Contacts of the strand formed by residues 533 - 538 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499D ILE* 3.2 29.2 - - + +
501D PRO* 4.0 13.2 - - + -
520D ILE* 3.8 40.6 - - + +
523D TRP* 3.8 31.9 - - + -
524D LEU* 3.6 17.7 - - + -
531D ARG 3.9 0.2 + - - -
532D PRO* 1.3 74.9 - - - +
534D ILE* 1.3 65.2 + - - +
535D LEU* 4.2 13.2 - - + +
556D PHE* 6.0 1.0 - - + -
561D ARG 2.9 10.9 + - - +
562D LEU* 3.8 8.9 - - + +
563D GLN 3.0 25.6 + - - -
564D GLY 4.1 2.2 + - - +
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Residues in contact with ILE 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D LEU* 3.7 32.8 - - + -
351D ILE* 4.0 17.5 - - + -
455D ILE* 5.0 4.0 - - + -
485D GLN* 5.2 3.7 + - - +
498D ILE* 3.8 24.7 - - + +
499D ILE 3.0 6.7 + - - -
500D CYS* 3.2 22.0 - - - +
532D PRO* 5.2 1.3 - - + -
533D LEU* 1.3 83.2 - - - +
535D LEU* 1.3 64.5 + - - +
536D CYS* 3.3 0.9 + - - -
563D GLN* 3.9 20.9 - - + +
564D GLY 3.4 13.2 - - - +
565D GLY* 3.7 12.6 - - - +
566D PHE* 3.9 22.7 - - + -
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Residues in contact with LEU 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D PRO* 3.3 25.4 - - + +
504D ALA* 3.6 38.6 - - + +
520D ILE* 4.3 9.0 - - + -
533D LEU* 4.2 9.4 - - + +
534D ILE* 1.3 70.6 - - - +
536D CYS* 1.3 60.1 + - - +
537D GLU 3.7 15.3 - - - +
538D TYR* 3.9 14.6 - - + -
552D TYR* 4.0 13.7 - - + -
556D PHE* 3.9 33.0 - - + -
564D GLY 3.1 10.4 + - - +
565D GLY* 3.1 4.4 - - - -
566D PHE* 2.9 31.8 + - - -
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Residues in contact with CYS 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D ASN* 3.0 20.6 + - - +
388D ARG* 3.3 33.5 + - - +
485D GLN* 3.9 19.1 - - - +
487D GLU* 3.8 21.8 - - + -
500D CYS* 3.3 22.3 + - + +
501D PRO 3.0 9.3 + - - -
502D MET* 4.1 6.1 - - - -
534D ILE 3.3 4.8 + - - -
535D LEU* 1.3 73.5 - - - +
537D GLU* 1.4 72.1 + - - +
566D PHE* 3.4 14.1 - - - +
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Residues in contact with GLU 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D ASN* 4.0 0.4 - - - +
388D ARG* 3.1 22.6 + - - +
460D ASN* 3.4 2.6 - - - +
501D PRO 3.7 0.2 + - - -
502D MET* 3.2 25.2 - - + +
503D TYR* 2.9 42.0 + - + +
535D LEU* 3.2 5.2 - - - +
536D CYS* 1.4 86.7 - - - +
538D TYR* 1.3 61.3 + - - +
566D PHE 3.2 7.9 - - - -
568D TRP* 3.7 17.0 - - + -
2001D 2DG 1.5 65.2 - - - +
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Residues in contact with TYR 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D GLY 5.1 0.2 + - - -
503D TYR* 3.8 12.9 - - - +
535D LEU* 3.9 21.1 - - + -
537D GLU* 1.3 76.3 - - - +
539D ALA* 1.3 77.1 + - + +
540D HIS 3.5 1.8 - - - -
549D PHE* 3.3 27.6 - + - -
552D TYR* 3.6 46.4 - + + +
553D TRP* 2.9 33.4 + - - -
556D PHE* 4.0 8.3 - + - -
565D GLY* 3.4 29.0 + - - -
566D PHE 3.1 20.9 + - - -
567D VAL* 3.2 20.2 - - + +
568D TRP 3.1 15.5 + - - +
624D GLN* 4.2 0.9 + - - -
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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