Contacts of the strand formed by residues 533 - 538 (chain A) in PDB entry 1JZ3
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 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A ILE* 3.3 34.8 - - + +
501A PRO* 4.1 9.6 - - + -
520A ILE* 3.9 46.9 - - + +
523A TRP* 3.9 15.5 - - + -
524A LEU* 3.5 19.7 - - + -
531A ARG 3.8 0.2 + - - -
532A PRO* 1.3 74.0 - - - +
534A ILE* 1.3 63.9 + - - +
535A LEU* 4.1 18.2 - - + +
556A PHE* 5.9 0.6 - - + -
561A ARG 3.0 9.8 + - - +
562A LEU* 3.8 8.6 - - + -
563A GLN 2.9 28.1 + - - -
564A GLY 4.1 1.0 + - - +
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Residues in contact with ILE 534 (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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342A LEU* 3.7 33.4 - - + -
351A ILE* 4.1 14.6 - - + -
455A ILE* 5.2 4.0 - - + -
485A GLN* 5.2 4.9 + - - +
498A ILE* 3.8 21.9 - - + +
499A ILE 2.9 7.3 + - - -
500A CYS* 3.1 23.2 - - - +
532A PRO* 5.2 1.6 - - + -
533A LEU* 1.3 80.8 - - - +
535A LEU* 1.3 66.8 + - - +
536A CYS* 3.3 1.0 + - - -
563A GLN* 3.7 26.0 - - + +
564A GLY 3.4 19.1 - - - +
565A GLY* 3.8 7.6 - - - +
566A PHE* 3.9 22.9 - - + -
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Residues in contact with LEU 535 (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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501A PRO* 3.3 26.0 - - + +
504A ALA* 3.7 35.9 - - + +
520A ILE* 4.2 9.0 - - + -
533A LEU* 4.1 11.2 - - + -
534A ILE* 1.3 71.9 - - - +
536A CYS* 1.3 59.9 + - - +
537A GLU 3.8 14.1 - - - +
538A TYR* 4.0 14.4 - - + -
552A TYR* 4.1 13.9 - - + -
556A PHE* 3.8 24.5 - - + -
564A GLY 3.1 18.5 + - - +
565A GLY* 3.2 5.1 - - - -
566A PHE* 3.0 29.5 + - - -
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Residues in contact with CYS 536 (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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355A ASN* 2.9 21.8 + - - +
388A ARG* 3.2 32.5 + - - +
485A GLN* 4.1 18.8 - - - +
487A GLU* 3.8 20.9 - - + -
500A CYS* 3.2 24.1 + - + +
501A PRO 2.9 10.5 + - - -
502A MET* 4.1 6.7 - - - -
534A ILE 3.3 4.5 + - - -
535A LEU* 1.3 73.1 - - - +
537A GLU* 1.4 70.9 + - - +
566A PHE* 3.4 14.0 - - - +
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Residues in contact with GLU 537 (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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355A ASN* 3.7 9.0 - - - +
388A ARG* 3.1 20.1 + - - +
460A ASN* 3.5 3.1 - - - +
501A PRO 3.6 2.6 - - - +
502A MET* 3.1 27.2 - - + +
503A TYR* 2.8 51.6 + - + +
535A LEU* 3.2 2.5 - - - +
536A CYS* 1.4 88.7 - - - +
538A TYR* 1.4 59.6 + - - +
566A PHE 3.1 7.4 - - - -
568A TRP* 3.7 8.9 - - + -
2001A 2DG 1.5 58.4 - - - +
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Residues in contact with TYR 538 (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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503A TYR* 3.8 12.7 - - - +
535A LEU* 4.0 20.2 - - + -
537A GLU* 1.4 74.6 - - - +
539A ALA* 1.3 77.3 + - + +
540A HIS 3.5 2.0 - - - -
549A PHE* 3.3 29.5 - + - -
552A TYR* 3.6 45.8 - + + +
553A TRP* 2.9 33.8 + - - -
556A PHE* 4.0 8.3 - + - -
565A GLY* 3.3 29.8 + - - -
566A PHE 3.1 19.1 + - - -
567A VAL* 3.3 19.9 - - + +
568A TRP 3.1 15.0 + - - +
624A GLN* 4.1 1.4 + - - -
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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