Contacts of the strand formed by residues 67 - 70 (chain B) in PDB entry 1OLY
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 PHE 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.9 14.4 - - + -
42B ARG 3.8 0.6 + - - -
43B ALA* 3.2 34.3 - - + -
44B CYS 3.2 20.3 + - - -
65B PRO* 3.8 1.3 - - - +
66B GLU* 1.4 87.5 - - + +
68B ILE* 1.3 75.5 + - - +
69B ASN* 3.9 18.6 - - + -
88B CYS 5.0 0.2 - - - -
89B GLU* 2.9 30.7 - - + +
91B ILE* 4.4 3.8 - - + -
104B CYS* 3.9 7.0 - - - -
107B MET* 3.5 40.6 - - + -
108B LEU* 4.0 23.6 - - + -
111B LYS* 4.1 12.6 - - + -
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Residues in contact with ILE 68 (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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44B CYS* 3.0 44.2 - - + +
46B ASP 4.4 1.1 - - - +
49B ALA* 3.9 15.5 - - + -
65B PRO* 3.1 31.9 - - + -
67B PHE* 1.3 80.6 - - - +
69B ASN* 1.3 65.6 + - - +
72B PHE* 5.5 0.9 - - - -
75B ILE* 3.5 32.5 - - + +
83B TYR* 4.6 11.7 - - + -
88B CYS* 4.9 2.5 - - + -
89B GLU 2.8 5.3 + - - -
90B LEU* 3.3 23.4 - - + +
91B ILE 2.8 23.4 + - - +
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Residues in contact with ASN 69 (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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44B CYS 2.9 17.2 + - - -
45B ALA* 3.7 1.2 - - - +
46B ASP* 2.7 32.6 + - - -
67B PHE* 3.9 11.1 - - + -
68B ILE* 1.3 78.5 - - - +
70B GLY* 1.3 55.1 + - - +
72B PHE* 6.2 0.7 - - - -
75B ILE* 5.4 2.2 - - - -
91B ILE* 3.0 23.3 - - + +
93B THR* 4.2 10.7 + - + +
100B ASP 3.5 4.6 - - - +
103B LYS 3.5 4.0 - - - +
104B CYS* 2.7 56.1 + - - +
107B MET* 4.9 4.0 - - + -
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Residues in contact with GLY 70 (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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46B ASP* 4.2 2.2 - - - -
69B ASN* 1.3 79.2 - - - +
71B ASP* 1.3 66.6 + - - -
72B PHE* 3.4 7.2 + - - -
75B ILE* 5.8 1.3 - - - -
91B ILE 3.1 4.4 + - - +
92B SER* 3.6 7.8 - - - -
93B THR* 3.1 33.3 + - - -
100B ASP* 3.5 17.0 - - - -
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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