Contacts of the helix formed by residues 34 - 57 (chain B) in PDB entry 4TZM
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 ASP 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 4.3 4.0 - - - +
33B SER* 1.3 85.9 + - - +
35B PRO* 1.4 74.4 - - + +
36B ASP* 3.0 14.4 + - - +
37B ARG* 3.0 46.4 + - - +
38B SER* 3.0 20.6 + - - -
239B HIS* 3.4 3.6 - - - -
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Residues in contact with PRO 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 1.4 88.1 - - + +
36B ASP* 1.3 61.4 + - - +
38B SER* 3.9 2.0 - - - -
39B SER* 2.8 27.5 + - - -
134B ASN 5.4 2.2 - - - +
239B HIS* 3.1 39.0 - - + +
240B HIS* 3.8 6.4 - - + -
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 2.9 34.7 + - - +
34B ASP* 3.0 8.9 + - - +
35B PRO* 1.3 80.9 - - - +
37B ARG* 1.3 66.3 + - + +
39B SER* 3.2 4.9 + - - -
40B ASN* 3.1 34.3 + - - +
101B LYS* 3.8 17.6 - - - +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 4.1 8.3 - - + +
31B ILE* 3.1 60.8 - - - +
32B VAL* 4.0 2.0 - - - +
34B ASP* 3.0 36.8 + - - +
36B ASP* 1.3 78.9 - - - +
38B SER* 1.3 57.2 + - - +
40B ASN* 3.3 13.6 + - - +
41B PHE* 2.8 34.8 + - - +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 3.6 18.3 + - - +
34B ASP 3.0 17.2 + - - -
35B PRO* 3.8 5.6 - - - -
37B ARG* 1.3 79.1 - - - +
39B SER* 1.3 60.0 + - - +
41B PHE* 3.5 3.9 + - - +
42B MET* 3.3 24.6 + - - +
237B PRO* 3.4 15.9 - - - +
239B HIS 2.9 21.8 + - - -
240B HIS* 2.7 25.5 + - - -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO 2.8 14.0 + - - -
36B ASP* 3.2 10.0 + - - -
38B SER* 1.3 76.1 - - - +
40B ASN* 1.3 65.0 + - - +
42B MET* 3.2 7.8 + - - +
43B ILE* 3.0 29.5 + - - +
100B THR* 4.2 1.9 + - - -
101B LYS* 3.3 43.2 - - - +
240B HIS* 3.5 22.0 - - - -
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 4.5 10.7 - - + +
36B ASP* 3.1 23.0 + - - +
37B ARG* 3.3 15.2 + - - +
39B SER* 1.3 78.3 + - - +
41B PHE* 1.3 62.2 + - - +
43B ILE* 3.2 11.0 + - - +
44B ARG* 3.0 29.3 + - + +
101B LYS* 2.2 32.0 + - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.7 21.5 - + - -
28B PHE* 3.6 28.7 - + - -
29B PRO* 3.9 14.3 - - + +
32B VAL* 3.7 24.2 - - + -
37B ARG 2.8 19.6 + - - +
38B SER 3.7 3.8 - - - +
39B SER 3.3 0.2 - - - -
40B ASN* 1.3 72.5 - - - +
42B MET* 1.3 57.9 + - - +
44B ARG* 3.2 3.3 + - - +
45B ALA* 2.7 33.1 + - + +
167B VAL* 3.5 28.3 - - + -
171B MET* 3.7 24.0 - - + -
235B LEU* 3.9 28.5 - - + -
237B PRO* 4.2 15.0 - - + -
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Residues in contact with MET 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER 3.3 13.9 + - - +
39B SER 3.2 8.9 + - - +
41B PHE* 1.3 89.8 - - - +
43B ILE* 1.3 59.2 + - - +
45B ALA* 3.5 3.3 - - - +
46B ILE* 2.8 37.5 + - + +
100B THR* 4.2 12.8 - - - +
