Contacts of the helix formed by residues 28 - 49 (chain F) in PDB entry 2VT5
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 28 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F THR* 1.3 78.5 - - - +
29F GLU* 1.3 57.0 + - - +
31F THR 3.5 0.4 + - - -
32F GLN* 3.0 33.1 + - - +
1337F ROK 3.0 36.6 + - - -
18H MET* 3.3 17.4 - - - +
22H ARG* 4.1 4.0 - - - -
1337H ROK 4.6 0.7 - - - -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F THR* 3.5 10.9 + - - +
28F GLY* 1.3 76.2 - - - +
30F LEU* 1.3 60.6 + - - +
32F GLN* 3.5 4.7 + - - +
33F LEU* 3.1 21.3 + - - +
89F PHE 4.2 9.6 - - - +
90F ALA* 3.2 31.8 - - + +
111F GLY* 3.5 4.6 - - - -
112F LYS* 2.7 58.2 + - - +
113F TYR* 4.0 6.1 - - + -
1337F ROK 3.2 1.2 + - - +
22H ARG* 3.2 35.2 + - - +
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Residues in contact with LEU 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLU* 1.3 75.4 - - - +
31F THR* 1.3 59.4 + - - +
33F LEU* 3.4 5.6 + - + +
34F LEU* 2.9 48.1 + - + +
113F TYR* 3.7 22.2 - - + +
138F ILE* 4.3 23.8 - - + -
140F ARG* 5.0 0.9 - - - +
160F VAL* 4.1 30.5 - - + -
161F ALA* 4.8 2.2 - - + -
177F MET* 4.4 12.8 - - - -
1337F ROK 2.9 49.5 + - + +
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Residues in contact with THR 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F THR 4.8 2.2 - - - +
17F VAL* 3.4 25.8 - - + +
18F MET* 3.8 22.8 - - + +
28F GLY 3.6 8.5 - - - -
29F GLU 3.3 0.2 - - - -
30F LEU* 1.3 74.0 - - - +
32F GLN* 1.3 64.5 + - - +
34F LEU* 3.2 1.6 + - - +
35F ASN* 2.8 46.0 + - - +
1337F ROK 2.6 32.6 + - - -
18H MET* 3.5 19.1 - - + -
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Residues in contact with GLN 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLY 3.0 17.1 + - - +
29F GLU* 3.5 11.8 - - - +
31F THR* 1.3 76.4 - - - +
33F LEU* 1.3 61.9 + - - +
35F ASN* 3.4 6.2 + - - +
36F SER* 3.0 25.8 + - - -
88F SER* 3.6 27.9 - - - +
89F PHE* 4.9 3.3 - - - +
90F ALA* 4.7 0.4 - - + -
15H ARG* 5.5 10.6 + - + +
18H MET* 3.8 33.0 + - + +
19H GLU* 3.7 17.6 + - - +
22H ARG* 3.0 48.6 + - - +
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLU 3.1 10.3 + - - +
30F LEU* 3.7 7.4 - - + +
32F GLN* 1.3 75.6 - - - +
34F LEU* 1.3 63.2 + - + +
36F SER* 3.3 4.2 + - - -
37F LEU* 2.9 28.7 + - + +
85F LEU* 3.6 19.8 - - + +
88F SER* 4.0 12.1 - - - +
90F ALA* 3.5 14.8 - - + +
91F THR* 3.7 17.0 - - + -
113F TYR* 3.6 37.5 - - + -
115F VAL* 3.9 10.1 - - + -
138F ILE* 3.7 32.1 - - + -
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU* 4.8 8.1 - - + +
17F VAL* 3.9 36.1 - - + -
30F LEU* 2.9 39.3 + - + +
31F THR 3.9 2.7 - - - +
33F LEU* 1.3 75.5 - - - +
35F ASN* 1.3 60.0 + - - +
37F LEU* 3.6 10.3 - - + +
38F CYS* 2.9 29.6 + - - +
136F PHE* 4.3 9.0 - - + -
138F ILE* 3.7 25.1 - - + -
161F ALA* 5.1 0.4 - - + -
173F LEU* 6.5 0.4 - - + -
175F LEU* 4.1 29.6 - - + -
177F MET* 4.4 6.7 - - - -
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Residues in contact with ASN 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU* 5.8 1.6 - - - +
14F THR* 3.2 38.0 + - - +
17F VAL* 5.6 1.6 - - - +
31F THR* 2.8 32.0 + - - +
32F GLN* 3.6 6.2 - - - +
34F LEU* 1.3 73.4 - - - +
