Contacts of the helix formed by residues 24 - 51 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 1.3 77.3 - - - +
25B SER* 1.3 64.2 + - - +
26B LYS* 3.3 5.3 + - - +
27B ALA* 3.1 21.0 + - - +
28B MET* 3.1 18.0 + - - +
160B ARG* 3.9 34.0 - - - +
161B ILE 2.9 14.3 + - - -
162B THR* 4.3 6.7 - - - -
163B PRO* 3.6 10.8 - - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 5.8 2.7 - - - -
23B ILE 3.7 0.6 + - - -
24B SER* 1.3 73.6 - - - +
26B LYS* 1.3 62.5 + - - +
28B MET* 3.5 7.8 + - - +
29B GLY* 3.3 17.3 + - - -
160B ARG* 5.5 0.2 - - - +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.2 5.4 + - - +
25B SER* 1.3 78.3 - - - +
27B ALA* 1.3 65.7 + - - +
29B GLY* 3.4 2.9 + - - +
30B ILE* 3.3 25.5 + - + +
163B PRO* 3.7 23.1 - - + -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.6 14.6 - - + -
24B SER* 3.1 16.0 + - - +
26B LYS* 1.3 76.4 - - - +
28B MET* 1.3 57.9 + - - +
30B ILE* 3.1 4.7 + - - +
31B MET* 2.9 30.8 + - - +
161B ILE* 3.6 18.6 - - + +
162B THR 3.8 12.1 - - - +
163B PRO* 3.8 4.2 - - - +
166B LEU* 3.5 22.3 - - + +
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.3 45.3 - - - +
10B VAL* 3.7 34.8 - - + -
11B TYR* 3.4 43.3 - - + +
23B ILE* 3.9 15.9 - - + +
24B SER 3.1 16.1 + - - +
25B SER* 3.7 8.5 - - - +
26B LYS 3.2 0.2 - - - -
27B ALA* 1.3 77.6 - - - +
29B GLY* 1.3 57.5 + - - +
31B MET* 3.3 4.1 + - - +
32B ASN* 2.8 27.8 + - - +
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 6.1 0.2 - - - -
25B SER 3.3 11.7 + - - -
26B LYS 3.4 4.2 + - - -
27B ALA 3.3 0.4 - - - -
28B MET* 1.3 78.9 - - - +
30B ILE* 1.3 57.4 + - - +
32B ASN* 3.3 7.6 + - - +
33B SER* 3.0 30.3 + - - -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS 3.3 14.8 + - - +
27B ALA 3.1 7.3 + - - +
29B GLY* 1.3 78.0 - - - +
31B MET* 1.3 58.9 + - - +
33B SER* 3.2 9.1 + - - -
34B PHE* 3.0 27.7 + - + +
163B PRO* 4.0 28.5 - - + +
166B LEU* 3.6 22.7 - - + -
167B GLN* 6.2 0.7 - - + +
170B ILE* 5.9 5.4 - - + -
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Residues in contact with MET 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.3 13.7 - - + -
23B ILE* 4.0 18.8 - - + -
27B ALA 2.9 17.2 + - - +
28B MET* 3.4 11.2 - - - +
30B ILE* 1.3 78.0 - - - +
32B ASN* 1.3 55.8 + - - +
34B PHE* 3.3 16.6 + - + +
35B VAL* 3.0 34.3 + - + +
142B THR* 3.8 35.4 - - + +
145B VAL* 3.7 28.5 - - + -
146B LEU* 4.0 17.0 - - + -
166B LEU* 4.0 15.0 - - + -
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 5.0 7.9 - - - +
4B GLU 3.1 20.0 + - - +
5B SER* 3.6 2.9 - - - +
6B TYR* 2.7 37.5 + - - +
7B SER* 3.5 15.9 + - - +
10B VAL* 5.4 2.7 - - - -
28B MET* 2.8 21.0 + - + +
29B GLY* 3.7 9.0 - - - +
30B ILE 3.3 0.2 - - - -
31B MET* 1.3 70.6 - - - +
33B SER* 1.3 64.7 + - - +
35B VAL* 3.6 5.6 + - - +
36B ASN* 3.0 34.3 + - - +
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 3.3 27.1 - - - +
29B GLY 3.0 14.4 + - - -
30B ILE* 3.5 10.8 - - - -
32B ASN* 1.3 75.9 - - - +
34B PHE* 1.3 58.3 + - - +
36B ASN* 3.3 2.1 + - - +
37B ASP* 2.8 42.0 + - - +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.0 15.1 + - + +
31B MET* 3.4 25.1 - - + +
33B SER* 1.3 74.7 - - - +