127B MET* 6.0 0.9 - - - +
129B PHE* 4.3 15.9 - - + -
235B LEU* 4.3 11.7 - - + +
237B PRO* 3.6 16.2 - - + -
240B HIS* 3.6 27.8 - - + -
241B ALA 3.6 31.9 - - - +
242B ALA* 3.6 19.3 - - + +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER 3.0 16.0 + - - +
40B ASN* 3.5 21.5 - - - +
42B MET* 1.3 77.3 - - - +
44B ARG* 1.3 67.3 + - - +
46B ILE* 3.5 3.3 + - - +
47B TYR* 3.3 21.2 + - + +
93B LEU 5.2 2.1 - - - +
94B ARG* 3.9 32.7 - - - +
97B GLY* 3.3 40.4 - - - +
98B ASP* 3.7 18.4 - - - +
100B THR* 4.3 0.2 - - - +
101B LYS* 4.4 15.3 - - + +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS 5.3 0.8 + - - -
27B LEU* 3.0 39.9 + - - +
28B PHE* 3.7 19.3 - - + -
29B PRO* 4.1 12.6 - - + -
40B ASN* 3.0 15.7 + - + +
41B PHE 3.6 6.5 - - - +
43B ILE* 1.3 82.6 - - - +
45B ALA* 1.3 57.4 + - - +
47B TYR* 3.4 41.3 + - - +
48B VAL* 3.0 35.8 + - - +
81B PHE* 6.0 4.0 - - - -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 3.9 8.5 - - - -
41B PHE* 2.7 23.6 + - + +
42B MET* 3.2 9.8 + - - +
44B ARG* 1.3 70.9 - - - +
46B ILE* 1.3 61.0 + - - +
49B VAL* 2.8 38.8 + - + +
127B MET* 5.0 2.9 - - - -
171B MET* 3.6 24.2 - - + -
235B LEU* 3.7 19.1 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET 2.8 22.1 + - - +
43B ILE 3.7 4.3 - - - +
45B ALA* 1.3 73.9 - - - +
47B TYR* 1.3 63.5 + - - +
50B PHE* 3.2 44.6 + - + +
93B LEU* 3.9 30.1 - - + +
96B ALA 4.5 2.0 - - - -
97B GLY* 3.7 28.0 - - - +
100B THR* 4.1 8.5 - - + -
105B LEU* 4.6 3.1 - - + -
108B ILE* 4.5 9.9 - - + -
127B MET* 4.0 11.2 - - - -
129B PHE* 3.7 33.0 - - + -
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 5.3 1.6 - - + -
43B ILE* 3.3 11.2 + - + +
44B ARG* 3.6 43.1 - - - +
45B ALA 3.2 0.6 - - - -
46B ILE* 1.3 80.2 - - - +
48B VAL* 1.3 67.4 + - + +
51B SER* 2.9 40.3 + - - -
78B THR* 3.4 31.0 + - + -
79B LEU* 2.5 28.8 + - + -
81B PHE* 3.4 27.8 - + - -
90B ALA* 4.0 22.9 - - + -
93B LEU* 4.2 19.6 - - + +
94B ARG* 6.1 0.4 - - - +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.4 12.6 - - + +
28B PHE* 3.6 32.1 - - + -
44B ARG* 3.0 24.4 + - - +
45B ALA 4.1 1.3 - - - +
47B TYR* 1.3 86.8 - - + +
49B VAL* 1.3 66.8 + - + +
51B SER* 3.6 2.3 + - - -
52B ALA* 3.2 21.5 + - - +
70B ILE* 4.7 2.0 - - + -
76B CYS* 4.2 23.9 - - + +
77B MET 5.0 0.5 - - - +
78B THR* 4.3 13.3 - - + +
171B MET* 4.9 1.1 - - - -
175B VAL* 4.4 17.5 - - + -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 2.8 27.4 + - + +
48B VAL* 1.3 73.9 - - - +
50B PHE* 1.3 58.9 + - + +
52B ALA* 3.1 9.4 + - - +
53B VAL* 3.0 28.2 + - + +
127B MET* 4.0 19.7 - - + -
171B MET* 4.2 19.5 - - + -
174B ILE* 3.9 28.5 - - + -
175B VAL* 5.0 4.7 - - + -
178B VAL* 4.7 4.5 - - + -
235B LEU* 5.2 2.2 - - + -
244B MET* 3.7 31.2 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.2 33.7 + - + +
