Contacts of the helix formed by residues 22 - 34 (chain A) in PDB entry 1OZ7
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 THR 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 1.3 77.1 - - - +
23A TRP* 1.3 69.0 + - - +
24A ASP* 3.3 28.0 - - + +
25A GLU* 3.2 26.1 + - + +
26A ALA* 2.9 21.1 + - - +
66A TRP* 3.9 0.7 - - - -
117A CYS* 3.6 13.0 - - + +
118A GLU* 3.5 19.2 + - - -
119A ASN 3.6 8.1 - - - -
120A THR* 4.5 4.4 - - - +
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Residues in contact with TRP 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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22A THR* 1.3 75.1 - - - +
24A ASP* 1.3 100.5 + - - +
26A ALA* 3.7 0.3 - - - +
27A GLU* 2.9 53.3 + - + +
39A LEU* 3.7 17.2 - - + +
66A TRP* 3.7 22.1 - + + +
67A THR 4.3 11.0 + - - -
68A GLY 4.6 1.2 - - - -
69A LEU 4.0 5.1 + - - -
70A SER* 3.1 45.3 - - - +
100A CYS* 2.8 40.2 - - + -
117A CYS* 3.1 16.0 + - + +
80B SER* 4.4 17.7 - - - -
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Residues in contact with ASP 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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22A THR* 3.2 13.7 - - + +
23A TRP* 1.3 108.4 - - - +
25A GLU* 1.3 60.2 + - + +
27A GLU* 3.6 2.6 - - - +
28A LYS* 2.9 28.6 + - - +
117A CYS* 5.2 6.0 - - - +
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Residues in contact with GLU 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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21A LYS* 4.0 18.2 - - + +
22A THR* 3.2 35.9 + - + +
24A ASP* 1.3 76.2 - - + +
26A ALA* 1.3 62.1 + - - +
28A LYS* 3.3 7.0 + - - +
29A PHE* 2.8 29.5 + - - +
120A THR* 5.7 1.2 - - - +
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Residues in contact with ALA 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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21A LYS* 4.0 15.1 - - + +
22A THR 2.9 17.3 + - - +
23A TRP 3.7 2.9 - - - +
25A GLU* 1.3 73.4 - - - +
27A GLU* 1.3 66.8 + - - +
29A PHE* 3.1 5.6 + - - +
30A CYS* 2.9 27.7 + - - -
39A LEU* 3.8 11.0 - - + -
66A TRP* 4.6 5.6 - - + -
123A PHE* 3.6 34.9 - - + -
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Residues in contact with GLU 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 TRP* 2.9 41.0 + - + +
24A ASP 3.6 4.7 - - - +
26A ALA* 1.3 76.2 - - - +
28A LYS* 1.3 63.1 + - - +
30A CYS* 3.2 13.5 + - - +
31A ASN* 3.2 15.6 + - - +
38A HIS* 2.5 33.4 + - - +
39A LEU* 3.1 33.4 + - + +
80B SER* 2.6 31.0 + - - -
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Residues in contact with LYS 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 ASP 2.9 19.4 + - - +
25A GLU* 3.5 8.3 - - - +
27A GLU* 1.3 77.6 - - - +
29A PHE* 1.3 61.4 + - - +
31A ASN* 2.7 65.2 + - - +
32A LYS* 3.3 38.5 - - - +
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Residues in contact with PHE 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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17A PHE* 4.0 29.8 - + - -
19A GLU* 5.8 6.5 - - + -
21A LYS* 3.7 24.7 - - - -
25A GLU 2.8 20.9 + - - +
26A ALA* 3.3 8.5 - - - +
28A LYS* 1.3 74.5 - - - +
30A CYS* 1.3 59.4 + - - +
32A LYS* 3.1 16.6 + - + +
33A GLN* 2.5 59.7 + - + +
123A PHE* 3.3 30.7 - + - -
125A CYS* 4.0 2.2 - - - -
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Residues in contact with CYS 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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6A TRP* 5.8 0.3 - - - -
26A ALA 2.9 17.4 + - - -
27A GLU 3.2 6.0 + - - +
29A PHE* 1.3 76.2 - - - +
31A ASN* 1.3 60.1 + - - +
32A LYS 3.1 1.8 + - - -
33A GLN* 3.6 14.1 + - - +
34A GLY 4.2 0.3 - - - +
37A GLY* 3.2 17.5 - - - -
38A HIS* 3.5 28.5 - - - +
39A LEU* 4.1 6.3 - - - -
123A PHE* 3.7 11.0 - - - -
125A CYS* 2.0 56.9 - - + +
127A TYR* 5.8 0.3 - - - -
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Residues in contact with ASN 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 GLU* 3.2 10.1 + - - +
28A LYS* 2.7 65.1 + - - +
30A CYS* 1.3 76.7 - - - +
32A LYS* 1.3 69.0 + - - +
34A GLY 3.8 12.1 + - - +
35A LYS* 5.2 0.5 - - - -
36A ASP* 4.9 3.3 + - - -
37A GLY 3.3 20.1 + - - +
38A HIS* 5.0 9.0 - - + +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.3 45.6 - - - +
29A PHE* 3.1 15.8 + - + +
31A ASN* 1.3 90.3 + - - +
33A GLN* 1.3 70.7 + - - +
34A GLY 3.3 3.0 + - - -
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Residues in contact with GLN 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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6A TRP* 4.0 32.5 - - + -
17A PHE* 4.9 3.3 - - + -
29A PHE* 2.5 65.4 + - + +
30A CYS* 3.9 11.7 - - - +
31A ASN 3.5 0.6 - - - -
32A LYS* 1.3 89.4 - - - +
34A GLY* 1.3 56.8 + - - +
125A CYS* 4.7 0.4 - - - -
127A TYR* 5.2 6.4 - - + -
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Residues in contact with GLY 34 (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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30A CYS 4.2 1.2 + - - -
31A ASN 3.8 8.5 - - - +
32A LYS 3.3 2.7 - - - -
33A GLN* 1.3 81.1 - - - +
35A LYS* 1.3 68.7 + - - -
36A ASP 2.9 0.7 + - - -
37A GLY* 2.8 19.3 + - - -
127A TYR* 5.0 18.1 - - - -
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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