Contacts of the helix formed by residues 54 - 68 (chain E) in PDB entry 4ADV
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 GLU 54 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C LYS* 4.3 20.2 + - - -
32E PHE* 3.4 7.6 - - - -
52E ALA* 3.1 1.9 - - - +
53E ARG* 1.3 100.2 + - + +
55E VAL* 1.3 66.2 + - - +
56E PRO* 3.8 16.4 - - + +
57E ALA* 3.6 21.0 - - + +
58E ALA* 3.1 24.8 + - - +
60E GLN* 5.7 0.5 + - - -
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Residues in contact with VAL 55 (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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17E VAL* 4.9 21.8 - - + +
32E PHE* 3.4 37.5 - - + -
34E ALA* 5.6 0.7 - - - +
54E GLU* 1.3 72.6 - - - +
56E PRO* 1.3 69.2 - - + +
58E ALA* 3.7 12.0 - - - +
59E ILE* 3.8 8.7 + - - +
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Residues in contact with PRO 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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54E GLU* 3.4 18.2 - - + +
55E VAL* 1.3 96.8 - - + +
57E ALA* 1.3 64.0 + - - +
58E ALA 3.1 2.0 - - - -
59E ILE* 2.8 30.6 - - + +
60E GLN* 3.0 18.6 - - + +
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Residues in contact with ALA 57 (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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1072A G 5.9 1.6 - - - +
1073A U 4.3 5.0 + - - +
52E ALA* 3.5 18.4 - - + -
53E ARG 5.1 0.2 - - - +
54E GLU* 3.3 26.4 + - + +
56E PRO* 1.3 82.3 - - - +
58E ALA* 1.3 65.3 + - - +
60E GLN* 3.1 32.7 - - - +
61E LYS* 3.4 10.6 + - - +
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Residues in contact with ALA 58 (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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32E PHE* 3.9 13.9 - - + +
33E THR 3.1 23.8 - - - +
34E ALA* 4.6 1.3 - - + -
50E GLY 3.7 8.9 - - - +
51E LYS 3.9 4.7 - - - -
52E ALA* 3.1 16.4 - - + +
54E GLU 3.1 17.0 + - - +
55E VAL 3.7 6.3 - - - +
57E ALA* 1.3 71.7 - - - +
59E ILE* 1.3 64.4 + - - +
60E GLN 2.8 5.7 + - - -
61E LYS* 2.8 17.2 + - - +
62E ALA 3.3 8.1 + - - -
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Residues in contact with ILE 59 (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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14E LEU* 3.8 30.5 - - + -
33E THR 4.3 0.6 + - - -
34E ALA* 4.5 10.7 - - + +
36E THR* 4.0 13.2 - - + -
55E VAL 3.8 5.0 + - - +
56E PRO* 2.8 37.2 - - + +
58E ALA* 1.3 76.0 - - - +
60E GLN* 1.3 62.4 + - + +
62E ALA* 4.0 7.6 - - - +
63E MET* 3.1 43.8 + - + +
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Residues in contact with GLN 60 (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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1073A U 5.8 0.2 - - - +
54E GLU* 5.7 0.6 + - - -
56E PRO* 3.0 22.8 + - + +
57E ALA* 3.1 31.1 - - - +
58E ALA 2.8 2.0 + - - -
59E ILE* 1.3 81.3 - - + +
61E LYS* 1.3 60.0 + - + +
63E MET* 3.7 4.4 - - - +
64E GLU* 3.4 20.1 + - - +
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Residues in contact with LYS 61 (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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1072A G 2.3 11.9 + - - -
1073A U 0.3 102.1 + - - +
1074A G 3.6 22.0 - - - +
50E GLY* 4.0 8.7 - - - -
51E LYS 3.0 28.0 - - - +
52E ALA* 4.2 8.5 - - - -
57E ALA* 3.5 9.6 - - - +
58E ALA 2.8 12.5 + - - +
60E GLN* 1.3 70.5 - - + +
62E ALA* 1.3 66.3 + - - +
