Contacts of the strand formed by residues 37 - 41 (chain O) in PDB entry 1J0B
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 ASP 37 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O TYR* 3.3 27.1 + - + -
31O SER* 3.5 3.3 - - - -
36O ALA* 1.3 67.7 - - - +
38O VAL* 1.3 60.0 + - - +
39O TYR* 4.0 14.9 + - + -
301O GLU* 3.0 24.6 + - - +
302O LYS* 4.0 16.0 - - + +
303O ILE* 2.8 28.5 + - - +
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Residues in contact with VAL 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O TYR* 4.2 1.0 - - - -
27O LEU* 2.9 46.0 + - + +
30O ILE* 3.6 33.9 - - + -
31O SER* 2.7 25.1 + - - +
34O ILE* 5.3 4.0 - - + -
36O ALA 3.2 4.0 + - - +
37O ASP* 1.3 72.6 - - - +
39O TYR* 1.3 60.5 + - - +
287O PHE* 4.9 0.4 - - + -
290O LEU* 3.4 39.3 - - + -
303O ILE* 3.8 7.2 - - + +
305O PHE* 4.5 9.2 - - + -
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Residues in contact with TYR 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O ILE* 4.3 10.1 - - + -
25O GLN 2.9 11.0 - - - +
26O TYR* 3.1 52.0 - + + -
37O ASP* 4.5 21.8 + - + -
38O VAL* 1.3 72.9 - - - +
40O ILE* 1.3 61.4 + - - +
180O VAL* 3.2 38.2 - - + +
182O PHE* 3.1 32.5 - + + -
302O LYS* 5.0 4.0 - - + -
303O ILE 2.8 13.7 + - - +
304O LEU* 3.2 9.0 - - - +
305O PHE* 3.0 22.7 + - - +
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Residues in contact with ILE 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O PRO 3.7 0.7 - - - +
24O ILE* 4.6 1.1 - - - -
25O GLN* 2.8 37.9 + - + +
27O LEU* 3.4 36.5 - - + +
38O VAL 4.0 2.6 + - - -
39O TYR* 1.3 71.4 - - - +
41O LYS* 1.3 62.5 + - - +
42O ARG* 3.6 12.6 + - - +
276O ILE* 3.5 24.2 - - + -
278O LEU* 5.5 0.4 - - + -
287O PHE* 5.6 1.6 - - + -
304O LEU* 4.7 0.2 - - - -
305O PHE* 3.2 32.1 - - + -
307O HIS* 3.2 44.2 - - + -
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Residues in contact with LYS 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O THR* 2.7 34.8 + - - -
23O PRO 3.8 5.4 - - - +
24O ILE* 3.7 14.4 - - + -
39O TYR 3.9 0.2 + - - -
40O ILE* 1.3 72.7 - - - +
42O ARG* 1.3 50.2 + - - +
43O ASP* 2.5 36.8 + - - +
56O ARG* 3.9 4.1 - - - +
167O TYR* 6.5 0.2 - - - -
170O ALA* 5.1 5.2 - - - -
173O GLU* 3.2 14.7 + - - -
174O ILE* 3.1 35.0 - - + +
177O GLN* 2.9 24.7 - - - +
304O LEU* 3.3 18.6 - - + -
305O PHE 2.7 10.5 + - - +
306O ILE* 4.1 7.6 - - + -
307O HIS 3.7 10.1 + - - -
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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