36F SER* 1.3 66.0 + - - +
38F CYS* 3.2 9.8 + - - +
39F THR* 3.0 26.5 + - - -
14H THR* 3.4 32.1 - - + +
15H ARG* 5.4 5.8 - - + +
18H MET* 4.2 7.9 - - - -
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Residues in contact with SER 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLN 3.0 9.4 + - - -
33F LEU 3.4 8.7 - - - -
35F ASN* 1.3 76.0 - - - +
37F LEU* 1.3 64.7 + - - +
39F THR* 3.2 5.4 + - - -
40F ALA 3.0 17.7 + - - -
84F MET* 3.4 40.9 - - - +
85F LEU* 4.3 1.8 - - - -
88F SER* 3.1 19.0 - - - -
15H ARG* 3.1 25.2 + - - +
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 2.9 24.4 + - + +
34F LEU* 3.6 16.4 - - + +
36F SER* 1.3 76.3 - - - +
38F CYS* 1.3 56.8 + - - +
40F ALA* 3.2 6.5 + - + +
41F VAL* 2.9 43.5 + - + +
81F VAL* 4.0 33.0 - - + -
84F MET* 5.3 0.2 - - - -
85F LEU* 4.2 14.3 - - + +
115F VAL* 5.5 1.8 - - + -
117F PHE* 5.9 0.4 - - + -
134F THR* 5.0 4.5 - - + -
136F PHE* 3.6 54.3 - - + -
138F ILE* 5.0 0.7 - - + -
173F LEU* 5.9 2.2 - - + -
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Residues in contact with CYS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 3.5 25.6 - - + -
14F THR* 4.9 9.4 - - - -
34F LEU 2.9 18.6 + - - +
35F ASN* 3.2 9.4 + - - +
37F LEU* 1.3 76.9 - - - +
39F THR* 1.3 57.1 + - - +
41F VAL* 3.3 8.8 + - - +
42F LYS* 3.1 44.6 + - - +
173F LEU* 4.4 4.2 - - + +
193F PHE* 3.6 24.9 - - + -
192H GLU* 4.9 2.5 - - - -
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Residues in contact with THR 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ASN 3.0 13.5 + - - -
36F SER* 3.2 9.7 + - - -
38F CYS* 1.3 73.8 - - - +
40F ALA* 1.3 64.6 + - - +
42F LYS* 3.5 6.4 + - - +
43F ALA* 3.2 20.8 + - - +
84F MET* 3.5 26.2 - - + +
59G ILE* 4.0 16.3 - - + +
12H THR* 4.7 8.9 + - + +
190H ILE* 4.7 1.8 - - + +
192H GLU* 2.8 42.2 + - + -
194H ILE* 5.9 0.9 - - + -
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Residues in contact with ALA 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F SER 3.0 12.0 + - - +
37F LEU* 3.2 11.9 + - + +
39F THR* 1.3 74.5 - - - +
41F VAL* 1.3 52.4 + - - +
43F ALA* 3.1 9.6 + - - +
44F ILE* 2.8 38.2 + - - +
80F LEU* 3.9 26.6 - - + +
81F VAL* 3.9 23.3 - - + +
84F MET* 3.9 9.1 - - + +
59G ILE* 5.2 0.4 - - - -
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Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 2.9 33.2 + - + +
38F CYS* 3.6 7.4 - - - +
39F THR 3.3 0.4 - - - -
40F ALA* 1.3 76.6 - - + +
42F LYS* 1.3 55.4 + - - +
44F ILE* 3.3 2.6 + - + -
45F SER* 2.8 27.4 + - - -
134F THR* 4.6 13.7 - - + +
136F PHE* 5.9 2.9 - - + -
165F ALA* 3.5 31.2 - - + -
167F TYR* 3.5 20.5 + - + +
171F THR* 4.7 2.2 - - + -
173F LEU* 4.4 9.4 - - + -
193F PHE* 3.5 24.5 - - + -
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Residues in contact with LYS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F CYS* 3.1 36.0 + - - +
39F THR* 3.9 6.1 - - - +
41F VAL* 1.3 72.1 - - - +
43F ALA* 1.3 60.6 + - - +
45F SER* 3.6 8.1 - - - -
46F SER* 3.0 28.9 + - - -
186F LEU* 3.7 25.6 - - + +
191F GLY* 3.0 26.6 + - - +
192F GLU* 5.0 1.6 + - - +
193F PHE* 3.5 17.9 - - + -
42H LYS* 4.4 1.6 - - - +
189H ALA 4.5 1.4 - - - +
190H ILE* 3.0 28.7 + - + +
