Contacts of the helix formed by residues 81 - 90 (chain F) in PDB entry 4P9U
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 HIS 81 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58F ASP* 3.1 59.9 + - + -
60F TRP* 4.6 2.7 - - - -
79F GLY* 3.0 22.5 + - - -
80F LEU* 1.3 74.8 - - - +
82F ILE* 1.3 93.5 + - + +
83F LEU 3.0 3.6 + - - -
84F ASP* 3.3 19.6 + - - +
85F THR* 4.1 6.4 + - - -
207F GLY* 4.0 14.5 + - - +
210F LYS* 5.9 4.8 - - + +
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Residues in contact with ILE 82 (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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203E LEU* 3.9 16.2 - - + -
60F TRP* 3.8 28.5 - - + -
74F PHE* 4.7 3.8 - - + -
75F MET* 3.6 37.5 - - + +
78F SER* 3.6 26.7 - - - +
79F GLY 3.1 16.2 - - - +
81F HIS* 1.3 103.3 + - + +
83F LEU* 1.3 60.9 + - + +
84F ASP 3.1 0.4 - - - -
85F THR* 3.2 7.7 + - - +
86F LEU* 2.8 36.8 + - + +
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Residues in contact with LEU 83 (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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199E GLN* 3.2 31.4 - - + +
200E ILE* 3.6 34.8 - - + -
203E LEU* 4.9 9.9 - - + -
75F MET* 5.2 3.4 - - + -
80F LEU* 3.8 15.2 + - + +
81F HIS 3.0 1.6 + - - -
82F ILE* 1.3 77.5 - - + +
84F ASP* 1.3 56.7 + - - +
86F LEU* 3.4 9.7 - - + +
87F MET* 3.0 32.5 + - - +
97F ILE* 4.0 21.9 - - + +
100F ASP* 5.8 3.8 - - + +
208F LEU* 3.7 19.3 - - + -
211F LEU* 3.9 19.1 - - + -
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Residues in contact with ASP 84 (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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80F LEU 5.1 0.2 + - - -
81F HIS 3.3 11.5 + - - +
82F ILE 3.1 0.2 - - - -
83F LEU* 1.3 77.5 - - - +
85F THR* 1.3 67.4 + - - +
87F MET* 3.1 24.2 + - - +
88F THR* 3.5 6.4 + - - +
210F LYS* 3.2 31.7 - - + +
211F LEU* 3.2 29.5 + - + +
214F ARG* 2.8 46.0 + - - -
277F ASP* 5.9 0.7 - - - -
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Residues in contact with THR 85 (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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17F ILE* 4.1 21.5 - - + +
60F TRP* 4.5 11.6 - - + -
81F HIS* 4.5 7.4 + - - -
82F ILE* 3.2 13.8 + - - +
84F ASP* 1.3 80.5 + - - +
86F LEU* 1.3 56.7 + - - +
88F THR* 2.9 21.2 + - + +
89F LEU* 2.9 46.7 + - + +
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Residues in contact with LEU 86 (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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199E GLN* 5.4 1.8 - - - +
21F TRP* 3.8 26.5 - - + -
60F TRP* 4.9 4.3 - - + -
74F PHE* 4.7 9.0 - - + -
75F MET* 3.7 33.7 - - + -
82F ILE* 2.8 35.7 + - + +
83F LEU* 3.4 11.7 - - + +
85F THR* 1.3 74.3 - - - +
87F MET* 1.3 65.1 + - - +
89F LEU* 4.3 12.8 - - + -
90F ASP* 2.8 45.8 + - - +
97F ILE* 3.8 13.2 - - + +
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Residues in contact with MET 87 (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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83F LEU 3.0 19.8 + - - +
84F ASP* 3.1 12.5 + - - +
86F LEU* 1.3 79.2 - - - +
88F THR* 1.3 56.7 + - - +
91F ALA* 3.6 15.8 - - - -
94F ALA* 3.5 31.8 - - + +
97F ILE* 3.6 28.5 - - + +
98F VAL* 4.1 10.5 - - + -
211F LEU* 3.6 22.2 - - + -
214F ARG* 4.4 19.1 - - - -
215F VAL* 5.2 0.4 - - + -
274F PHE* 3.7 30.5 - - + -
275F THR* 3.5 22.9 - - + +
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Residues in contact with THR 88 (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 GLU* 5.8 0.2 - - - +
84F ASP* 3.5 3.5 + - - +
85F THR* 2.9 33.8 + - + +
87F MET* 1.3 77.5 - - - +
89F LEU* 1.3 66.8 + - + +
91F ALA* 4.9 2.2 - - - -
214F ARG* 5.4 3.6 - - - +
275F THR* 3.2 29.2 + - - +
276F GLU* 3.4 18.7 - - - -
277F ASP* 4.2 9.4 + - + +
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Residues in contact with LEU 89 (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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17F ILE* 3.8 19.1 - - + -
18F GLU* 3.9 28.0 - - + +
21F TRP* 3.0 59.9 + - + +
60F TRP* 4.3 10.5 - - + -
85F THR* 2.9 38.7 + - + +
86F LEU* 3.3 10.7 + - + +
88F THR* 1.3 86.9 - - + +
90F ASP* 1.3 60.4 + - - +
91F ALA 4.0 0.7 - - - -
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Residues in contact with ASP 90 (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 TRP* 3.3 34.7 - - + +
86F LEU* 2.8 28.7 + - - +
87F MET 4.1 3.0 - - - +
89F LEU* 1.3 74.8 - - - +
91F ALA* 1.3 63.4 + - - +
92F GLU* 3.1 12.2 - - + +
93F ASN* 3.0 30.2 + - - +
94F ALA* 3.5 5.5 + - - -
97F ILE* 4.8 3.8 - - - +
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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