Contacts of the strand formed by residues 82 - 87 (chain F) in PDB entry 2IO1
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 82 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LYS* 3.2 38.6 + - + +
22F ALA* 4.0 18.8 - - + +
28F VAL* 5.9 0.4 - - + -
60F ARG 4.8 0.5 - - - +
61F PHE* 3.5 20.4 - - - -
62F ASP 5.2 1.2 + - - -
80F GLU 3.8 0.9 + - - -
81F ASP* 1.3 73.5 - - - +
83F ILE* 1.3 70.5 + - - +
84F ASP* 3.6 20.6 + - - +
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 4.0 20.4 - - + -
20F LYS 2.7 13.1 + - - +
21F VAL* 3.3 15.4 - - + +
22F ALA 3.0 23.7 + - - -
39F LEU* 4.7 6.3 - - + -
42F LEU* 4.6 17.7 - - + -
43F MET* 6.2 1.3 - - + -
59F PHE* 4.2 19.1 - - + -
60F ARG 3.7 9.0 - - - +
61F PHE* 4.5 1.6 - - + -
66F ILE* 4.2 20.4 - - + -
77F MET* 3.5 33.4 - - + -
82F THR* 1.3 73.3 - - - +
84F ASP* 1.3 77.0 + - - +
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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
----------------------------------------------------------
445E LYS* 2.9 42.2 + - - +
457E TRP* 4.5 7.5 + - - -
22F ALA* 3.8 9.2 - - - +
59F PHE* 3.5 0.7 - - - -
60F ARG* 2.8 37.0 + - + +
62F ASP 6.2 1.3 - - - -
82F THR* 3.6 18.4 + - - +
83F ILE* 1.3 82.2 - - - +
85F VAL* 1.3 67.8 + - - +
86F PHE* 3.4 22.5 - - + -
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F VAL* 3.5 29.8 - - + -
22F ALA 3.3 11.4 + - - +
23F GLY* 4.1 2.3 - - - -
24F GLN* 3.9 22.2 + - - +
46F TYR* 4.0 21.1 - - + +
52F LEU* 5.3 1.8 - - + -
57F ILE* 3.7 37.0 - - + -
58F ARG 3.1 9.6 - - - +
59F PHE* 3.6 18.8 - - + -
84F ASP* 1.3 80.7 - - - +
86F PHE* 1.3 60.9 + - - +
87F GLN* 5.7 0.5 - - - +
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Residues in contact with PHE 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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441E PHE* 3.3 55.6 - + + -
444E PRO* 5.1 4.5 - - + -
445E LYS* 3.7 34.8 - - + -
457E TRP* 4.0 22.7 - + - -
24F GLN* 3.8 24.9 - - + -
57F ILE* 3.4 6.5 - - - +
58F ARG* 2.8 34.1 + - + +
60F ARG* 4.4 13.2 - - + -
84F ASP* 3.4 28.7 - - + -
85F VAL* 1.3 79.9 - - - +
87F GLN* 1.3 63.6 + - - +
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Residues in contact with GLN 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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441E PHE* 3.4 16.5 - - - -
24F GLN* 2.9 29.7 + - + +
56F GLN* 3.8 6.7 - - + +
57F ILE* 4.7 8.7 - - + +
58F ARG* 4.5 1.1 - - - -
85F VAL 5.7 0.4 - - - +
86F PHE* 1.3 76.0 - - - +
88F GLN* 1.3 71.5 + - + +
89F GLN* 3.4 6.8 + - - +
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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