - - - +
52B TYR* 2.5 43.7 + - + +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE 2.8 22.6 + - - +
43A ALA* 3.7 5.4 - - - +
45A GLU* 1.3 73.2 - - - +
47A SER* 1.3 61.7 + - - +
49A LEU* 3.5 3.7 + - - +
50A ALA* 3.3 21.5 + - - +
58A ILE* 3.9 13.6 - - + +
62A GLU* 3.9 25.0 - - - +
63A ILE* 3.6 30.7 - - + -
66A ALA* 4.0 0.6 - - + +
----------------------------------------------------------
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 2.8 17.2 + - - -
44A GLY* 3.8 6.1 - - - -
46A ALA* 1.3 79.1 - - - +
48A ARG* 1.3 61.3 + - - +
50A ALA* 3.4 15.1 + - - +
51A HIS* 4.0 4.7 + - - +
58A ILE* 4.0 17.8 - - - +
119A ARG 3.5 23.8 + - - -
120A THR* 3.9 10.0 + - - -
121A THR* 4.0 16.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.4 8.5 + - - +
45A GLU* 3.4 40.6 + - - +
47A SER* 1.3 75.9 - - - +
49A LEU* 1.3 70.4 + - - +
50A ALA 3.4 0.2 + - - -
51A HIS* 2.8 38.2 + - - +
52A TYR* 4.1 7.3 - - - -
45B GLU* 2.9 36.8 + - - -
48B ARG* 2.9 63.3 + - - +
49B LEU* 4.0 8.3 - - - +
51B HIS* 5.7 0.2 - - - -
52B TYR* 4.7 2.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 3.2 45.3 + - + +
46A ALA* 3.9 4.3 - - - +
48A ARG* 1.3 85.9 - - - +
50A ALA* 1.3 63.5 + - - +
52A TYR* 3.2 24.7 + - + +
53A ASN 4.2 1.4 + - - -
62A GLU* 3.8 33.6 - - + +
65A THR* 3.7 29.6 - - + -
66A ALA 4.1 1.8 - - - +
69A LEU* 4.6 0.7 - - + -
45B GLU* 4.5 1.8 - - - +
49B LEU* 4.9 3.6 - - + -
69B LEU* 3.8 37.8 - - + +
----------------------------------------------------------
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.3 12.5 + - - +
47A SER 3.5 12.6 - - - +
48A ARG 3.2 0.6 - - - -
49A LEU* 1.3 73.5 - - - +
51A HIS* 1.3 60.7 + - - +
52A TYR 3.0 5.8 - - - -
53A ASN* 3.0 31.3 + - - +
56A SER* 3.3 15.6 - - - +
57A THR 3.8 4.7 - - - +
58A ILE* 3.8 32.5 - - + +
62A GLU* 4.1 3.4 - - + -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 4.0 4.4 + - - +
48A ARG* 2.8 30.4 + - + +
49A LEU 3.3 0.8 - - - -
50A ALA* 1.3 78.0 - - - +
52A TYR* 1.3 97.1 + + - +
53A ASN 3.2 7.4 + - - +
56A SER* 4.6 11.6 - - - +
----------------------------------------------------------
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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