35B VAL* 1.3 74.5 + - + +
37B ASP* 3.3 4.3 + - - +
38B ILE* 3.0 35.2 + - + +
141B LEU* 4.1 34.1 - - + -
142B THR* 4.5 5.2 - - - -
145B VAL* 4.1 25.1 - - + -
170B ILE* 5.9 2.0 - - + -
176B LEU* 5.4 1.1 - - + -
179B LEU* 4.1 18.4 - - + -
180B ILE* 3.6 34.8 - - + -
183B THR* 6.5 0.9 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.5 32.3 - - + -
10B VAL* 4.5 11.7 - - + -
31B MET* 3.0 18.3 + - + +
32B ASN* 3.9 5.6 - - - +
34B PHE* 1.3 83.2 - - + +
36B ASN* 1.3 61.9 + - - +
38B ILE* 4.2 1.3 - - - +
39B PHE* 3.1 23.1 + - + +
107B PHE* 3.9 23.8 - - + -
138B LEU* 4.0 17.3 - - + +
142B THR* 3.6 24.2 - - + +
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Residues in contact with ASN 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 25.9 - - + +
3B LYS* 3.5 25.8 - - + +
4B GLU* 2.9 45.8 + - - +
6B TYR* 4.0 11.5 - - - -
32B ASN* 3.0 28.7 + - - +
33B SER 3.7 4.0 - - - +
35B VAL* 1.3 78.2 - - - +
37B ASP* 1.3 59.6 + - - +
39B PHE* 3.8 3.9 - - - +
40B GLU* 2.9 24.3 + - - +
115B HIS* 3.7 9.9 - - - -
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.9 0.2 - - - +
3B LYS* 2.8 26.9 + - - -
33B SER* 2.8 26.0 + - - +
34B PHE* 4.0 3.9 - - - +
36B ASN* 1.3 73.7 - - - +
38B ILE* 1.3 67.1 + - - +
40B GLU* 3.4 17.5 + - - +
41B ARG* 3.3 27.0 + - - +
183B THR* 3.7 21.2 - - + +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.0 25.8 + - + +
35B VAL* 4.2 3.1 - - - +
37B ASP* 1.3 78.2 - - - +
39B PHE* 1.3 59.7 + - - +
41B ARG* 3.1 12.3 + - + +
42B ILE* 2.9 40.4 + - + +
70B LEU* 5.2 4.0 - - + -
71B LEU* 4.1 16.2 - - + -
138B LEU* 3.9 18.4 - - + -
141B LEU* 3.9 24.7 - - + -
179B LEU* 3.9 33.2 - - + -
183B THR* 4.3 12.5 - - + +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.3 0.4 - - - -
6B TYR* 4.7 4.9 - + - -
35B VAL* 3.1 19.0 + - + +
36B ASN* 3.8 3.6 - - - +
38B ILE* 1.3 80.8 - - - +
40B GLU* 1.3 60.0 + - - +
42B ILE* 4.4 10.5 - - + +
43B ALA* 2.8 43.6 + - + +
63B ILE* 6.1 0.2 - - + -
112B ILE* 4.2 12.1 - - + -
115B HIS* 3.3 52.5 - + + -
116B LEU* 3.7 33.9 - - + -
134B SER* 4.1 22.4 - - - -
138B LEU* 3.7 27.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.5 52.9 + - + +
36B ASN 2.9 18.0 + - - +
37B ASP* 3.7 19.3 - - - +
38B ILE 3.3 0.4 - - - -
39B PHE* 1.3 76.0 - - - +
41B ARG* 1.3 59.8 + - + +
43B ALA* 4.2 2.6 - - - +
44B GLY* 2.9 25.8 + - - -
119B ARG* 4.6 9.0 + - - +
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 4.9 8.2 + - - -
37B ASP 3.3 6.2 + - - +
38B ILE* 3.1 14.1 + - + +
40B GLU* 1.3 79.8 - - + +
42B ILE* 1.3 64.3 + - - +
44B GLY* 5.0 0.4 - - - -
45B GLU* 3.0 21.0 + - - +
70B LEU* 3.4 51.9 + - + +
179B LEU* 4.2 6.9 + - - +
182B ALA* 3.5 31.3 + - - +
183B THR* 2.6 62.2 + - - +
185B ALA 5.2 3.8 + - - -
186B GLY* 5.7 4.0 - - - -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 2.9 42.3 + - + +
39B PHE* 4.0 13.7 - - + +
41B ARG* 1.3 73.3 - - - +
43B ALA* 1.3 62.2 + - - +
45B GLU 3.5 0.2 + - - -
46B ALA* 2.8 28.6 + - - +
63B ILE* 4.1 29.8 - - + -
66B ALA* 3.7 10.7 - - + +
67B VAL* 3.9 24.0 - - + -
70B LEU* 3.7 19.5 - - + -
71B LEU* 5.3 2.9 - - + -
134B SER* 5.5 1.3 - - - +
