Contacts of the strand formed by residues 52 - 55 (chain B) in PDB entry 2EZ9
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 HIS 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP* 2.9 43.4 + - - +
28B HIS* 3.1 31.0 - - + +
29B LEU* 3.1 6.9 + - - -
48B ARG 3.4 19.0 + - - -
49B ASP 3.6 20.4 + - - -
50B ARG 4.8 6.1 - - - -
51B ILE* 1.3 73.6 - - - +
53B TYR* 1.3 64.9 + - - +
54B ILE* 3.6 8.9 + - + +
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Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.6 19.0 - - + +
31B GLY 2.8 29.0 + - - -
33B PRO* 3.5 18.5 - - + +
41B MET* 3.8 20.6 - - + +
44B LEU* 4.6 20.0 - - + -
48B ARG* 5.9 5.4 - - + -
51B ILE 3.7 4.4 + - - +
52B HIS* 1.3 73.0 - - - +
54B ILE* 1.3 75.7 + - - +
55B GLN* 3.3 25.4 - - + +
80B PHE* 3.4 32.3 - + - -
463B TYR* 3.8 12.0 + - - -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 4.2 7.2 - - + -
29B LEU 2.8 16.7 + - - +
30B TYR* 3.3 26.1 - - + +
31B GLY 3.2 22.9 + - - -
52B HIS* 3.9 15.9 - - + +
53B TYR* 1.3 82.7 - - - +
55B GLN* 1.3 62.0 + - - +
56B VAL* 3.4 3.8 + - + -
430B ILE* 5.0 2.0 - - + -
434B LEU* 4.0 38.1 - - + -
459B THR* 4.1 14.6 - - + -
463B TYR* 3.8 36.6 - - + -
465B LEU* 6.0 0.4 - - + -
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY 3.4 7.4 - - - +
32B ILE* 5.0 2.9 - - + +
33B PRO* 4.8 9.2 - - + -
53B TYR* 3.3 28.0 - - + +
54B ILE* 1.3 68.5 - - - +
56B VAL* 1.3 79.6 + - - +
57B ARG* 3.3 25.1 + - - +
459B THR* 4.1 5.7 + - - +
462B GLN* 2.9 25.6 + - - +
463B TYR* 2.9 30.9 + - - +
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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
------------------------------------------------------------
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