Contacts of the strand formed by residues 52 - 58 (chain X) in PDB entry 1JPY
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 TRP 52 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40X MET* 5.8 0.2 - - - -
44X ILE* 3.1 43.7 - - + -
45X GLU* 2.9 37.4 + - + +
48X SER* 4.0 3.4 - - - -
50X SER 3.5 13.5 - - - -
51X PRO* 1.3 74.8 - - - +
53X ASN* 1.3 71.3 + - - +
54X TYR* 3.1 32.8 + + - -
70X ALA* 3.6 11.9 - - + -
71X GLN 3.1 20.6 - - - +
73X ARG* 2.7 29.4 + - - -
120X VAL 3.9 4.9 + - - -
121X GLY* 3.7 11.0 - - - -
122X CYS* 3.2 43.1 - - - -
93Y ILE* 3.9 20.9 - - + -
123Y THR* 3.8 7.9 - - + -
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Residues in contact with ASN 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D NAG 1.5 69.7 + - - +
45X GLU* 5.5 0.4 - - - -
52X TRP* 1.3 74.8 - - - +
54X TYR* 1.3 64.7 + - - +
55X THR* 4.2 2.9 - - - +
70X ALA* 3.0 10.6 - - - +
71X GLN* 2.6 43.1 + - + +
73X ARG* 3.0 23.1 + - - -
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Residues in contact with TYR 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 5.7 0.3 + - - -
35B ASN* 6.4 2.2 - - + -
40X MET* 4.1 18.5 - - - +
44X ILE* 4.6 1.4 - - - +
45X GLU* 3.7 37.2 + - + +
52X TRP* 3.1 34.9 + + - -
53X ASN* 1.3 80.8 - - - +
55X THR* 1.3 61.9 + - - +
56X VAL* 4.1 4.4 + - + +
68X VAL* 3.5 28.0 - - + -
69X GLN 3.4 0.2 - - - -
70X ALA* 4.2 5.8 - - + -
120X VAL* 4.1 12.5 + - - -
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Residues in contact with THR 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 4.8 8.7 - - + -
53X ASN* 5.4 3.3 - - - +
54X TYR* 1.3 73.1 + - - +
56X VAL* 1.3 73.1 + - - +
57X THR* 3.9 8.0 + - + +
68X VAL* 3.4 2.9 - - - -
69X GLN* 2.6 51.5 + - + +
70X ALA 5.9 0.2 - - - -
71X GLN* 5.0 11.1 + - - +
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Residues in contact with VAL 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 2.9 62.9 + - + +
9A THR* 4.1 1.9 + - - -
34B GLU* 4.4 15.9 - - + +
37B ARG* 5.8 3.4 - - - +
54X TYR* 4.1 4.8 + - + +
55X THR* 1.3 77.3 - - - +
57X THR* 1.3 71.9 + - - +
66X GLU* 3.4 28.3 - - + +
67X VAL 4.3 2.0 - - - -
68X VAL* 3.7 22.2 - - + -
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Residues in contact with THR 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.9 4.7 - - - -
55X THR* 4.2 13.5 - - + +
56X VAL* 1.3 79.8 - - - +
58X TRP* 1.3 61.2 + - - +
62X ARG* 3.2 18.7 + - - -
66X GLU* 3.0 26.3 - - - +
67X VAL* 2.9 25.7 + - + +
69X GLN* 4.3 15.7 - - + -
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Residues in contact with TRP 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS 4.3 7.2 - - - +
9A THR* 3.1 36.2 + - + +
10A PHE* 3.3 53.9 - + + -
60B PRO 3.6 18.6 - - - -
63B TYR* 5.2 4.6 - + - -
65B SER* 2.8 29.7 + - - +
102B ARG* 5.3 8.5 - - - -
57X THR* 1.3 76.4 - - - +
59X ASP* 1.3 63.5 + - - +
60X PRO* 3.2 44.0 - - + +
62X ARG* 4.1 0.4 - - - -
65X SER* 3.3 10.6 - - - -
66X GLU* 4.0 24.9 - - + -
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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
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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