Contacts of the helix formed by residues 21 - 30 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F VAL* 3.8 6.9 - - + +
20F ASP* 1.3 88.2 - - - +
22F GLU* 1.3 65.3 + - - +
23F GLY 4.5 2.5 - - - -
24F ALA* 3.5 20.1 + - - +
25F LEU* 3.2 20.1 + - - +
49F GLN* 6.2 1.3 - - - +
76F HIS* 3.8 28.5 + - + +
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Residues in contact with GLU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASP 3.7 3.0 + - - -
21F THR* 1.3 70.9 - - - +
23F GLY* 1.3 57.3 + - - +
25F LEU* 3.3 9.5 + - - +
26F LYS* 2.9 50.3 + - + +
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Residues in contact with GLY 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F THR* 3.3 2.6 + - - -
22F GLU* 1.3 78.4 - - - +
24F ALA* 1.3 56.2 + - - +
26F LYS* 3.5 6.9 + - - +
27F ALA* 3.0 28.4 + - - +
76F HIS* 5.8 1.6 - - - -
103F ASN* 6.1 0.7 - - - -
104F CYS* 3.5 28.8 - - - -
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL* 3.8 19.7 - - + -
21F THR* 3.3 22.3 + - - +
23F GLY* 1.3 72.3 - - - +
25F LEU* 1.3 66.4 + - - +
27F ALA* 3.2 4.1 + - - +
28F HIS 3.0 19.2 + - - -
69F PHE* 3.3 24.2 - - + -
72F ILE* 4.0 23.0 - - + +
73F CYS* 4.3 4.7 - - - -
76F HIS* 5.1 1.5 - - + +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL* 4.0 8.1 - - + +
20F ASP* 3.9 22.9 - - + +
21F THR 3.2 19.9 + - - +
22F GLU* 3.7 6.7 - - - +
24F ALA* 1.3 76.3 - - - +
26F LYS* 1.3 63.3 + - + +
28F HIS* 3.4 8.5 + - + +
29F LYS* 3.4 18.2 + - - +
42F THR* 3.6 31.6 - - + -
69F PHE* 5.0 0.7 - - + -
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Residues in contact with LYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLU* 2.9 34.7 + - + +
23F GLY* 3.8 6.5 - - - +
25F LEU* 1.3 76.0 - - + +
27F ALA* 1.3 66.0 + - - +
29F LYS* 3.1 16.5 + - - +
30F THR* 3.4 17.8 + - + +
103F ASN* 6.4 0.2 - - - +
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Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F GLY 3.0 18.5 + - - +
24F ALA* 3.2 5.8 + - - +
26F LYS* 1.3 75.5 - - - +
28F HIS* 1.3 63.8 + - - +
30F THR* 2.7 22.8 + - - -
39F GLN* 4.7 0.2 - - - -
67F VAL* 3.4 12.9 - - - +
69F PHE* 4.6 7.6 - - - -
72F ILE* 3.7 22.4 - - + -
100F ASN* 3.7 27.8 - - + +
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Residues in contact with HIS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ALA 3.0 12.7 + - - +
25F LEU* 3.5 14.1 - - + +
26F LYS 3.2 0.2 - - - -
27F ALA* 1.3 76.0 - - - +
29F LYS* 1.3 63.0 + - - +
30F THR 3.3 0.7 + - - -
31F ALA* 3.5 6.2 + - - +
36F ARG* 3.9 18.2 - - + +
37F MET* 4.5 15.7 - - + -
39F GLN* 3.1 47.6 + - - +
40F LEU 3.0 29.5 + - - -
41F GLY* 4.4 5.5 - - - -
42F THR* 5.4 4.0 - - + -
69F PHE* 3.6 28.5 - + + -
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU 3.4 8.9 + - - +
26F LYS* 3.1 12.9 + - - +
28F HIS* 1.3 80.9 + - - +
30F THR* 1.3 59.6 + - + +
31F ALA 3.3 5.7 + - - +
36F ARG* 5.4 8.6 - - - +
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Residues in contact with THR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LYS* 3.4 15.9 - - + +
27F ALA 2.7 19.3 + - - +
29F LYS* 1.3 75.7 - - + +
31F ALA* 1.3 66.3 + - - +
32F PRO* 3.6 3.5 - - - +
67F VAL* 3.4 10.0 - - - +
96F THR* 3.5 16.6 - - + +
100F ASN* 2.8 32.0 + - - +
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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