Contacts of the helix formed by residues 55 - 77 (chain E) in PDB entry 1VQ7
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 ASN 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11390 U 4.7 1.3 - - - +
11400 C 3.4 22.0 - - - +
53E GLU* 3.5 30.1 + - - -
54E ASP* 1.3 84.4 - - - +
56E ALA* 1.3 65.8 + - - +
57E LYS* 3.2 13.0 + - - +
58E THR* 2.8 46.2 + - - -
59E MET* 3.1 7.8 + - - +
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Residues in contact with ALA 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11390 U 3.5 38.1 + - - +
11400 C 2.8 17.3 + - - +
27840 A 3.6 15.1 + - - +
54E ASP 3.7 0.8 + - - -
55E ASN* 1.3 70.5 - - - +
57E LYS* 1.3 57.2 + - - +
59E MET* 3.3 4.7 + - - +
60E SER* 2.7 33.6 + - - -
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11170 A 4.6 35.5 + - - +
11180 A 4.9 3.8 + - - -
11380 G 3.7 24.6 + - - -
11390 U 4.0 25.0 + - - +
27920 A 4.5 20.4 + - - +
35E TYR* 3.5 24.7 + - - +
55E ASN* 3.2 10.1 + - - +
56E ALA* 1.3 76.2 - - - +
58E THR* 1.3 61.1 + - - +
60E SER* 3.4 9.3 - - - -
61E THR* 3.4 18.0 + - - -
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Residues in contact with THR 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TYR* 4.4 11.9 - - + -
36E PRO 5.1 4.3 + - - +
38E ILE* 4.1 10.8 - - + -
51E SER* 3.8 21.1 - - - +
53E GLU* 3.4 29.8 + - + +
55E ASN* 2.8 33.2 + - - -
57E LYS* 1.3 73.0 - - - +
59E MET* 1.3 67.4 + - - +
60E SER 3.1 1.1 - - - -
61E THR* 3.0 5.2 + - - -
62E ILE* 2.8 28.9 + - + +
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Residues in contact with MET 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27830 A 3.8 2.6 + - - -
27840 A 4.4 19.1 - - - +
1E PRO* 3.5 41.3 - - + -
54E ASP* 3.4 28.9 - - + +
55E ASN 3.1 4.2 + - - +
56E ALA* 3.8 7.0 - - - +
58E THR* 1.3 76.4 - - - +
60E SER* 1.3 65.7 + - - +
62E ILE* 3.6 13.9 - - + +
63E GLY* 2.9 21.1 + - - -
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11390 U 5.1 2.6 + - - -
27830 A 2.7 32.0 + - - -
27840 A 3.2 29.8 + - - -
27920 A 3.9 12.6 - - - -
56E ALA 2.7 21.7 + - - -
57E LYS* 3.4 13.6 - - - -
58E THR 3.1 0.2 - - - -
59E MET* 1.3 77.1 - - - +
61E THR* 1.3 56.1 + - - +
64E THR* 2.7 26.0 + - - -
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Residues in contact with THR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27920 A 3.8 12.6 - - - -
27930 A 4.1 5.2 - - - +
35E TYR* 3.2 35.6 + - + -
38E ILE* 3.4 20.2 - - + -
57E LYS 3.4 5.1 + - - -
58E THR 3.0 3.8 + - - -
60E SER* 1.3 75.0 - - - +
62E ILE* 1.3 67.2 + - - +
64E THR* 2.9 8.5 + - - -
65E PHE* 2.8 56.6 + - + -
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E PRO* 3.9 27.6 - - + -
3E VAL* 4.0 27.6 - - + -
38E ILE* 3.7 18.2 - - + -
49E ILE* 4.0 23.0 - - + +
50E GLU* 4.8 3.6 - - - -
51E SER* 4.4 15.0 - - - +
58E THR* 2.8 34.9 + - + +
59E MET* 3.6 19.3 - - + +
61E THR* 1.3 74.0 - - - +
63E GLY* 1.3 64.7 + - - +
65E PHE* 3.2 11.1 + - - +
66E GLN* 3.2 12.1 + - - +
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Residues in contact with GLY 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27830 A 3.7 23.4 - - - +