64E GLU* 3.0 8.8 + - - +
65E LYS* 2.9 28.2 + - + +
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Residues in contact with ALA 62 (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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34E ALA 4.0 8.3 - - - +
36E THR* 3.3 17.7 - - + +
48E GLY* 3.2 16.9 - - - +
49E TYR* 3.8 5.6 - - - +
50E GLY 3.4 26.3 - - - +
58E ALA 3.3 6.6 + - - +
59E ILE* 4.0 10.5 - - - +
61E LYS* 1.3 77.2 - - - +
63E MET* 1.3 57.3 + - - +
65E LYS* 3.5 1.5 + - - -
66E ALA* 2.8 29.3 + - - +
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Residues in contact with MET 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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12E GLU* 3.5 57.2 - - + +
13E LYS 5.3 0.4 - - - +
14E LEU* 5.9 1.6 - - + +
36E THR* 3.6 25.0 + - + -
38E VAL* 4.6 1.6 - - + -
59E ILE* 3.1 40.3 + - + +
60E GLN* 3.7 6.1 - - - +
62E ALA* 1.3 73.8 - - - +
64E GLU* 1.3 58.5 + - - +
66E ALA* 2.7 24.5 + - - +
67E ARG* 2.9 20.9 + - - +
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Residues in contact with GLU 64 (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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1074A G 5.4 0.9 - - - +
104B LYS* 4.1 24.6 - - + +
60E GLN 3.4 9.4 + - - +
61E LYS* 3.0 11.1 + - - +
63E MET* 1.3 78.4 - - - +
65E LYS* 1.3 76.2 + - + +
66E ALA 3.0 1.2 + - - -
67E ARG* 3.2 20.9 + - - +
68E ARG* 3.4 18.6 + - - +
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Residues in contact with LYS 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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1074A G 2.2 66.0 + - - +
1075A U 3.1 24.4 + - - -
101B THR* 4.7 7.2 - - - -
104B LYS* 4.3 8.5 - - + +
47E PHE 4.1 5.6 - - - +
48E GLY* 4.7 5.4 - - - -
49E TYR 4.8 11.9 + - - +
50E GLY* 5.8 0.2 - - - -
61E LYS* 2.9 23.6 + - + +
62E ALA* 3.8 7.2 - - - +
64E GLU* 1.3 82.2 - - + +
66E ALA* 1.3 56.7 + - - +
68E ARG* 2.9 25.1 - - - +
69E ASN* 4.4 8.1 - - - +
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Residues in contact with ALA 66 (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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36E THR 4.0 3.1 - - - +
38E VAL* 3.5 26.0 - - + -
46E GLY 3.3 19.9 - - - +
47E PHE 3.5 9.6 - - - -
48E GLY* 3.9 9.4 - - - +
62E ALA 2.8 14.6 + - - +
63E MET* 2.7 17.0 + - - +
65E LYS* 1.3 75.1 - - - +
67E ARG* 1.3 56.9 + - - +
68E ARG 2.7 18.5 - - - +
70E MET* 3.7 7.3 - - - +
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Residues in contact with ARG 67 (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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10E LEU* 4.1 31.7 + - + +
12E GLU* 2.7 29.4 + - - +
38E VAL* 4.7 7.8 - - + +
63E MET* 2.9 24.0 + - + +
64E GLU* 3.2 13.4 + - - +
66E ALA* 1.3 72.0 - - + +
68E ARG* 1.3 57.0 + - - +
70E MET* 3.1 31.4 - - - +
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Residues in contact with ARG 68 (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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155B GLY* 4.8 4.0 - - - -
156B LEU* 2.5 62.8 + - - +
178B LEU* 4.6 6.2 - - + +
47E PHE 5.0 0.5 - - - +
64E GLU* 3.4 18.1 + - - +
65E LYS* 2.9 16.1 - - - +
66E ALA 2.7 15.7 - - - +
67E ARG* 1.3 78.6 - - - +
69E ASN* 1.3 84.7 + - + +
70E MET 3.3 0.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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