Contacts of the helix formed by residues 18 - 33 (chain A) in PDB entry 5ONS
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 LYS 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN 5.0 5.2 - - - +
17A LEU* 1.3 80.1 - - - +
19A THR* 1.3 59.2 + - - +
20A SER* 3.2 6.7 - - - +
21A VAL* 2.8 35.9 + - + +
22A ILE* 3.0 11.5 + - - +
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 4.2 0.2 + - - -
18A LYS* 1.3 73.3 - - - +
20A SER* 1.3 64.5 + - - +
22A ILE* 3.9 13.1 - - + +
23A LYS* 3.2 25.5 + - + +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.2 6.0 - - - +
19A THR* 1.3 80.6 - - - +
21A VAL* 1.3 68.5 + - - +
23A LYS* 3.6 5.7 + - - +
24A GLY* 3.5 14.7 + - - -
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.2 17.9 - - + -
18A LYS* 2.8 29.7 + - + +
20A SER* 1.3 79.5 - - - +
22A ILE* 1.3 62.6 + - - +
24A GLY* 3.2 2.8 + - - -
25A ILE* 3.0 40.7 + - + +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.7 35.7 - - + +
18A LYS 3.0 13.7 + - - +
19A THR* 3.3 12.1 + - + +
21A VAL* 1.3 77.9 - - - +
23A LYS* 1.3 63.0 + - - +
25A ILE* 3.3 6.1 + - - +
26A LYS* 2.9 49.4 + - + +
44A MET* 4.1 13.7 - - + -
48A ASP 5.6 1.1 - - - +
49A PRO* 5.8 0.9 - - + -
50A VAL* 3.8 30.3 - - + +
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.2 18.1 + - + +
20A SER* 4.1 4.7 - - - +
21A VAL 3.3 0.2 - - - -
22A ILE* 1.3 76.6 - - - +
24A GLY* 1.3 58.9 + - - +
26A LYS* 3.4 9.0 + - - +
27A ASN* 3.0 51.4 + - - +
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER 3.5 8.0 + - - -
21A VAL* 3.2 6.3 + - - -
22A ILE 3.2 0.6 - - - -
23A LYS* 1.3 82.4 - - - +
25A ILE* 1.3 60.8 + - - +
27A ASN* 3.4 10.2 + - - +
28A GLN* 3.0 31.9 + - - +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.6 30.7 - - + -
21A VAL* 3.0 26.9 + - + +
22A ILE* 3.3 4.7 + - - +
24A GLY* 1.3 71.7 - - - +
26A LYS* 1.3 60.8 + - - +
28A GLN* 3.0 20.3 + - - +
29A LEU* 2.8 32.6 + - + +
44A MET* 5.4 4.0 - - + -
52A ILE* 4.4 7.9 - - + -
62A LEU* 4.0 28.9 - - + -
72A ARG* 4.4 14.8 - - - +
78A PHE* 3.9 23.6 - - + -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 2.9 38.9 + - + +
23A LYS* 3.6 8.7 - - - +
25A ILE* 1.3 76.0 - - - +
27A ASN* 1.3 58.9 + - - +
29A LEU* 3.1 10.5 + - - +
30A ILE* 2.8 35.3 + - + +
40A LEU* 4.0 29.1 - - + +
41A ASN* 5.6 4.3 - - - -
44A MET* 3.6 50.0 + - + +
45A PRO 5.5 1.0 + - - -
46A LYS* 5.6 2.4 - - - +
50A VAL* 5.4 1.2 - - - +
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.0 45.5 + - - +
24A GLY* 3.5 11.9 - - - +
25A ILE 3.2 0.2 - - - -
26A LYS* 1.3 76.4 - - - +
28A GLN* 1.3 58.0 + - + +
30A ILE* 3.1 11.7 + - - +
31A GLU* 2.9 45.1 + - - +
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 3.0 18.5 + - - +
25A ILE* 3.0 21.1 + - - +
27A ASN* 1.3 76.8 - - + +
29A LEU* 1.3 62.7 + - - +
31A GLU* 3.4 16.2 + - - +
32A GLN* 3.0 32.0 + - + +
72A ARG* 3.5 29.7 + - - +
75A GLU* 4.2 11.0 + - - +
76A GLY 5.6 1.2 + - - -
78A PHE* 4.5 10.2 - - + -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 2.8 22.0 + - + +
26A LYS* 3.1 9.6 + - - +
28A GLN* 1.3 76.6 - - - +
30A ILE* 1.3 52.3 + - - +
32A GLN* 3.3 0.7 + - - -
33A PHE* 2.8 45.2 + - + +
36A ILE* 3.9 12.3 - - + +
40A LEU* 4.5 9.0 - - + -
44A MET* 4.2 15.9 - - - -
62A LEU* 4.1 15.3 - - + -
70A PHE* 3.7 42.8 - - + -
78A PHE* 3.7 38.8 - - + -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 2.8 21.0 + - + +
27A ASN* 3.1 13.7 + - - +
29A LEU* 1.3 75.8 - - - +
31A GLU* 1.3 66.4 + - + +
33A PHE 4.2 2.2 - - - -
34A PRO* 3.3 27.9 - - + +
36A ILE* 3.9 2.2 - - + -
37A GLU* 3.4 52.5 - - + +
40A LEU* 3.4 20.9 - - + -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 2.9 36.5 + - - +
28A GLN* 3.8 14.1 + - - +
30A ILE* 1.3 78.7 - - + +
32A GLN* 1.3 62.9 + - + +
34A PRO* 4.1 8.5 - - - +
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLN* 3.0 19.5 + - - +
29A LEU 3.8 2.5 - - - +
31A GLU* 1.3 81.6 - - + +
33A PHE* 1.3 84.0 + - + +
34A PRO* 3.4 8.5 - - - +
77A PRO* 3.5 17.9 - - + +
78A PHE* 2.8 58.3 + - - +
131A ILE* 3.7 7.1 - - - +
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 2.8 24.9 + - + +
30A ILE* 3.4 3.8 - - - +
32A GLN* 1.3 101.8 - - + +
34A PRO* 1.3 69.6 - - - +
35A GLY 3.3 2.7 - - - -
36A ILE* 2.8 32.3 + - + +
70A PHE* 3.8 32.5 - + - -
78A PHE* 3.3 30.1 - - + -
80A PRO* 4.1 10.3 - - + -
91A ILE* 4.0 28.3 - - + +
92A LEU* 3.7 21.1 - - + -
131A ILE* 4.5 7.4 - - + -
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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