27840 A 5.6 1.6 - - - -
59E MET 2.9 14.8 + - - -
62E ILE* 1.3 80.1 - - - +
64E THR* 1.3 60.8 + - - +
66E GLN* 3.7 10.3 - - - +
67E SER* 3.5 24.6 + - - -
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Residues in contact with THR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27820 G 3.1 27.8 + - + +
27830 A 3.3 4.4 - - - -
27920 A 2.8 23.9 + - - +
27930 A 3.9 15.9 - - + +
60E SER 2.7 19.6 + - - -
61E THR* 2.9 10.9 + - - -
63E GLY* 1.3 77.0 - - - +
65E PHE* 1.3 65.9 + - + +
67E SER* 3.6 2.3 + - - -
68E HIS* 3.1 51.7 + - + +
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Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27930 A 4.4 15.7 - + - -
33E LEU* 3.6 57.4 - - + -
34E TRP 4.0 3.1 - - - -
35E TYR* 3.8 11.2 - - + -
38E ILE* 3.4 37.2 - - + -
40E VAL* 4.0 12.1 - - + -
49E ILE* 3.6 16.6 - - + -
61E THR* 2.8 36.5 + - + -
62E ILE 3.6 7.4 - - - +
64E THR* 1.3 77.2 - - - +
66E GLN* 1.3 67.4 + - - +
68E HIS* 3.0 10.4 + + - +
69E ILE* 2.8 25.6 + - - +
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Residues in contact with GLN 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL* 4.3 17.7 - - + +
5E LEU* 3.5 33.2 - - + +
49E ILE* 3.5 13.6 - - + +
62E ILE* 3.2 9.5 + - + +
63E GLY* 3.7 13.7 - - - +
65E PHE* 1.3 76.4 - - - +
67E SER* 1.3 60.2 + - - +
69E ILE* 2.7 24.9 + - - +
70E GLU* 2.9 37.4 + - - +
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Residues in contact with SER 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27820 G 3.5 17.4 + - - +
27830 A 2.6 32.0 + - - -
63E GLY 3.5 14.3 + - - -
64E THR 4.1 2.0 - - - -
65E PHE 3.4 0.2 - - - -
66E GLN* 1.3 81.6 + - - +
68E HIS* 1.3 58.5 + - - +
70E GLU* 4.1 14.6 + - - -
71E ASN* 2.8 36.9 + - - +
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Residues in contact with HIS 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27810 U 3.4 28.0 + - - -
27820 G 4.1 13.6 - - - -
27930 A 2.9 33.5 + + - -
27940 G 5.9 0.2 - - - -
31E ARG* 2.7 33.7 + - - +
33E LEU* 4.6 7.6 - - + -
64E THR* 3.1 34.4 + - + +
65E PHE* 3.0 16.1 + + - +
66E GLN 2.9 1.0 + - - -
67E SER* 1.3 76.4 - - - +
69E ILE* 1.3 63.9 + - + +
71E ASN* 3.5 7.4 + - - +
72E MET* 3.1 26.6 + - + +
138E ILE* 5.9 1.8 - - - +
139E GLU* 3.8 7.8 + - - -
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Residues in contact with ILE 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.0 12.1 - - + -
20E ILE* 4.4 4.7 - - + -
22E VAL* 5.2 1.3 - - + -
33E LEU* 4.0 20.2 - - + -
40E VAL* 4.2 3.4 - - + -
47E VAL* 3.9 25.1 - - + -
49E ILE* 3.8 23.6 - - + -
65E PHE 2.8 16.3 + - - +
66E GLN 2.7 11.8 + - - +
68E HIS* 1.3 68.2 - - - +
70E GLU* 1.3 57.1 + - - +
71E ASN 3.0 1.6 - - - -
72E MET* 2.6 50.8 + - + +
73E PHE* 2.9 40.0 + - + -
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.0 21.2 - - + +
66E GLN* 2.9 50.9 + - - +
67E SER* 4.1 12.0 + - - +
69E ILE* 1.3 71.9 - - - +
71E ASN* 1.3 65.6 + - - +
73E PHE* 3.1 18.6 + - + +
74E HIS* 3.0 22.7 + - - +
