Contacts of the helix formed by residues 28 - 32 (chain F) in PDB entry 1FSK
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 28 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F TYR* 1.3 80.3 - - - +
29F PHE* 1.3 54.0 + - - +
30F THR* 3.6 16.4 - - - +
31F SER* 2.8 54.4 + - - +
32F TYR* 5.1 2.3 - - - -
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Residues in contact with PHE 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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22F CYS 5.3 0.7 - - - -
24F ALA* 3.5 26.7 - - + -
27F TYR* 3.0 25.4 + - - +
28F THR* 1.3 70.5 - - - +
30F THR* 1.3 62.9 + - + +
31F SER 3.3 3.3 + - - -
32F TYR 3.4 9.7 + - - +
34F ILE* 4.6 14.8 - - + -
53F PRO* 2.9 39.0 - - + +
72F VAL* 4.0 21.1 - - + -
74F LYS* 4.2 13.9 - - - +
77F SER* 3.6 41.5 - - - -
78F THR* 3.6 26.9 - - - -
79F ALA* 4.0 5.4 - - + -
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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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28F THR* 3.6 14.2 - - - +
29F PHE* 1.3 78.8 - - + +
31F SER* 1.3 59.6 + - - +
32F TYR 3.4 0.7 - - - -
52F PHE* 3.1 23.0 - - - -
53F PRO* 3.4 10.8 - - + -
54F SER* 3.6 35.0 - - - +
74F LYS* 4.1 23.3 - - + +
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Residues in contact with SER 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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44D ILE* 5.4 2.9 - - - +
45D GLU* 4.3 0.9 - - - +
53D ILE* 4.7 10.6 - - - +
68D LYS* 5.2 7.1 + - - -
87D GLU* 4.0 17.5 + - - -
28F THR* 2.8 34.9 + - - +
30F THR* 1.3 79.1 + - - +
32F TYR* 1.3 78.8 + - - +
52F PHE* 3.4 17.5 - - - -
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Residues in contact with TYR 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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44D ILE* 3.7 29.9 + - + +
45D GLU* 3.0 42.2 - - + +
27F TYR* 3.1 43.4 + + + -
28F THR* 4.7 2.5 - - - -
29F PHE 3.4 4.0 + - - +
30F THR 3.4 1.2 - - - -
31F SER* 1.3 95.9 - - - +
33F TRP* 1.3 66.5 + - - +
34F ILE* 4.5 2.6 - - - +
52F PHE* 3.7 6.5 - - - -
53F PRO* 2.9 26.2 - - - +
98F ARG* 3.5 35.8 + - + -
99F GLY 4.7 0.7 - - - -
100F ALA* 4.8 0.6 - - - -
101F ARG 5.8 0.2 + - - -
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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