Contacts of the strand formed by residues 53 - 60 (chain J) in PDB entry 2ZHX
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47J TYR* 4.1 1.1 - - - -
48J ASP* 3.3 29.3 + - - +
51J THR* 3.0 39.6 + - - +
52J ASP* 1.3 76.7 - - - +
54J ASN* 1.3 65.6 + - - +
55J VAL* 3.6 9.9 + - + +
72J ILE* 3.4 31.3 - - + +
73J GLN 3.2 11.7 - - - +
74J ASP* 4.3 9.4 - - + +
80J LYS* 4.2 12.8 + - - -
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Residues in contact with ASN 54 (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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92I ARG* 3.1 25.5 + - - +
96I ASN* 5.4 4.0 + - - +
194I PRO* 3.7 19.8 - - + +
45J THR* 4.6 6.7 - - + -
46J ALA 4.0 4.0 - - - -
47J TYR* 3.1 25.2 - - - -
52J ASP* 5.2 0.7 - - - +
53J GLU* 1.3 72.1 - - - +
55J VAL* 1.3 59.0 + - - +
56J MET* 3.8 6.7 - - + +
72J ILE* 3.7 2.6 - - - +
73J GLN* 2.9 65.1 + - + +
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Residues in contact with VAL 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ILE* 3.9 36.9 - - + +
12J THR* 5.0 5.6 - - + +
14J LYS* 6.4 0.7 - - + -
16J LEU* 4.1 18.6 - - + -
44J HIS 3.9 0.5 - - - +
45J THR* 3.8 0.2 - - - -
46J ALA* 2.9 41.4 + - + +
48J ASP* 4.9 3.4 - - + +
53J GLU* 4.0 16.4 - - + +
54J ASN* 1.3 75.6 - - - +
56J MET* 1.3 62.5 + - - +
57J LEU 4.2 0.3 + - - -
70J LEU* 4.4 14.8 - - + -
71J VAL 3.8 2.5 - - - -
72J ILE* 4.5 19.7 - - + -
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Residues in contact with MET 56 (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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194I PRO* 4.1 7.9 - - - -
195I LEU* 3.8 39.3 - - + -
43J VAL* 4.2 11.7 - - + -
44J HIS 3.0 6.5 - - - +
45J THR* 3.7 26.0 - - + +
54J ASN* 3.8 10.8 - - + +
55J VAL* 1.3 77.5 - - - +
57J LEU* 1.3 60.9 + - - +
58J LEU* 4.1 2.8 - - + +
70J LEU* 3.5 8.2 - - - +
71J VAL* 2.9 63.0 + - + +
73J GLN* 3.6 36.6 - - + +
79J ASN* 4.5 0.7 - - - +
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Residues in contact with LEU 57 (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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4J LEU* 3.5 24.2 - - + -
7J ILE* 3.4 43.5 - - + -
8J ILE* 3.7 29.6 - - + +
44J HIS* 2.7 46.8 + - + +
55J VAL 4.2 0.6 + - - -
56J MET* 1.3 73.4 - - - +
58J LEU* 1.3 70.1 + - - +
59J THR* 3.9 12.8 - - + -
67J PRO* 4.6 5.2 - - + -
68J TRP 4.8 0.2 - - - +
69J ALA 3.4 17.3 - - - +
70J LEU* 4.8 7.0 - - + +
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Residues in contact with LEU 58 (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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195I LEU* 3.8 22.9 - - + -
29J VAL* 3.9 7.4 - - + -
33J ILE* 3.7 21.8 - - + -
41J ILE* 3.6 23.8 - - + -
42J LEU 3.4 3.6 - - - -
43J VAL* 4.1 15.7 - - + -
56J MET 4.1 8.5 - - - +
57J LEU* 1.3 76.6 - - - +
59J THR* 1.3 60.9 + - - +
68J TRP* 2.9 32.1 + - + +
69J ALA* 3.1 27.1 + - + +
71J VAL* 3.5 30.7 - - + -
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Residues in contact with THR 59 (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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4J LEU* 4.8 7.4 - - + -
41J ILE* 3.3 10.9 - - - +
42J LEU* 2.8 30.6 + - - +
44J HIS* 3.3 31.6 - - + +
57J LEU* 3.9 20.9 - - + -
58J LEU* 1.3 79.7 - - - +
60J SER* 1.3 69.7 + - - +
65J TYR* 4.0 16.3 - - - +
66J LYS 3.3 15.7 - - - -
67J PRO* 4.1 8.7 - - + -
68J TRP* 4.4 2.7 - - - +
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Residues in contact with SER 60 (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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39J SER* 6.1 3.4 - - - -
40J ASP 3.8 10.1 - - - -
41J ILE* 4.8 2.7 - - - +
42J LEU* 3.6 6.5 - - - +
59J THR* 1.3 89.3 + - - +
61J ASP* 1.3 68.7 + - - +
64J GLU 2.7 27.7 + - - +
65J TYR* 4.4 0.2 - - - -
66J LYS* 3.0 25.4 + - - +
68J TRP* 5.0 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