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Residues in contact with ASN 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27810 U 3.7 2.8 + - - -
27820 G 2.9 27.7 + - - -
67E SER* 2.8 27.6 + - - +
68E HIS* 3.6 8.1 - - - +
69E ILE 3.0 0.8 - - - -
70E GLU* 1.3 79.5 - - - +
72E MET* 1.3 58.5 + - - +
74E HIS* 4.4 0.2 - - - -
75E GLY 2.9 21.1 + - - -
80E TRP* 3.0 34.9 + - + -
138E ILE* 3.0 39.5 - - + +
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Residues in contact with MET 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 4.4 14.8 - - + +
22E VAL* 4.0 29.8 - - + -
29E VAL* 3.9 32.5 - - + +
31E ARG* 4.1 25.4 - - + -
33E LEU* 5.2 4.0 - - + -
68E HIS* 3.1 12.3 - - + +
69E ILE* 2.6 59.6 + - + +
71E ASN* 1.3 69.6 - - - +
73E PHE* 1.3 64.2 + - - +
75E GLY* 2.9 3.8 + - - -
76E VAL* 2.8 28.9 + - - +
136E PRO 4.8 4.9 - - - +
138E ILE* 6.5 0.4 - - + -
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Residues in contact with PHE 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.6 9.9 - - + -
6E GLU 3.9 8.5 - - - -
7E ILE* 3.8 33.7 - - + -
8E PRO* 3.5 33.0 - - + -
11E VAL* 4.1 6.1 - - + -
13E ALA* 4.4 3.1 - - + -
22E VAL* 3.7 25.8 - - + -
47E VAL* 4.2 13.2 - - + -
69E ILE* 2.9 34.6 + - + -
70E GLU* 3.3 22.0 - - + +
72E MET* 1.3 75.9 - - - +
74E HIS* 1.3 64.6 + - - +
76E VAL* 2.8 25.4 - - - +
77E THR* 3.0 13.1 + - - +
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Residues in contact with HIS 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLU 3.0 9.5 + - - +
71E ASN 3.7 1.1 - - - +
73E PHE* 1.3 77.8 - - - +
75E GLY* 1.3 54.7 + - - +
77E THR* 3.6 7.1 + - - -
78E GLU* 3.0 46.6 + - + +
79E GLY 2.5 57.3 + - - -
80E TRP* 3.6 42.7 - + + -
172E PRO* 5.7 1.4 - - - +
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Residues in contact with GLY 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ASN* 2.7 31.7 + - - -
71E ASN 2.9 7.7 + - - -
72E MET 2.9 8.0 + - - -
74E HIS* 1.3 77.5 - - - +
76E VAL* 1.3 54.1 + - - +
79E GLY* 3.4 7.9 - - - -
80E TRP* 3.4 11.4 - - - +
136E PRO* 3.1 29.5 - - - +
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.5 33.9 - - + -
22E VAL* 3.3 25.4 - - + +
23E GLU 4.1 0.4 - - - -
24E GLY* 3.4 18.1 - - - +
25E ASP 3.5 0.7 + - - -
26E ASN* 2.7 32.3 + - - +
27E GLY 3.2 24.9 - - - +
28E SER* 4.5 1.3 - - - -
29E VAL* 4.6 7.2 - - + +
72E MET 2.8 18.4 + - - +
73E PHE* 2.8 24.2 - - - +
75E GLY* 1.3 74.9 - - - +
77E THR* 1.3 60.0 + - - +
136E PRO* 4.7 0.4 - - + -
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Residues in contact with THR 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PRO* 4.5 8.7 - - + -
10E ASP* 4.0 25.1 - - + -
11E VAL* 3.2 33.9 - - + -
25E ASP* 5.7 1.1 - - - +
26E ASN* 3.4 10.9 + - - +
73E PHE 3.0 7.9 + - - +
74E HIS* 3.2 13.0 + - - -
76E VAL* 1.3 81.3 - - - +
78E GLU* 1.3 83.2 + - - +
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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) + - + + + + + -
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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