Contacts of the helix formed by residues 26 - 33 (chain F) in PDB entry 5WC9
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 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F ARG* 2.9 9.0 - - - +
24F GLY 4.0 3.8 + - - +
25F TYR* 1.3 72.1 - - - +
27F GLN* 1.3 60.8 + - - +
28F THR* 3.7 8.0 + - - -
29F ASN* 2.2 58.1 + - - +
30F VAL* 3.0 14.7 + - - +
170G C 4.0 23.3 - - - +
171G C 3.7 10.1 - - - +
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Residues in contact with GLN 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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20F ARG* 2.6 19.6 - - - +
26F THR* 1.3 72.2 - - - +
28F THR* 1.3 62.7 + - - +
30F VAL* 3.5 3.9 + - - +
31F GLY* 3.1 18.9 + - - -
44F GLN* 3.5 34.3 - - + +
47F ILE* 3.9 16.7 - - + +
48F CYS* 3.6 18.1 - - - +
51F GLU* 2.5 37.3 + - - +
171G C 2.9 40.7 + - + +
172G A 3.1 18.6 + - - -
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Residues in contact with THR 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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26F THR* 3.1 7.4 + - - -
27F GLN* 1.3 77.3 - - - +
29F ASN* 1.3 58.7 + - - +
31F GLY* 3.3 2.2 + - - +
32F GLU* 2.9 53.1 + - + +
42F PHE 5.5 0.2 - - - +
43F SER* 6.0 0.4 - - - +
44F GLN* 3.6 28.8 - - + +
171G C 4.6 1.5 + - - -
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Residues in contact with ASN 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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24F GLY 5.4 0.8 - - - +
25F TYR* 3.8 19.3 - - + -
26F THR* 2.2 48.7 + - - +
28F THR* 1.3 76.3 - - - +
30F VAL* 1.3 59.6 + - - +
32F GLU* 3.1 14.6 + - - +
33F ALA* 2.8 33.5 + - - +
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Residues in contact with VAL 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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16F PHE* 3.9 17.9 - - + -
20F ARG* 3.8 21.3 - - + -
25F TYR* 3.8 22.0 - - + -
26F THR 3.0 15.2 + - - +
27F GLN* 4.0 4.3 - - - +
29F ASN* 1.3 75.3 - - - +
31F GLY* 1.3 63.7 + - - +
32F GLU 3.3 0.5 + - - -
33F ALA 3.5 7.5 + - - +
34F LEU* 3.5 18.1 + - + +
47F ILE* 4.7 9.6 - - + -
67F LEU* 4.5 9.0 - - + -
70F TRP* 3.6 38.4 - - + -
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Residues in contact with GLY 31 (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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27F GLN 3.1 15.6 + - - -
28F THR 3.6 4.3 - - - -
29F ASN 3.2 0.2 - - - -
30F VAL* 1.3 78.3 - - - +
32F GLU* 1.3 56.8 + - - +
34F LEU* 3.0 11.2 - - - +
41F GLU* 3.2 3.1 - - - +
42F PHE* 2.8 50.9 + - - -
43F SER* 4.4 2.0 - - - -
47F ILE* 4.2 7.9 - - - +
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Residues in contact with GLU 32 (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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28F THR* 2.9 38.4 + - + +
29F ASN* 3.1 14.1 + - - +
31F GLY* 1.3 78.8 - - - +
33F ALA* 1.3 56.6 + - + +
34F LEU 3.1 7.6 + - - -
35F ALA* 3.8 11.1 + - - +
41F GLU* 4.0 28.0 - - - +
42F PHE 5.6 1.8 - - - +
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Residues in contact with ALA 33 (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 TYR* 4.8 11.0 - - + +
29F ASN 2.8 20.6 + - - +
30F VAL 3.5 1.7 + - - -
32F GLU* 1.3 71.9 - - - +
34F LEU* 1.3 51.7 + - - -
35F ALA 3.6 1.1 - - - -
36F ALA* 4.7 6.7 + - - +
70F TRP* 2.3 44.4 + - + +
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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