49B VAL* 1.3 76.9 - - + +
51B SER* 1.3 60.6 + - - +
53B VAL* 3.7 9.1 - - + +
54B LEU* 2.9 35.7 + - - +
93B LEU* 4.1 17.7 - - + -
108B ILE* 3.6 40.4 - - + -
110B LEU* 3.7 23.1 - - + -
125B PHE* 3.5 26.2 - - + -
127B MET* 3.6 32.3 - - + -
197B PHE* 3.7 20.0 - + + -
244B MET* 4.5 6.1 - - + -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 2.9 26.3 + - - -
48B VAL* 3.7 5.2 - - - -
50B PHE* 1.3 76.0 - - - +
52B ALA* 1.3 63.9 + - - +
54B LEU* 3.1 6.2 + - - -
55B ARG* 3.0 20.3 + - - +
65B PHE* 3.3 15.0 - - - -
77B MET 3.3 18.2 - - - -
78B THR* 3.7 8.7 - - - -
79B LEU* 3.1 32.5 + - - +
93B LEU* 4.8 1.4 - - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL 3.2 9.2 + - - +
49B VAL* 3.1 12.8 + - - +
51B SER* 1.3 77.4 - - - +
53B VAL* 1.3 53.4 + - - +
55B ARG* 3.3 2.5 + - - -
56B GLN* 2.8 47.9 + - - +
76B CYS* 5.1 8.3 - - + -
77B MET 3.7 9.3 + - - +
175B VAL* 4.8 18.4 - - + -
178B VAL* 4.2 15.3 - - + -
179B GLN* 5.4 3.1 - - + +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL 3.0 16.1 + - - +
50B PHE* 3.7 10.3 - - + +
52B ALA* 1.3 75.8 - - - +
54B LEU* 1.3 62.1 + - - +
56B GLN* 4.6 1.3 - - - -
57B ARG* 3.0 27.5 + - + +
59B ILE* 4.5 0.2 - - - +
110B LEU* 3.7 17.5 - - + -
125B PHE* 3.5 44.2 - - + -
178B VAL* 3.8 21.8 - - + -
182B CYS* 4.9 1.3 - - - -
244B MET* 4.1 24.7 - - + -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE 2.9 22.9 + - - +
51B SER* 3.4 4.5 - - - +
53B VAL* 1.3 77.8 - - - +
55B ARG* 1.3 57.9 + - - +
58B ASN 3.4 0.2 + - - -
59B ILE* 2.9 59.2 + - + -
60B LEU* 3.4 13.6 + - + -
65B PHE* 3.7 12.6 - - + -
79B LEU* 4.2 15.9 - - + -
89B ILE* 4.0 26.9 - - + -
93B LEU* 5.4 0.7 - - + -
110B LEU* 4.0 24.2 - - + -
197B PHE* 4.2 10.8 - - + -
496D ILE* 4.2 12.1 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER 3.0 15.0 + - - +
52B ALA 3.9 2.7 - - - +
54B LEU* 1.3 77.6 - - - +
56B GLN* 1.3 65.9 + - - +
58B ASN* 3.1 35.8 + - - +
60B LEU 2.8 25.7 + - - -
62B LYS* 3.7 32.6 - - - +
65B PHE* 3.5 36.8 - - + -
77B MET* 3.8 30.3 - - + +
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA* 2.8 27.6 + - - +
55B ARG* 1.3 80.4 - - - +
57B ARG* 1.3 60.3 + - - +
58B ASN* 3.1 6.4 + - - +
77B MET* 5.4 5.9 + - - +
178B VAL* 4.7 1.3 - - + +
179B GLN* 3.9 43.9 + - + +
182B CYS* 3.6 44.3 - - + +
183B THR* 5.0 10.0 + - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.0 20.4 + - + +
56B GLN* 1.3 75.3 + - - +
58B ASN* 1.3 71.1 + - - +
59B ILE* 3.1 18.2 + - + -
123B GLU* 2.8 42.8 + - - +
125B PHE* 4.0 10.1 - - + -
182B CYS* 3.4 46.9 + - - -
186B LEU* 3.5 16.2 + - - +
187B GLU 2.7 31.9 + - - -
188B PRO* 4.2 6.5 - - - +
189B LEU* 3.7 38.1 + - + +
250B SER* 3.7 7.3 + - - -
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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