Contacts of the strand formed by residues 589 - 598 (chain A) in PDB entry 1QZJ
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 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A PHE* 4.2 9.4 - - + -
585A PRO 4.0 1.1 + - - +
586A ARG* 3.3 16.3 + - - +
587A ASN 3.4 2.0 - - - -
588A ARG* 1.3 74.7 - - - +
590A SER* 1.3 58.9 + - - +
591A PHE* 3.3 40.2 + - + -
606A ALA* 3.8 21.1 - - + -
607A THR 4.0 0.2 - - - -
608A ALA* 4.0 15.9 - - + -
620A VAL* 4.0 12.6 - - + -
622A VAL* 3.9 28.9 - - + -
660A CYS* 4.4 9.6 - - - -
667A LEU* 4.3 9.4 - - + -
669A ILE* 4.1 23.8 - - + -
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Residues in contact with SER 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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587A ASN 5.7 0.9 - - - -
588A ARG 3.4 0.6 + - - -
589A LEU* 1.3 69.6 - - - +
591A PHE* 1.3 67.4 + - - +
606A ALA* 3.3 0.8 - - - -
607A THR* 2.9 40.9 + - - -
609A TYR* 3.5 36.8 + - - -
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Residues in contact with PHE 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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586A ARG 5.5 4.0 - - - -
589A LEU* 3.6 30.3 - - + -
590A SER* 1.3 79.8 + - - +
592A GLY* 1.3 60.0 + - - +
604A VAL* 4.1 19.5 - - + -
605A GLU 3.7 3.6 - - - -
606A ALA* 3.9 8.1 - - + -
622A VAL* 4.4 2.7 - - + -
624A MET* 3.8 21.8 - - + -
667A LEU* 3.9 23.6 - - + -
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Residues in contact with GLY 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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591A PHE* 1.3 77.0 - - - +
593A LYS* 1.3 65.7 + - - +
594A THR 3.8 0.5 + - - -
604A VAL* 3.9 10.9 - - - +
605A GLU* 2.9 26.2 + - - +
606A ALA* 4.8 0.4 - - - -
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Residues in contact with LYS 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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592A GLY* 1.3 70.9 - - - +
594A THR* 1.3 76.4 + - - +
595A LEU* 3.3 2.6 + - + +
604A VAL* 3.5 0.3 - - - -
605A GLU* 2.9 52.2 + - + +
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Residues in contact with THR 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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592A GLY 3.8 0.6 + - - -
593A LYS* 1.3 88.0 + - - +
595A LEU* 1.3 61.2 + - - +
596A GLY* 3.4 31.6 - - - +
597A ALA* 4.5 5.6 - - + -
602A LYS* 3.3 31.5 + - - -
603A VAL 3.8 4.5 - - - -
604A VAL* 4.2 3.4 - - - +
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Residues in contact with LEU 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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593A LYS* 3.3 3.1 + - + +
594A THR* 1.3 74.1 - - - +
596A GLY* 1.3 55.7 + - - +
603A VAL* 3.0 23.2 + - + +
604A VAL 3.7 2.0 - - - -
605A GLU* 3.5 33.7 - - + +
621A ALA* 3.6 30.3 - - + -
672A TYR* 4.4 18.4 - - + +
673A CYS* 4.0 21.5 - - + +
674A CYS 4.7 8.7 - - - +
799A LEU* 6.1 2.0 - - + +
811A PHE 4.9 3.2 - - - +
813A LEU* 5.0 1.6 - - - +
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Residues in contact with GLY 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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594A THR* 3.4 9.3 - - - +
595A LEU* 1.3 76.5 - - - +
597A ALA* 1.3 59.8 + - - +
602A LYS* 3.3 6.2 - - - +
603A VAL* 3.0 37.0 + - - +
811A PHE 4.4 1.1 - - - -
813A LEU* 3.8 18.4 - - - -
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Residues in contact with ALA 597 (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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594A THR* 4.5 7.9 - - + -
596A GLY* 1.3 76.2 - - - +
598A GLY* 1.3 58.1 + - - +
601A GLY 4.1 4.3 - - - -
602A LYS* 4.2 14.4 - - + +
626A LYS* 4.5 13.2 - - - +
812A GLY 3.4 5.4 + - - -
813A LEU* 3.4 17.6 - - - +
816A ASP* 3.4 20.7 - - - +
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Residues in contact with GLY 598 (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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597A ALA* 1.3 71.3 - - - +
599A ALA* 1.3 57.0 + - - -
600A PHE 3.0 8.7 + - - -
601A GLY 2.8 24.5 + - - +
626A LYS* 2.8 15.8 + - - -
812A GLY 3.0 18.6 + - - -
814A ALA* 3.7 13.5 - - - -
816A ASP* 3.0 8.1 - - - -
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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