Contacts of the helix formed by residues 21 - 30 (chain A) in PDB entry 4OA5
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.8 6.9 - - + +
20A ASP* 1.3 88.6 - - - +
22A GLU* 1.3 65.8 + - - +
24A ALA* 3.3 19.4 + - - +
25A LEU* 3.2 20.4 + - - +
49A GLN* 6.3 0.7 - - - +
76A HIS* 3.8 30.4 + - + +
306A IOD 4.4 8.3 - - - -
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Residues in contact with GLU 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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20A ASP 3.7 3.6 + - - +
21A THR* 1.3 71.7 - - - +
23A GLY* 1.3 56.3 + - - +
25A LEU* 3.3 24.6 + - - +
26A LYS* 2.9 70.4 + - - +
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Residues in contact with GLY 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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21A THR 3.3 0.8 - - - -
22A GLU* 1.3 78.5 - - - +
24A ALA* 1.3 55.6 + - - +
26A LYS* 3.5 2.3 + - - +
27A ALA* 3.0 28.4 + - - +
100A ASN* 5.6 0.2 - - - +
104A CYS* 3.5 29.4 - - - -
306A IOD 3.6 16.4 - - - +
315A IOD 3.9 16.9 - - - +
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Residues in contact with ALA 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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19A VAL* 3.8 20.4 - - + -
21A THR* 3.3 21.0 + - - +
23A GLY* 1.3 71.3 - - - +
25A LEU* 1.3 66.1 + - - +
27A ALA* 3.2 4.4 + - - +
28A HIS 3.0 19.9 + - - -
69A PHE* 3.3 24.0 - - + -
72A ILE* 3.9 24.5 - - + +
73A CYS* 4.3 4.5 - - - +
76A HIS* 5.2 1.3 - - + +
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Residues in contact with LEU 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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19A VAL* 4.0 8.5 - - + +
20A ASP* 3.9 21.5 - - + +
21A THR 3.2 17.1 + - - +
22A GLU* 3.7 25.4 - - - +
24A ALA* 1.3 77.8 - - + +
26A LYS* 1.3 62.6 + - - +
28A HIS* 3.5 8.5 + - + +
29A LYS* 3.4 24.0 + - - +
42A THR* 3.6 31.2 - - + -
69A PHE* 5.4 0.7 - - + -
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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 GLU* 2.9 44.8 + - - +
23A GLY* 3.8 4.7 - - - +
25A LEU* 1.3 75.3 - - - +
27A ALA* 1.3 66.1 + - - +
29A LYS* 3.1 23.2 + - - +
30A THR* 3.4 16.8 + - + +
100A ASN* 5.3 0.7 - - - +
315A IOD 3.8 28.4 - - + +
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Residues in contact with ALA 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 GLY 3.0 18.3 + - - +
24A ALA* 3.2 6.0 + - - +
26A LYS* 1.3 75.3 - - - +
28A HIS* 1.3 63.8 + - - +
30A THR* 2.7 22.4 + - - -
67A VAL* 3.4 13.2 - - - +
69A PHE* 4.6 7.2 - - - -
72A ILE* 3.8 23.3 - - + -
100A ASN* 3.7 28.0 - - + +
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Residues in contact with HIS 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 ALA 3.0 12.5 + - - +
25A LEU* 3.5 13.2 - - + +
26A LYS 3.2 0.2 - - - -
27A ALA* 1.3 77.0 - - - +
29A LYS* 1.3 59.9 + - - +
30A THR 3.3 0.7 + - - -
31A ALA* 3.5 6.2 + - - +
36A ARG* 3.3 40.4 + - - +
39A GLN* 3.1 47.0 + - - +
40A LEU 3.0 29.3 + - - -
41A GLY* 4.4 5.3 - - - -
42A THR* 5.4 4.0 + - + -
69A PHE* 3.6 29.1 - + + -
307A IOD 4.3 10.8 - - + -
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Residues in contact with LYS 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 LEU 3.4 12.8 + - - +
26A LYS* 3.1 16.6 + - - +
28A HIS* 1.3 76.4 - - - +
30A THR* 1.3 61.2 + - + +
31A ALA 3.3 5.3 + - - +
36A ARG* 3.4 22.7 + - - +
316A IOD 3.8 31.7 - - + +
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Residues in contact with THR 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* 3.4 16.6 - - + +
27A ALA 2.7 19.3 + - - -
29A LYS* 1.3 74.7 - - + +
31A ALA* 1.3 66.1 + - - +
32A PRO* 3.6 3.3 - - - +
67A VAL* 3.4 9.9 - - - +
96A THR* 3.5 16.4 - - + +
100A ASN* 2.9 32.1 + - - +
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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