Contacts of the strand formed by residues 79 - 84 (chain B) in PDB entry 5ODS
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 VAL 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE 4.4 0.2 - - - +
73B MET* 3.6 4.6 - - - +
74B ASN* 2.8 38.6 + - + +
77B SER* 2.9 18.8 + - - -
78B LYS* 1.3 82.2 - - - +
80B ILE* 1.3 64.2 + - - +
90B ILE* 3.7 16.8 - - + -
91B PHE 3.7 5.6 - - - +
92B ASN* 4.1 12.3 - - - +
99B MET* 3.7 38.6 - - + -
113B TRP* 4.4 6.6 - - + -
132B MET* 4.0 14.8 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 4.3 4.0 - - - -
50B VAL* 4.3 10.3 - - + -
52B ILE* 4.6 4.7 - - + -
66B ILE* 5.5 1.3 - - + -
71B ALA* 3.9 15.5 - - + -
72B ILE 3.8 11.4 - - - +
73B MET* 3.6 33.7 - - + -
78B LYS 4.3 0.4 - - - -
79B VAL* 1.3 79.1 - - - +
81B ALA* 1.3 62.7 + - - +
82B LEU* 3.7 32.1 - - + -
90B ILE* 3.6 1.7 - - - -
91B PHE* 2.7 57.3 + - + +
93B ILE* 3.8 19.9 - - + +
113B TRP* 4.8 0.7 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 3.4 1.7 - - - -
72B ILE* 2.9 49.5 + - + +
80B ILE* 1.3 75.3 - - - +
82B LEU* 1.3 59.8 + - - +
89B GLN 3.5 6.1 - - - +
90B ILE* 4.5 10.8 - - + -
111B TRP* 3.3 27.6 - - + -
113B TRP* 3.9 17.5 - - + +
119B VAL* 5.3 2.7 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 5.2 0.4 - - + -
66B ILE* 3.8 34.3 - - + -
68B ALA* 3.9 10.8 - - + -
70B SER 3.2 7.6 - - - +
71B ALA* 4.3 7.2 - - + -
80B ILE* 3.7 36.3 - - + -
81B ALA* 1.3 74.3 - - - +
83B LYS* 1.3 60.3 + - - +
87B THR 3.9 1.0 - - - +
88B LEU* 3.7 2.3 - - - -
89B GLN* 3.0 69.7 + - + +
91B PHE* 4.1 11.7 - - + -
111B TRP* 3.4 5.5 - - - -
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA* 3.3 5.9 - - - +
69B ASP* 2.8 53.5 + - - +
70B SER* 2.8 31.1 + - - -
82B LEU* 1.3 73.8 - - - +
84B ALA* 1.3 62.2 + - - +
85B GLY* 3.1 28.7 + - - +
87B THR 3.7 5.6 - - - +
88B LEU* 4.6 10.5 - - + +
107B ASP* 3.6 11.0 + - - -
108B VAL* 3.5 36.8 - - + +
111B TRP* 3.6 15.4 - - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B SER 4.5 14.1 - - - +
68B ALA* 5.0 0.9 - - + -
69B ASP* 3.5 7.0 - - - +
82B LEU 4.2 0.2 + - - -
83B LYS* 1.3 76.2 - - - +
85B GLY* 1.3 58.6 + - - +
86B LYS 3.2 0.5 + - - -
87B THR* 2.7 41.8 + - + +
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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