Contacts of the helix formed by residues 59 - 65 (chain F) in PDB entry 1S9C
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 59 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F TYR* 2.7 34.6 + - - -
34F VAL* 5.5 0.2 - - - +
57F LEU* 3.2 4.5 + - - +
58F PRO* 1.3 71.9 - - - +
60F PHE* 1.3 61.2 + - - +
61F GLY 2.9 6.1 - - - -
62F VAL* 3.0 19.7 + - + +
63F ILE 4.1 0.2 + - - -
94F LEU* 3.8 8.1 - - + -
220F PHE* 3.5 29.6 - - + -
221F GLY* 4.0 8.9 + - - -
224F ALA* 3.5 29.6 - - + +
225F ARG 5.7 0.2 + - - -
239F PHE* 4.6 10.5 - - + -
242F VAL* 4.8 3.4 - - + -
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Residues in contact with PHE 60 (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 TYR* 3.5 28.5 - + - -
22F TYR* 3.7 42.2 - + + -
26F GLU* 3.8 24.7 - - + -
27F ALA* 4.3 3.6 - - - -
30F TYR* 3.8 35.1 - + + -
56F CYS* 3.3 24.9 - - - -
57F LEU 2.8 19.7 + - - +
59F THR* 1.3 78.6 + - - +
61F GLY* 1.3 57.0 + - - +
63F ILE* 2.9 41.5 + - + +
64F ILE* 3.3 15.2 + - + -
100F LEU* 4.2 2.2 - - + -
191F SER* 5.6 0.2 - - - -
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Residues in contact with GLY 61 (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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58F PRO 3.1 8.9 + - - -
59F THR 2.9 1.8 - - - -
60F PHE* 1.3 76.6 - - - +
62F VAL* 1.3 63.9 + - - +
64F ILE* 3.1 21.4 + - - +
65F GLY 3.2 3.3 + - - -
94F LEU* 4.0 11.4 - - - -
100F LEU* 3.5 15.9 - - - +
138F CYS* 4.4 4.9 - - - -
140F ASN* 3.0 22.7 + - - -
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Residues in contact with VAL 62 (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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30F TYR* 5.2 2.0 - - - +
59F THR 3.0 14.7 + - - +
61F GLY* 1.3 77.6 - - - +
63F ILE* 1.3 61.0 + - + +
65F GLY 3.7 0.7 + - - -
66F GLN* 2.8 29.9 + - - +
92F GLN* 4.0 14.6 - - + +
94F LEU* 3.9 13.7 - - + +
140F ASN* 3.6 11.4 - - - +
142F PHE* 4.1 4.6 - - + -
188F TYR* 5.6 1.1 - - - +
217F LEU* 3.2 43.3 - - + -
220F PHE* 3.6 30.1 - - + -
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Residues in contact with ILE 63 (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 TYR* 3.6 33.4 - - + +
30F TYR* 3.2 35.0 - - + -
60F PHE* 2.9 20.2 + - + +
62F VAL* 1.3 80.2 - - + +
64F ILE* 1.3 65.2 + - - +
66F GLN* 3.3 27.7 + - - +
67F LYS* 3.8 4.9 + - - +
188F TYR* 4.5 8.5 - - + +
191F SER* 3.2 46.0 - - - +
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Residues in contact with ILE 64 (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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18F PHE* 3.6 18.7 - - - -
20F TYR* 3.6 36.2 - - + +
22F TYR* 3.8 11.9 - - + -
60F PHE* 3.9 15.0 - - + +
61F GLY* 3.1 15.0 + - - +
63F ILE* 1.3 81.3 - - - +
65F GLY* 1.3 59.5 + - - +
66F GLN 3.5 0.3 + - - -
67F LYS* 4.0 1.4 + - - +
100F LEU* 4.1 23.1 - - + -
106F LEU* 3.5 27.8 - - + -
108F CYS* 3.9 7.3 - - - -
130F SER* 3.5 29.2 - - - +
138F CYS* 4.4 2.9 - - - -
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Residues in contact with GLY 65 (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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18F PHE* 4.0 5.9 - - - -
61F GLY 3.2 7.9 + - - -
64F ILE* 1.3 79.3 - - - +
66F GLN* 1.3 62.8 + - - +
67F LYS 3.3 2.5 - - - -
68F SER* 3.5 15.4 + - - -
126F MET* 5.1 0.2 - - - +
128F VAL* 3.8 25.6 - - - +
130F SER* 4.6 0.7 - - - -
140F ASN* 3.9 10.9 - - - +
142F PHE* 3.6 18.8 - - - -
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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