191H GLY 3.3 11.9 + - - -
192H GLU* 2.8 29.4 + - - -
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Residues in contact with ALA 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F THR 3.2 11.2 + - - +
40F ALA 3.1 9.8 + - - +
42F LYS* 1.3 76.9 - - - +
44F ILE* 1.3 64.7 + - - +
46F SER* 3.5 3.8 + - - -
47F ALA* 3.2 22.7 + - - +
80F LEU* 3.6 21.5 - - + +
55G HIS* 4.8 9.6 + - - +
59G ILE* 3.7 23.3 - - + -
190H ILE* 3.5 15.8 - - + +
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Residues in contact with ILE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ALA 2.8 24.7 + - - +
41F VAL* 3.3 2.7 + - - +
43F ALA* 1.3 69.5 - - - +
45F SER* 1.3 54.5 + - - +
47F ALA* 3.0 5.9 + - - +
48F VAL* 2.7 44.0 + - + +
77F SER* 3.5 33.0 - - - +
80F LEU* 3.8 16.4 - - + -
81F VAL* 3.7 29.2 - - + -
119F PRO 4.1 2.9 - - - +
120F LEU* 3.8 4.5 - - + -
134F THR* 3.9 14.8 - - + +
167F TYR* 3.4 34.3 - - + +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F VAL 2.8 20.6 + - - -
42F LYS 3.6 5.8 - - - -
44F ILE* 1.3 72.8 - - - +
46F SER* 1.3 57.5 + - - +
48F VAL* 3.2 3.0 + - - +
49F ARG* 2.9 44.4 + - - +
167F TYR* 3.7 19.9 - - - -
171F THR* 2.8 22.7 + - - -
186F LEU* 3.6 20.5 - - - +
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Residues in contact with SER 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LYS 3.0 18.3 + - - -
43F ALA 3.6 5.8 - - - -
44F ILE 3.3 0.2 - - - -
45F SER* 1.3 74.9 + - - +
47F ALA* 1.3 62.6 + - - +
49F ARG* 3.6 5.5 + - - +
50F LYS 3.3 4.0 + - - -
51F ALA* 3.2 40.3 + - - +
189H ALA* 3.4 31.8 + - - +
190H ILE* 4.2 6.1 - - - -
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Residues in contact with ALA 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ALA 3.2 9.3 + - - +
44F ILE* 3.0 9.6 + - - +
46F SER* 1.3 76.9 - - - +
48F VAL* 1.3 62.3 + - - +
50F LYS* 3.0 26.2 + - - +
51F ALA* 4.8 7.0 - - - +
73F LEU* 3.9 25.3 - - + +
76F LEU* 4.0 20.0 - - + -
80F LEU* 5.7 0.2 - - + -
55G HIS* 6.1 2.2 - - - +
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Residues in contact with VAL 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E SER* 3.3 38.6 + - - +
170E ALA* 3.6 9.0 - - - +
44F ILE* 2.7 40.3 + - + +
45F SER* 3.6 6.1 - - - +
47F ALA* 1.3 74.2 - - - +
49F ARG* 1.3 56.7 + - - +
50F LYS* 3.3 12.0 + - - +
73F LEU* 4.3 14.3 - - + +
77F SER* 5.2 0.4 - - - +
120F LEU* 3.9 26.5 - - + -
126F ILE* 4.7 3.3 - - + +
132F VAL* 3.9 11.9 - - + -
167F TYR* 3.9 14.4 - - + -
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Residues in contact with ARG 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ARG* 3.6 28.6 - - + +
168E GLY 3.3 7.3 + - - -
169E SER* 2.7 36.3 + - - +
170E ALA* 3.8 8.0 - - - +
171E THR 5.0 0.9 + - - -
186E LEU 3.8 3.3 - - - +
188E PRO* 3.3 26.3 - - + +
45F SER* 2.9 34.0 + - - +
46F SER* 4.0 6.1 - - - +
47F ALA 3.3 0.2 - - - -
48F VAL* 1.3 75.6 - - - +
50F LYS* 1.3 69.0 + - - +
51F ALA 3.5 1.1 - - - -
167F TYR* 3.8 9.3 - - - +
168F GLY 2.8 31.3 + - - +
169F SER 3.9 2.6 + - - -
170F ALA* 3.2 21.2 - - - +
171F THR* 3.1 27.2 + - - +
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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