Contacts of the strand formed by residues 72 - 77 (chain O) in PDB entry 4WNC
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 ASN 72 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23O PHE* 3.6 24.3 - - + -
30O ILE 5.5 2.5 - - - +
67O LEU 3.4 1.4 - - - +
68O VAL* 3.4 3.1 - - - +
69O ILE* 2.9 41.2 + - - +
70O ASN* 3.3 16.5 + - - +
71O GLY* 1.3 79.0 - - - +
73O PRO* 1.3 70.7 - - + +
74O ILE* 3.7 6.0 + - + +
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Residues in contact with PRO 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O ILE 4.8 1.0 - - - +
31O VAL* 4.5 9.7 - - - +
66O LYS* 4.2 28.3 - - + +
67O LEU 3.5 4.5 - - - +
68O VAL* 4.1 13.0 - - + -
71O GLY 3.5 9.6 - - - +
72O ASN* 1.3 86.7 - - + +
74O ILE* 1.3 61.0 + - - +
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Residues in contact with ILE 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O THR* 5.1 0.2 - - + -
23O PHE* 3.9 20.2 - - + -
30O ILE* 3.8 19.5 - - + +
31O VAL* 3.7 3.8 - - - -
32O ALA* 3.6 22.4 - - - +
33O ILE* 3.8 24.7 - - + -
66O LYS* 3.4 10.4 - - - +
67O LEU* 2.7 41.4 + - + +
69O ILE* 3.7 31.4 - - + -
72O ASN 3.7 5.4 - - - +
73O PRO* 1.3 78.9 - - - +
75O THR* 1.3 71.7 + - - +
76O ILE* 3.6 3.3 + - + +
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Residues in contact with THR 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O VAL 3.0 15.5 + - - -
32O ALA* 3.2 3.1 - - - +
33O ILE 3.0 26.0 + - - +
66O LYS* 3.5 25.5 + - - +
73O PRO 4.3 0.2 - - - -
74O ILE* 1.3 71.7 - - - +
76O ILE* 1.3 64.8 + - - +
77O PHE* 3.6 34.7 - - + -
90O ALA* 4.1 17.2 + - + +
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Residues in contact with ILE 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O ILE* 3.4 13.7 - - + -
40O LEU* 4.0 24.0 - - + +
43O MET* 3.6 32.1 - - + -
65O GLY 4.5 12.8 + - - +
67O LEU* 3.7 28.0 - - + +
74O ILE* 3.6 11.8 + - + +
75O THR* 1.3 85.0 - - - +
77O PHE* 1.3 68.8 + - - +
78O GLN* 3.9 27.3 - - + +
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Residues in contact with PHE 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O ALA* 4.1 10.3 - - + -
33O ILE 2.8 14.4 + - - +
34O ASN* 3.1 23.9 - - + +
35O ASP 3.2 10.9 + - - -
75O THR* 3.6 26.0 - - + -
76O ILE* 1.3 78.2 - - - +
78O GLN* 1.3 79.4 + - - +
79O GLU* 4.6 9.2 - - + -
85O ILE* 3.5 27.6 - - + -
86O LYS* 3.5 40.6 - - + -
87O TRP* 4.4 8.1 - + - -
89O ASP* 5.7 1.1 - - + -
90O ALA* 4.0 13.0 - - + -
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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