Contacts of the strand formed by residues 42 - 48 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22M ASP* 5.7 0.7 - - - +
53M GLU* 3.6 31.4 - - + +
24N ARG* 3.5 59.9 - - + +
25N GLU 3.6 14.1 - - - +
26N ARG* 3.5 17.2 - - + +
40N SER* 3.2 16.0 + - - +
41N SER* 1.3 78.2 + - - +
43N THR* 1.3 66.4 + - - +
44N GLU* 4.2 11.9 - - + +
57N THR* 4.6 1.9 + - - -
59N PRO* 3.2 22.9 - - - +
49P LYS* 5.5 2.4 - - - -
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Residues in contact with THR 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N PRO* 5.7 0.4 - - + -
14N ILE* 3.7 29.4 - - + -
23N SER 4.0 0.3 - - - +
24N ARG* 3.6 2.1 - - - -
25N GLU* 2.9 44.1 + - + +
27N TYR* 3.7 20.1 - - + +
41N SER 3.5 0.2 + - - -
42N LEU* 1.3 75.6 - - - +
44N GLU* 1.3 63.4 + - - +
56N TRP* 3.4 25.1 - - + +
57N THR* 2.8 28.3 + - - -
59N PRO* 4.6 0.9 - - - -
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Residues in contact with GLU 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M GLU 5.1 1.9 - - - +
22N TYR* 4.8 7.1 - - - +
23N SER 3.3 5.4 - - - +
24N ARG* 2.5 48.7 + - + +
42N LEU* 4.2 13.9 - - + +
43N THR* 1.3 77.5 + - - +
45N CYS* 1.3 63.2 + - - +
46N VAL* 4.4 9.6 - - + -
56N TRP* 3.2 6.7 - - - -
57N THR* 2.8 53.2 + - + +
55O GLY 4.8 7.8 - - - +
49P LYS* 5.4 4.3 + - - -
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Residues in contact with CYS 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N CYS* 2.1 54.7 - - - -
19N TYR 3.9 0.7 - - - -
20N SER 3.5 25.1 - - - +
21N LEU* 3.7 7.7 - - - +
22N TYR* 2.8 33.5 + - - +
23N SER 3.0 9.4 + - - +
44N GLU* 1.3 71.8 - - - +
46N VAL* 1.3 58.5 + - - +
54N ALA* 3.9 13.0 - - - -
55N HIS 3.6 0.4 - - - -
56N TRP* 3.3 16.8 - - + -
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Residues in contact with VAL 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N LEU* 3.6 9.0 - - - -
22N TYR* 4.4 14.6 - - + -
44N GLU* 4.4 11.0 - - + +
45N CYS* 1.3 79.7 - - - +
47N LEU* 1.3 61.1 + - - +
48N ASN 3.9 0.2 + - - -
54N ALA* 3.2 4.9 - - - +
55N HIS* 2.8 59.0 + - + +
57N THR* 3.6 31.6 - - + -
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Residues in contact with LEU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3N MET* 3.8 29.2 - - - -
1N ILE* 4.2 22.0 - - + -
21N LEU* 3.7 12.8 - - + +
22N TYR* 4.9 3.5 + - - +
46N VAL* 1.3 76.0 - - - +
48N ASN* 1.3 67.9 + - - +
49N LYS* 3.1 37.9 + - + +
52N ASN* 3.4 43.5 - - - +
53N VAL 3.8 8.1 - - - +
54N ALA* 3.9 3.6 - - - +
55N HIS* 4.6 3.2 - - - -
52O LEU* 4.2 13.2 - - + -
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Residues in contact with ASN 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N VAL 3.9 1.6 + - - -
47N LEU* 1.3 69.4 - - - +
49N LYS* 1.3 57.6 + - - +
50N ALA* 3.2 23.8 + - - +
51N THR* 3.2 23.0 + - - +
52N ASN* 2.9 27.9 + - - -
53N VAL 3.2 20.1 + - - +
55N HIS* 4.0 20.9 + - - +
58P THR* 5.6 1.2 - - - -
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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