Contacts of the helix formed by residues 24 - 50 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP* 3.9 1.6 - - - -
23D ILE* 1.3 76.4 - - - +
25D SER* 1.3 60.3 + - - +
26D LYS* 3.5 4.6 + - - +
27D ALA* 3.2 21.5 + - - +
28D MET* 3.0 26.5 + - - +
160D ARG* 3.4 39.2 - - - +
161D ILE 3.0 14.6 + - - -
162D THR* 4.3 6.7 - - - -
163D PRO* 3.7 10.2 - - - +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS* 6.0 0.9 - - - +
19C PRO* 3.9 23.9 + - - +
20C ASP* 2.9 31.7 + - - +
23D ILE 3.8 0.6 + - - -
24D SER* 1.3 73.5 - - - +
26D LYS* 1.3 62.3 + - - +
28D MET* 3.5 7.0 + - - +
29D GLY* 3.2 17.7 + - - -
8E VAL* 5.2 0.3 - - - +
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Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP* 5.5 0.4 - - - -
24D SER* 3.3 4.3 + - - +
25D SER* 1.3 76.6 - - - +
27D ALA* 1.3 64.8 + - - +
29D GLY* 3.1 3.1 + - - -
30D ILE* 3.0 25.3 + - + +
163D PRO* 4.1 15.9 - - + -
8E VAL* 3.7 27.3 - - + +
12E TYR* 2.8 48.7 + - + +
15E LYS* 5.4 0.4 - - - +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 3.6 13.0 - - + -
24D SER* 3.2 18.2 + - - +
26D LYS* 1.3 78.0 - - - +
28D MET* 1.3 56.3 + - - +
30D ILE* 3.1 6.3 + - - +
31D MET* 3.0 30.0 + - - +
161D ILE* 3.6 19.5 - - + +
162D THR 3.8 17.3 - - - +
163D PRO* 3.9 6.5 - - - +
166D LEU* 3.6 14.4 - - + +
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Residues in contact with MET 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 4.7 7.0 - - + +
7D SER* 3.4 52.5 - - - +
10D VAL* 3.8 20.4 - - + -
11D TYR* 4.0 20.9 - - + +
14D LEU* 5.8 0.2 - - + -
23D ILE* 3.6 32.5 - - + +
24D SER 3.0 17.1 + - - +
25D SER* 3.7 7.4 - - - +
27D ALA* 1.3 72.7 - - - +
29D GLY* 1.3 56.3 + - - +
31D MET* 3.1 3.3 + - - +
32D ASN* 2.8 33.7 + - - +
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Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 5.6 0.7 - - - -
25D SER 3.2 7.4 + - - -
26D LYS 3.1 8.1 + - - -
28D MET* 1.3 79.2 - - - +
30D ILE* 1.3 61.2 + - - +
32D ASN* 3.2 10.2 + - - +
33D SER* 3.1 25.1 + - - -
7E GLU* 5.9 1.6 - - - +
8E VAL* 3.4 20.0 - - - +
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LYS* 3.0 12.4 + - + +
27D ALA 3.1 8.0 + - - +
29D GLY* 1.3 73.5 - - - +
31D MET* 1.3 62.6 + - - +
33D SER* 3.1 6.1 + - - -
34D PHE* 2.9 26.4 + - + +
163D PRO* 4.0 18.8 - - + -
166D LEU* 3.8 16.8 - - + -
8E VAL* 4.1 14.1 - - + -
9E GLY 3.9 15.9 - - - +
10E LEU* 4.1 4.7 - - + +
12E TYR* 3.8 34.8 - - + -
13E LEU* 4.0 32.1 - - + -
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Residues in contact with MET 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 4.1 17.5 - - + -
23D ILE* 4.2 8.3 - - + -
27D ALA 3.0 16.9 + - - +
28D MET* 3.1 8.2 + - - +
30D ILE* 1.3 77.5 - - - +
32D ASN* 1.3 57.6 + - - +
34D PHE* 3.3 33.0 + - + +
35D VAL* 3.0 34.7 + - + +
142D THR* 4.2 24.7 - - + -
145D VAL* 3.8 30.3 - - + -
146D LEU* 4.2 19.1 - - + -
166D LEU* 3.9 18.8 - - + -
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Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SER* 4.3 11.1 + - - +
6D TYR* 2.8 33.1 + - - +
7D SER* 4.0 14.8 + - - +
10D VAL* 5.1 4.2 - - - +
