Contacts of the strand formed by residues 589 - 596 (chain A) in PDB entry 4DAY
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 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A LYS* 3.2 31.9 - - - -
512A ALA 3.4 14.8 - - - +
513A PHE* 4.1 12.8 - - + -
587A ASP 3.6 3.6 + - - -
588A LEU* 1.3 79.3 - - - +
590A CYS* 1.3 67.4 + - - +
610A ASP* 4.8 1.9 - - - +
59B TRP* 4.5 9.0 - - - -
61B GLN* 5.2 0.9 - - - -
103B MET* 5.1 3.6 - - - -
123B THR* 4.1 4.9 - - + -
125B LEU* 3.8 28.6 - - + +
131B HIS* 3.7 17.3 + - - -
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Residues in contact with CYS 590 (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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511A LYS* 3.8 14.1 - - - +
512A ALA 3.0 27.6 + - - +
588A LEU* 4.1 16.8 - - - -
589A CYS* 1.3 79.9 - - - +
591A LEU* 1.3 75.6 + - - +
592A MET* 3.5 4.3 + - - +
608A LEU* 3.8 27.8 - - - -
609A GLN 3.2 15.3 - - - +
610A ASP* 4.2 14.8 - - - +
611A VAL* 4.1 6.7 - - - +
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Residues in contact with LEU 591 (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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490A PRO* 4.1 1.8 - - + +
491A PHE* 3.8 25.8 - - + -
509A LYS* 3.8 26.7 - - + +
510A VAL 3.0 9.2 - - - +
511A LYS* 3.7 16.8 - - + -
590A CYS* 1.3 75.6 - - - +
592A MET* 1.3 59.4 + - - +
593A THR 4.1 0.4 - - - -
608A LEU* 3.3 4.9 - - - -
609A GLN* 2.8 49.1 + - + +
611A VAL* 3.6 25.3 - - + +
615A HIS* 3.3 42.4 - - + +
134B MET* 6.4 0.7 - - + -
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Residues in contact with MET 592 (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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508A VAL 3.4 0.2 - - - +
509A LYS* 3.4 4.9 - - - -
510A VAL* 2.7 30.4 + - + +
512A ALA* 3.6 40.8 - - + +
513A PHE* 4.5 3.1 - - - +
514A ILE* 4.8 0.2 - - + -
534A VAL* 4.6 18.2 - - + -
545A PHE* 5.7 2.7 - - + -
588A LEU* 3.7 30.1 - - + -
590A CYS* 3.9 4.9 - - - +
591A LEU* 1.3 74.0 - - - +
593A THR* 1.3 63.8 + - - +
594A ILE* 3.0 25.2 + - + +
605A VAL* 4.4 18.6 - - + -
607A ALA 3.6 6.1 - - - +
608A LEU* 3.3 20.6 - - + -
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Residues in contact with THR 593 (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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507A THR* 4.1 20.4 - - + -
508A VAL 3.3 5.6 - - - +
509A LYS* 3.6 18.9 - - - +
591A LEU 4.1 1.6 - - - -
592A MET* 1.3 69.6 - - - +
594A ILE* 1.3 56.4 + - - +
605A VAL* 3.7 2.9 - - - +
606A LEU* 2.8 54.6 + - + -
607A ALA* 3.2 30.9 + - + +
609A GLN* 5.0 4.7 + - - +
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Residues in contact with ILE 594 (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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494A LEU* 5.2 4.5 - - + -
506A THR 3.7 0.7 - - - +
507A THR* 3.6 4.5 - - - +
508A VAL* 3.0 44.9 + - + +
510A VAL* 3.5 28.0 - - + -
534A VAL* 4.7 6.3 - - + -
541A LEU* 4.1 20.4 - - + -
543A VAL* 4.5 6.5 - - + -
592A MET* 3.0 22.6 + - + +
593A THR* 1.3 77.7 - - - +
595A SER* 1.3 63.5 + - - +
596A PHE* 4.2 4.0 - - + +
603A ALA* 3.6 25.4 - - + -
604A MET 4.1 3.1 - - - +
605A VAL* 4.1 12.6 - - + -
606A LEU* 4.6 3.1 - - - -
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Residues in contact with SER 595 (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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505A VAL* 3.9 21.0 - - - +
506A THR 3.5 5.0 + - - -
507A THR* 4.7 4.6 + - - +
594A ILE* 1.3 70.4 - - - +
596A PHE* 1.3 61.1 + - - +
597A ASN 3.6 1.0 + - - -
603A ALA* 3.4 5.8 - - - -
604A MET* 3.1 38.0 + - - +
606A LEU* 3.5 28.2 - - - +
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Residues in contact with PHE 596 (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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494A LEU* 5.8 1.8 - - + -
497A LEU* 4.1 26.5 - - + -
498A MET* 4.7 19.5 - - + -
502A PRO* 4.4 17.7 - - + -
505A VAL* 3.5 7.9 - - - +
506A THR* 3.0 34.8 + - - +
508A VAL* 5.6 0.2 - - + -
541A LEU* 3.8 28.7 - - + -
594A ILE* 3.8 5.8 + - + +
595A SER* 1.3 71.7 - - - +
597A ASN* 1.3 60.3 + - - +
598A PRO* 3.2 39.5 - - + +
601A SER* 3.7 24.7 - - - -
603A ALA* 3.9 12.1 - - + -
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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