Contacts of the strand formed by residues 53 - 57 (chain C) in PDB entry 3OEE
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 GLU 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C ILE* 3.6 11.2 - - + +
50C GLN* 2.9 50.6 + - + +
51C ALA 3.3 0.6 + - - -
52C GLU* 1.3 78.6 - - - +
54C LEU* 1.3 71.3 + - - +
55C VAL* 3.6 2.0 + - - +
64C MET* 3.4 4.3 - - - -
65C ALA* 3.1 25.3 + - - +
92C ARG* 2.6 47.2 + - - +
93C THR 3.3 6.9 + - - -
94C GLY* 2.8 16.8 + - - -
95C ASN 3.4 19.5 - - - +
96C ILE* 4.1 2.7 - - + -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLU 3.9 1.0 + - - -
53C GLU* 1.3 77.6 - - - +
55C VAL* 1.3 64.9 + - - +
62C LYS* 4.3 28.0 - - + +
63C GLY 3.3 14.8 - - - +
64C MET* 4.7 0.2 - - - +
78C PHE* 3.7 25.1 - - + -
93C THR* 3.0 45.7 + - + +
95C ASN* 2.7 21.6 + - + +
97C VAL* 4.1 18.5 - - + +
98C ASP* 5.2 9.4 - - - +
113C LEU* 4.7 13.7 - - + -
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 4.4 1.1 - - + -
49C ILE* 3.3 34.3 - - + -
53C GLU 4.2 3.6 - - - +
54C LEU* 1.3 78.2 - - - +
56C GLU* 1.3 63.8 + - - +
57C PHE* 3.8 11.9 - - + -
62C LYS* 3.3 7.3 - - - +
63C GLY* 2.7 53.3 + - - +
64C MET 4.2 0.2 - - - +
75C ILE* 3.9 16.2 - - + -
90C VAL* 3.7 24.0 - - + -
91C LYS 3.3 14.4 - - - +
92C ARG* 4.8 0.4 - - - -
93C THR* 4.1 0.4 - - - -
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C VAL* 1.3 77.5 - - - +
57C PHE* 1.3 66.7 + - - +
58C SER 3.9 0.7 + - - -
60C GLY 5.3 1.8 - - - +
61C VAL 3.8 4.0 - - - +
62C LYS* 3.3 40.8 + - + -
89C LEU 4.0 0.2 - - - +
90C VAL* 3.4 1.8 - - - -
91C LYS* 2.8 59.2 + - + +
93C THR* 3.9 16.7 + - - +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.5 20.4 - - + -
41C ALA* 3.7 17.0 - - + -
43C VAL* 4.4 1.8 - - + -
55C VAL* 3.8 12.3 - - + -
56C GLU* 1.3 77.8 - - - +
58C SER* 1.3 55.9 + - - +
59C SER* 4.3 0.9 - - - +
60C GLY* 2.8 30.3 + - - +
61C VAL* 2.9 39.2 + - + +
63C GLY* 4.5 3.6 - - - -
75C ILE* 3.8 20.2 - - + -
77C LEU* 3.5 28.9 - - + -
84C VAL* 4.1 13.2 - - + -
88C GLU* 3.4 13.0 - - + +
89C LEU 3.8 2.9 - - - -
90C VAL* 3.5 31.9 - - + +
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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