28D MET 2.8 13.8 + - - +
29D GLY* 3.3 13.1 + - - +
30D ILE 3.2 0.2 - - - -
31D MET* 1.3 77.7 - - - +
33D SER* 1.3 62.5 + - - +
35D VAL* 3.4 5.2 + - - +
36D ASN* 3.0 43.7 + - - +
7E GLU* 5.9 4.8 - - - +
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLY 3.1 6.4 + - - -
30D ILE 3.5 7.6 - - - -
32D ASN* 1.3 77.2 + - - +
34D PHE* 1.3 55.6 + - - +
36D ASN* 3.2 6.1 + - - +
37D ASP* 2.8 49.3 + - - -
7E GLU* 4.5 9.9 - - - +
8E VAL 2.8 23.4 + - - -
9E GLY* 3.4 20.6 - - - -
10E LEU* 3.9 7.0 - - - -
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Residues in contact with PHE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ILE* 2.9 14.4 + - + +
31D MET* 3.4 34.8 - - + +
33D SER* 1.3 76.7 - - - +
35D VAL* 1.3 69.0 + - + +
37D ASP* 4.6 0.2 - - - +
38D ILE* 3.2 59.9 + - + +
138D LEU 5.5 0.2 - - - -
141D LEU* 3.9 18.4 - - + -
142D THR* 4.1 22.0 - - - -
145D VAL* 4.0 17.5 - - + -
170D ILE* 5.4 3.4 - - + -
179D LEU* 4.0 7.9 - - + -
180D ILE* 4.0 24.5 - - + -
10E LEU* 3.6 29.5 - - + +
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D TYR* 3.8 29.4 - - + -
10D VAL* 4.2 12.8 - - + -
31D MET* 3.0 17.2 + - + +
32D ASN 3.9 3.4 - - - +
34D PHE* 1.3 81.9 - - + +
36D ASN* 1.3 64.5 + - - +
38D ILE* 4.0 2.4 - - - +
39D PHE* 3.1 23.3 + - + +
107D PHE* 3.8 28.0 - - + -
138D LEU* 4.4 16.6 - - + +
142D THR* 3.7 23.6 - - + +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SER 4.7 7.5 + - - +
6D TYR* 3.7 22.8 - - - -
32D ASN* 3.0 47.3 + - - +
33D SER* 3.7 5.1 - - - +
35D VAL* 1.3 76.5 - - - +
37D ASP* 1.3 64.1 + - - +
39D PHE* 3.2 8.1 + - - +
40D GLU* 2.8 32.5 + - - +
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Residues in contact with ASP 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER* 2.8 35.9 + - - +
36D ASN* 1.3 75.7 - - - +
38D ILE* 1.3 64.5 + - - +
40D GLU* 3.8 16.1 - - - +
41D ARG* 3.1 26.9 + - - +
183D THR* 3.8 21.7 - - + +
9E GLY* 5.6 0.5 - - - -
10E LEU* 4.2 16.0 + - + +
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.2 58.2 + - + +
35D VAL* 4.0 1.8 - - - +
37D ASP* 1.3 76.5 - - - +
39D PHE* 1.3 59.3 + - - +
41D ARG* 3.3 3.3 + - - +
42D ILE* 2.9 48.2 + - + +
70D LEU* 4.0 12.7 - - + +
138D LEU* 3.9 14.8 - - + -
141D LEU* 4.2 14.1 - - + -
179D LEU* 4.0 17.5 - - + -
183D THR* 4.0 22.2 - - + +
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Residues in contact with PHE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D TYR* 4.0 24.0 - + + -
35D VAL* 3.1 20.1 + - + +
36D ASN* 3.5 6.5 - - - +
38D ILE* 1.3 76.1 - - - +
40D GLU* 1.3 59.9 + - - +
42D ILE* 4.5 8.1 - - + +
43D ALA* 2.8 46.6 + - + +
112D ILE* 3.7 38.8 - - + -
115D HIS* 3.3 40.6 - + + -
116D LEU* 4.2 11.0 - - + -
134D SER* 4.5 9.4 - - - -
138D LEU* 3.7 27.6 - - + -
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 2.8 18.9 + - - +
37D ASP* 3.8 19.3 - - - +
38D ILE 3.3 0.2 - - - -
39D PHE* 1.3 73.9 - - - +
41D ARG* 1.3 60.8 + - - +
44D GLY* 3.1 20.4 + - - -
115D HIS* 5.0 5.2 - - + +
119D ARG* 3.5 25.7 + - - +
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP 3.1 13.0 + - - +
38D ILE 3.6 8.1 - - - +