137B ILE* 4.2 17.0 - - + -
138B LEU* 5.2 3.6 - - + -
141B LEU* 5.2 1.6 - - + -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 2.8 30.5 + - + +
40B GLU* 4.2 2.0 - - - +
42B ILE* 1.3 72.8 - - - +
44B GLY* 1.3 60.2 + - - +
46B ALA* 3.7 5.7 - - - +
47B SER* 2.8 33.1 + - - -
58B ILE* 5.0 1.9 - - - +
116B LEU* 4.0 22.0 - - + -
119B ARG* 3.9 29.7 - - + +
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Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU 2.9 20.1 + - - -
41B ARG* 3.9 1.1 - - - -
42B ILE 3.3 0.2 - - - -
43B ALA* 1.3 78.9 - - - +
45B GLU* 1.3 60.9 + - - +
47B SER* 3.4 5.5 + - - -
48B ARG* 3.3 19.4 + - - +
119B ARG* 5.2 4.2 - - - +
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 2.9 31.6 + - - -
49A LEU* 4.5 0.2 - - - +
52A TYR* 2.5 43.0 + - + +
41B ARG 3.0 17.5 + - - +
44B GLY* 1.3 73.2 - - - +
46B ALA* 1.3 66.1 + - - +
47B SER 3.3 0.2 + - - -
48B ARG* 3.4 6.2 + - - +
49B LEU* 3.2 49.7 + - + +
66B ALA* 3.9 20.4 - - + -
69B LEU* 4.0 14.0 - - + +
70B LEU* 4.2 4.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE 2.8 23.8 + - - +
43B ALA* 3.7 5.2 - - - +
45B GLU* 1.3 74.1 - - - +
47B SER* 1.3 61.6 + - - +
49B LEU* 3.5 1.5 + - - -
50B ALA* 3.2 21.5 + - - +
58B ILE* 3.9 12.4 - - + +
62B GLU* 3.8 27.5 - - - +
63B ILE* 3.6 29.8 - - + -
66B ALA* 4.0 1.1 - - + +
116B LEU* 5.6 0.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA 2.8 16.1 + - - -
44B GLY* 3.7 6.3 - - - -
45B GLU 3.2 0.2 - - - -
46B ALA* 1.3 76.0 - - - +
48B ARG* 1.3 64.3 + - - +
50B ALA* 3.3 14.7 + - - +
51B HIS* 3.9 5.2 + - - +
58B ILE* 4.0 19.2 - - - +
119B ARG* 3.6 22.9 + - - -
120B THR* 3.9 10.4 + - - -
121B THR* 3.9 17.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 2.9 56.2 + - - +
44B GLY 3.3 9.8 + - - +
45B GLU* 3.4 12.5 + - - +
47B SER* 1.3 79.8 - - - +
49B LEU* 1.3 57.4 + - - +
50B ALA 3.4 0.3 + - - -
51B HIS* 2.9 37.2 + - + +
52B TYR* 4.2 1.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 4.4 3.1 - - - +
48A ARG* 4.0 9.9 - - - +
49A LEU* 4.9 4.7 - - + -
65A THR* 6.0 0.4 - - + -
69A LEU* 3.8 36.8 - - + +
45B GLU* 3.2 45.9 + - + +
46B ALA* 3.9 1.6 - - - +
47B SER 3.3 0.4 - - - -
48B ARG* 1.3 73.3 - - - +
50B ALA* 1.3 64.9 + - - +
51B HIS 3.2 0.2 - - - -
52B TYR* 3.2 25.7 + - + +
53B ASN 4.1 1.6 + - - -
62B GLU* 3.9 32.7 - - + +
65B THR* 3.1 26.0 - - - +
66B ALA 4.1 2.2 - - - +
69B LEU* 4.5 2.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 3.2 12.9 + - - +
47B SER* 3.5 12.1 - - - +
48B ARG 3.2 0.8 - - - -
49B LEU* 1.3 73.6 - - - +
51B HIS* 1.3 61.1 + - - +
52B TYR 3.0 5.6 - - - -
53B ASN* 3.1 31.0 + - - +
56B SER* 3.3 16.1 - - - +
57B THR 3.8 4.7 - - - +
58B ILE* 3.8 33.4 - - + +
62B GLU* 4.1 3.1 - - - -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 5.7 0.2 - - - -
47B SER 3.9 4.9 + - - +
48B ARG* 2.9 33.8 + - + +
49B LEU 3.2 1.2 - - - -
50B ALA* 1.3 77.4 - - - +
52B TYR* 1.3 94.9 + + - +
53B ASN 3.6 6.3 + - - +
56B SER* 4.7 11.5 - - - +
----------------------------------------------------------
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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