Contacts of the strand formed by residues 583 - 589 (chain B) in PDB entry 4KXY
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 THR 583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A GLY* 4.2 21.8 - - - +
554B GLY 2.9 11.0 + - - +
555B ARG* 3.7 19.8 - - - +
556B ILE* 3.0 26.5 + - - +
581B GLY 4.6 5.8 + - - +
582B ILE* 1.3 77.4 - - - +
584B VAL* 1.3 68.6 + - - +
585B THR* 5.7 1.8 - - - -
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Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A VAL* 4.0 33.6 + - + +
556B ILE* 3.4 24.5 - - + +
558B THR* 4.5 5.8 - - - +
569B GLY 4.7 3.1 - - - +
572B VAL* 4.4 11.4 - - + -
573B SER* 3.8 16.8 - - - +
576B VAL* 3.7 30.5 - - + -
582B ILE* 4.6 0.2 - - + -
583B THR* 1.3 82.6 - - - +
585B THR* 1.3 73.3 + - - +
586B HIS* 5.5 3.1 - - + +
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Residues in contact with THR 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B ILE 2.9 9.3 + - - -
557B LEU* 3.2 23.8 - - + +
558B THR 2.9 26.0 + - - -
583B THR* 5.6 2.8 - - - -
584B VAL* 1.3 78.7 + - - +
586B HIS* 1.3 66.9 + - - +
587B LEU* 5.6 2.2 - - + -
615B ALA* 5.1 10.1 - - + +
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Residues in contact with HIS 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A SER* 5.9 2.4 - - - -
558B THR* 3.6 6.7 - - - +
560B GLU* 2.7 26.1 + - + -
564B TYR* 3.5 52.4 + + + -
569B GLY* 3.4 32.9 - - - -
570B GLU* 3.9 4.6 - - + +
573B SER* 5.5 1.2 + - - -
584B VAL* 5.5 3.4 - - + +
585B THR* 1.3 79.7 - - - +
587B LEU* 1.3 89.5 + - - +
588B ALA* 3.6 8.8 - - + +
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Residues in contact with LEU 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B LEU* 4.1 15.3 - - + -
558B THR 2.8 12.6 + - - +
559B VAL* 3.3 12.6 - - + -
560B GLU 3.0 24.4 + - - -
564B TYR* 3.9 4.3 - - - +
585B THR* 5.7 2.2 - - + -
586B HIS* 1.3 81.7 - - - +
588B ALA* 1.3 62.5 + - - +
606B GLY 3.8 24.7 - - - +
607B ILE* 4.0 2.0 - - - -
611B ALA* 3.8 24.0 - - + +
612B ILE* 3.9 24.0 - - + -
615B ALA* 4.0 15.0 - - + -
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Residues in contact with ALA 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B GLU* 3.5 15.5 - - + -
562B HIS 3.4 13.0 - - - +
564B TYR* 3.1 39.5 + - + -
586B HIS* 3.6 19.3 - - - +
587B LEU* 1.3 75.9 - - - +
589B VAL* 1.3 61.1 + - - +
590B ASN* 3.7 1.4 + - - +
605B PHE 3.4 13.9 - - - +
606B GLY 4.9 0.7 - - - +
607B ILE* 3.8 8.1 - - - +
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Residues in contact with VAL 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B VAL* 4.2 6.1 - - + -
431B LEU* 4.2 4.9 - - + -
560B GLU 4.3 0.2 - - - +
561B ASP* 3.9 22.0 - - - +
562B HIS 3.0 21.9 + - - +
563B TYR* 3.3 29.6 - - + -
564B TYR* 3.4 10.9 + - - -
588B ALA* 1.3 75.7 - - - +
590B ASN* 1.3 59.5 + - - +
591B ARG 3.5 21.1 - - - +
593B PRO* 4.0 15.7 - - + -
605B PHE* 4.1 22.2 - - + -
607B ILE* 4.0 14.4 - - + -
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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