40D GLU* 1.3 76.4 - - + +
42D ILE* 1.3 66.5 + - - +
44D GLY* 4.0 0.6 - - - -
45D GLU* 3.1 35.5 + - - +
69D LEU* 4.6 11.3 + - - +
70D LEU* 4.3 28.5 - - + +
182D ALA* 2.8 31.7 + - - +
183D THR* 4.0 11.3 - - + +
186D GLY* 3.1 38.3 + - - +
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE* 2.9 38.0 + - + +
39D PHE* 4.0 9.9 - - + +
41D ARG* 1.3 76.3 - - - +
43D ALA* 1.3 59.7 + - - +
45D GLU* 4.8 0.2 - - - -
46D ALA* 2.9 28.8 + - - +
63D ILE* 4.3 20.4 - - + -
66D ALA* 3.6 16.5 - - + +
67D VAL* 3.8 40.4 - - + +
70D LEU* 4.4 13.9 - - + -
71D LEU* 5.3 2.2 - - + -
134D SER* 5.3 3.1 - - - +
137D ILE* 4.6 12.3 - - + -
138D LEU* 4.8 6.5 - - + -
141D LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PHE* 2.8 32.9 + - + +
42D ILE* 1.3 75.9 - - - +
44D GLY* 1.3 62.8 + - - +
46D ALA* 3.9 2.8 - - - +
47D SER* 3.1 25.8 + - - -
58D ILE* 5.0 1.7 - - - +
115D HIS* 4.3 6.1 - - + -
116D LEU* 4.0 22.2 - - + -
119D ARG* 3.8 29.2 - - + +
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Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU 3.1 15.5 + - - -
41D ARG 4.0 0.4 - - - -
43D ALA* 1.3 75.6 - - - +
45D GLU* 1.3 61.0 + - - +
47D SER* 3.0 21.2 + - - -
48D ARG* 3.2 11.4 + - - +
119D ARG* 3.5 24.8 - - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ARG* 3.1 28.1 + - - +
42D ILE* 3.8 2.7 - - - +
44D GLY* 1.3 72.6 - - - +
46D ALA* 1.3 61.1 + - - +
48D ARG* 3.1 43.8 + - - +
49D LEU* 2.9 32.4 + - + +
66D ALA* 3.9 15.0 - - + +
69D LEU* 3.8 32.5 - - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE 2.9 19.2 + - - +
43D ALA* 3.9 3.6 - - - +
45D GLU* 1.3 77.6 - - - +
47D SER* 1.3 56.6 + - - +
49D LEU* 3.2 4.3 + - - +
50D ALA* 2.9 31.3 + - - +
58D ILE* 4.2 9.2 - - + -
62D GLU* 3.8 29.2 - - - +
63D ILE* 4.0 24.0 - - + +
66D ALA* 3.8 3.5 - - + +
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ALA 3.1 14.7 + - - -
44D GLY* 3.0 14.0 + - - -
46D ALA* 1.3 72.7 - - - +
48D ARG* 1.3 69.4 + - - +
50D ALA* 3.1 2.4 + - - +
51D HIS* 3.0 22.7 + - - +
56D SER 5.3 0.7 - - - +
58D ILE* 3.7 27.5 - - - +
119D ARG* 3.8 25.4 + - - +
120D THR* 5.2 1.3 - - - -
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLY 3.2 9.5 + - - +
45D GLU* 3.1 33.0 + - - +
47D SER* 1.3 82.3 + - - +
49D LEU* 1.3 79.3 + - - +
51D HIS* 3.1 22.3 + - - +
52D TYR* 5.7 0.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 2.9 31.2 + - + +
46D ALA 3.2 5.1 + - - +
48D ARG* 1.3 96.7 - - - +
50D ALA* 1.3 56.9 + - - +
51D HIS 3.3 1.5 + - - -
52D TYR* 4.7 2.4 + - - +
53D ASN* 4.8 3.6 - - - +
62D GLU* 3.8 31.8 - - + +
65D THR* 3.2 30.1 - - + +
66D ALA* 4.0 7.6 - - - +
69D LEU* 4.6 7.0 - - + -
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA 2.9 16.9 + - - +
47D SER 3.6 4.5 - - - +
48D ARG 3.1 0.4 - - - -
49D LEU* 1.3 76.8 - - - +
51D HIS* 1.3 65.3 + - - +
52D TYR 3.1 3.1 - - - -
53D ASN* 3.0 22.3 + - - +
56D SER* 3.3 18.4 - - - +
57D THR 3.2 29.2 - - - +
58D ILE* 3.9 8.3 - - + -
62D GLU* 3.8 7.2 - - + -
----------------------------------------------------------
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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