Contacts of the strand formed by residues 62 - 65 (chain C) in PDB entry 2BX5
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 62 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLN* 4.0 11.4 - - - -
47C LEU* 3.6 20.4 - - + -
48C ILE* 4.0 12.8 - - + -
54C LEU* 3.3 24.6 - - - +
58C VAL* 3.3 29.8 - - + -
59C PRO* 3.4 19.0 + - + -
60C SER 3.5 2.1 - - - +
61C ARG* 1.3 89.9 - - - +
63C SER* 1.3 61.2 + - - +
73C LEU* 4.6 7.0 - - + -
74C THR 3.9 4.5 - - - -
75C ILE* 3.6 22.2 - - + -
82C ASP* 3.2 30.7 - - - -
86C TYR* 3.5 28.5 - + - -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 3.7 6.1 - - - +
52C SER 5.6 0.9 - - - -
54C LEU* 4.7 9.9 - - - -
60C SER 4.7 6.1 - - - -
61C ARG 4.5 2.9 + - - -
62C PHE* 1.3 76.9 - - - +
64C GLY* 1.3 64.1 + - - +
65C SER* 4.2 0.7 + - - -
72C THR* 5.0 0.5 - - - -
73C LEU* 4.2 3.0 - - - +
74C THR* 3.7 33.2 + - - -
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Residues in contact with GLY 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 4.9 2.2 - - - -
48C ILE* 3.2 18.0 - - - +
51C ALA 3.0 21.2 + - - +
52C SER* 3.7 19.4 + - - +
63C SER* 1.3 76.9 - - - +
65C SER* 1.3 64.1 + - - -
72C THR 3.6 11.4 - - - -
73C LEU* 4.9 1.8 - - - -
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Residues in contact with SER 65 (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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51C ALA 3.2 7.3 + - - -
52C SER* 5.3 1.8 - - - -
63C SER 5.3 0.4 + - - -
64C GLY* 1.3 75.9 - - - -
66C GLY* 1.3 58.5 + - - +
70C ASP 3.4 1.6 - - - +
71C PHE* 3.2 10.6 - - - -
72C THR* 3.1 44.1 + - - -
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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
------------------------------------------------------------
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