Contacts of the strand formed by residues 589 - 597 (chain B) in PDB entry 1PKG
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584B PHE* 3.5 29.4 - - + -
585B PRO 4.7 1.6 - - - +
586B ARG 3.8 13.8 + - - +
587B ASN* 3.3 8.9 - - - +
588B ARG* 1.3 80.6 - - - +
590B SER* 1.3 61.6 + - - +
591B PHE* 4.0 18.6 - - + -
606B ALA* 4.5 7.0 - - + -
607B THR 3.2 7.9 - - - +
608B ALA* 3.7 15.9 - - + -
609B TYR* 6.2 0.2 - - - -
620B VAL* 4.4 9.4 - - + -
622B VAL* 4.1 10.3 - - + -
660B CYS* 4.3 12.1 - - - -
667B LEU* 3.8 28.9 - - + -
669B ILE* 4.1 14.8 - - + -
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Residues in contact with SER 590 (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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589B LEU* 1.3 76.2 - - - +
591B PHE* 1.3 67.8 + - - +
592B GLY* 3.7 0.3 + - - -
606B ALA* 3.2 14.6 - - - +
607B THR* 2.9 27.2 + - - -
609B TYR* 5.7 5.2 - - - -
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Residues in contact with PHE 591 (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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586B ARG 5.5 4.0 - - - -
589B LEU* 4.0 15.0 - - + -
590B SER* 1.3 79.7 + - - +
592B GLY* 1.3 61.3 + - - +
604B VAL* 4.2 22.0 - - + -
605B GLU 3.7 1.3 - - - -
606B ALA* 3.8 11.9 - - + -
622B VAL* 3.7 31.0 - - + -
624B MET* 4.9 9.6 - - + -
667B LEU* 3.9 29.6 - - + -
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Residues in contact with GLY 592 (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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590B SER 3.7 1.9 + - - -
591B PHE* 1.3 75.5 - - - +
593B LYS* 1.3 67.7 + - - -
594B THR 3.7 0.7 + - - -
604B VAL* 3.3 9.5 - - - +
605B GLU* 2.6 22.3 + - - -
606B ALA* 5.0 0.4 - - - -
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Residues in contact with LYS 593 (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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592B GLY* 1.3 72.3 - - - -
594B THR* 1.3 69.6 + - - +
595B LEU* 4.0 18.8 - - + +
604B VAL* 3.1 3.0 - - - +
605B GLU* 2.8 62.3 + - + +
672B TYR* 5.2 3.1 - - - +
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Residues in contact with THR 594 (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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592B GLY 3.7 1.4 + - - -
593B LYS* 1.3 83.9 - - - +
595B LEU* 1.3 63.2 + - - +
596B GLY* 4.0 16.4 - - - +
597B ALA* 5.3 1.8 - - + +
602B LYS* 4.6 14.8 + - + -
603B VAL 3.9 7.2 - - - +
604B VAL* 3.9 16.3 - - + +
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Residues in contact with LEU 595 (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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593B LYS* 3.4 22.8 + - - +
594B THR* 1.3 75.0 - - - +
596B GLY* 1.3 55.4 + - - +
603B VAL* 2.8 17.4 + - + +
604B VAL 4.1 2.5 - - - -
605B GLU* 3.4 34.1 - - + +
621B ALA* 4.1 10.8 - - + -
672B TYR* 3.5 32.3 - - + +
676B GLY* 5.9 2.7 - - - -
677B ASP* 5.5 0.5 - - - +
1486B ADP 3.5 47.4 + - + +
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Residues in contact with GLY 596 (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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594B THR* 3.8 8.3 - - - +
595B LEU* 1.3 81.5 - - - +
597B ALA* 1.3 61.3 + - - -
602B LYS* 3.7 1.2 - - - +
603B VAL* 2.8 31.8 + - - +
1486B ADP 3.2 22.8 + - - -
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Residues in contact with ALA 597 (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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594B THR* 5.3 3.1 - - + +
596B GLY* 1.3 75.1 - - - -
598B GLY* 1.3 59.7 + - - +
601B GLY 3.7 6.3 - - - +
602B LYS* 4.3 7.0 - - + +
626B LYS* 4.0 21.3 - - - -
1486B ADP 3.5 13.7 + - - +
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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