Contacts of the strand formed by residues 539 - 544 (chain A) in PDB entry 2JI8
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 CYS 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A VAL 2.8 11.5 + - - +
473A THR* 4.1 6.1 - - + -
474A VAL* 3.0 22.0 + - - +
509A MET* 3.3 12.2 - - - +
515A LYS* 3.3 30.1 - - - +
517A TYR* 4.2 6.1 - - + -
532A ALA* 3.6 35.4 - - + -
535A SER* 3.6 14.8 - - - -
537A LYS 3.4 14.6 - - - -
538A PRO* 1.3 75.5 - - - +
540A LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A PHE* 4.4 2.5 - - + -
462A LEU* 3.4 38.4 - - + -
474A VAL* 3.2 22.7 - - + +
476A ILE* 4.0 13.5 - - + -
505A TYR* 3.6 40.4 - - + +
506A ASP* 3.6 5.4 - - - +
509A MET* 3.6 17.9 - - + -
515A LYS 2.9 5.7 + - - -
516A GLY* 3.5 2.9 - - - -
517A TYR* 2.9 26.4 + - - -
539A CYS* 1.3 76.2 - - - +
541A ILE* 1.3 76.0 + - - +
542A ASN* 4.0 2.0 - - - +
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Residues in contact with ILE 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A THR* 3.8 21.3 - - + -
474A VAL 2.6 11.7 + - - +
475A ILE* 3.4 10.7 - - + -
476A ILE 2.9 26.7 + - - -
517A TYR* 3.7 15.9 - - + -
519A ALA* 3.9 17.0 - - + -
525A LEU* 3.6 25.6 - - + -
528A ALA* 3.7 15.7 - - + +
529A LEU* 3.5 44.2 - - + +
540A LEU* 1.3 77.9 - - - +
542A ASN* 1.3 59.1 + - - +
543A ALA* 3.3 4.5 + - + +
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Residues in contact with ASN 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A ILE* 4.1 3.8 - - - +
478A ASN* 2.8 32.5 + - - +
503A GLY 3.0 23.6 + - - -
504A ARG* 3.8 6.5 - - - +
505A TYR* 3.6 13.8 - - - +
506A ASP* 3.4 25.8 + - - +
517A TYR 2.7 19.1 + - - +
518A VAL* 3.6 7.3 - - + +
519A ALA 3.0 20.8 + - - +
540A LEU* 4.0 4.1 - - + +
541A ILE* 1.3 68.7 - - - +
543A ALA* 1.3 63.3 + - - +
544A MET* 3.4 16.0 + - - +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A MET* 4.2 12.6 - - + -
380A SER* 5.7 0.2 - - - -
475A ILE* 4.1 20.0 - - + -
476A ILE 2.9 15.0 + - - +
477A MET* 4.6 10.3 - - - -
478A ASN* 2.9 28.9 + - - +
519A ALA* 3.6 8.3 - - - -
525A LEU* 4.2 15.3 - - + -
541A ILE 3.3 1.8 + - - +
542A ASN* 1.3 71.7 - - - +
544A MET* 1.3 61.2 + - - +
545A ILE* 3.3 5.6 + - + +
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Residues in contact with MET 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A GLY* 3.5 18.7 - - - +
375A MET* 3.3 28.6 + - - +
478A ASN* 3.9 6.5 - - - +
502A ARG* 3.4 49.1 - - + +
504A ARG* 6.5 0.2 - - - -
518A VAL* 4.0 8.5 - - + -
519A ALA 2.9 13.4 + - - +
520A ASN* 3.2 29.6 - - - +
542A ASN* 3.9 35.4 - - - +
543A ALA* 1.3 70.2 - - - +
545A ILE* 1.3 61.7 + - - +
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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