Contacts of the strand formed by residues 42 - 47 (chain J) in PDB entry 2Z3R
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 LEU 42 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I ASP* 5.7 1.1 - - - +
53I GLU* 3.7 40.6 - - + +
24J ARG* 3.8 47.3 - - + +
25J GLU 3.6 16.2 - - - +
26J ARG* 3.6 15.9 - - + +
40J SER* 3.3 15.3 + - - +
41J SER* 1.3 80.1 + - - +
43J THR* 1.3 67.5 + - - +
44J GLU* 4.2 14.4 - - + +
57J THR* 4.5 2.3 + - - +
59J PRO* 3.4 21.5 - - - +
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Residues in contact with THR 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J PRO* 5.5 0.4 - - + -
14J ILE* 3.7 29.8 - - + -
23J SER 4.0 0.2 - - - +
24J ARG* 3.6 2.1 - - - -
25J GLU* 2.8 40.9 + - + +
27J TYR* 3.8 21.0 + - + +
41J SER 3.6 0.2 + - - -
42J LEU* 1.3 75.9 - - - +
44J GLU* 1.3 63.8 + - - +
56J TRP* 3.4 30.4 - - + +
57J THR* 2.6 28.8 + - - -
59J PRO* 4.5 0.7 - - - -
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Residues in contact with GLU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I GLU 5.1 2.1 - - - +
22J TYR* 5.0 6.4 - - - +
23J SER 3.4 4.7 - - - +
24J ARG* 2.7 44.9 + - + +
42J LEU* 4.2 16.2 - - + +
43J THR* 1.3 77.6 + - - +
45J CYS* 1.3 62.2 + - - +
46J VAL* 3.6 16.3 + - + -
56J TRP* 3.2 7.0 - - - -
57J THR* 2.8 48.3 + - + +
55K GLY 4.9 8.1 - - - +
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Residues in contact with CYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR 4.4 0.2 - - - -
3J CYS* 2.0 57.9 - - + -
19J TYR 3.9 6.3 - - - +
20J SER 3.8 17.0 - - - +
21J LEU* 4.0 8.1 - - - -
22J TYR* 2.7 32.7 + - - +
23J SER 3.0 9.8 + - - +
44J GLU* 1.3 72.5 - - - +
46J VAL* 1.3 60.9 + - - +
54J ALA* 3.9 10.1 - - - -
56J TRP* 3.4 18.1 - - + -
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Residues in contact with VAL 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LEU* 3.7 8.7 - - - -
22J TYR* 4.3 15.7 - - + -
44J GLU* 4.1 14.4 - - + +
45J CYS* 1.3 80.3 - - - +
47J LEU* 1.3 64.1 + - - +
48J ASN 3.8 0.3 + - - -
54J ALA* 3.1 2.3 - - - -
55J HIS* 2.8 59.7 + - + +
57J THR* 3.7 33.0 - - + -
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Residues in contact with LEU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3J MET* 3.7 37.0 - - + -
1J ILE* 4.2 23.1 - - + -
21J LEU* 3.8 13.3 - - + +
22J TYR* 4.9 3.3 - - - +
46J VAL* 1.3 78.2 - - - +
48J ASN* 1.3 69.0 + - - +
49J LYS* 3.3 27.1 + - + +
52J ASN* 3.6 37.2 - - - +
53J VAL 3.9 6.5 - - - -
54J ALA* 4.0 3.4 - - - +
55J HIS* 4.7 2.9 - - - -
52K LEU* 3.9 19.3 - - + -
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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