Contacts of the strand formed by residues 618 - 624 (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 MET 618 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B THR* 3.6 3.8 - - - -
608B ALA* 3.0 30.7 + - - +
611B LEU* 3.4 34.1 - - + -
612B ILE* 3.2 43.1 - - + +
616B ALA* 4.3 13.5 - - + -
617B ALA* 1.3 75.7 - - - +
619B THR* 1.3 66.8 + - - +
620B VAL* 4.1 3.5 + - + -
657B LEU* 3.7 21.5 - - + -
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Residues in contact with THR 619 (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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605B GLU* 4.0 19.7 - - + -
606B ALA 3.5 11.4 - - - +
607B THR* 4.7 6.1 + - - +
618B MET* 1.3 80.0 - - - +
620B VAL* 1.3 67.8 + - - +
657B LEU* 5.1 0.2 - - - +
671B GLU* 4.8 1.4 - - - -
672B TYR* 3.3 44.8 + - + +
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Residues in contact with VAL 620 (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* 4.4 8.5 - - + -
605B GLU* 3.8 4.9 - - - +
606B ALA* 2.8 40.5 + - + +
608B ALA* 4.0 9.9 - - + -
611B LEU* 3.4 30.5 - - + -
618B MET* 4.4 5.2 - - - +
619B THR* 1.3 79.3 - - - +
621B ALA* 1.3 60.2 + - - +
622B VAL* 3.8 24.7 - - + -
657B LEU* 3.8 9.2 - - + -
669B ILE* 3.6 9.0 - - + -
670B THR 3.5 12.1 - - - +
671B GLU* 4.8 0.2 - - - +
672B TYR* 3.6 14.7 - - - +
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Residues in contact with ALA 621 (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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595B LEU* 4.1 6.5 - - + -
603B VAL* 3.8 14.6 - - + -
604B VAL 4.0 3.8 - - - -
620B VAL* 1.3 76.5 - - - +
622B VAL* 1.3 62.6 + - - +
668B VAL 3.6 0.5 - - - +
669B ILE* 3.4 4.9 - - - -
670B THR* 2.9 39.5 + - - +
672B TYR* 3.9 1.4 - - - +
1486B ADP 3.3 37.7 - - + +
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Residues in contact with VAL 622 (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* 4.1 8.1 - - + -
591B PHE* 3.7 29.6 - - + -
602B LYS 3.6 0.7 - - - +
603B VAL* 3.2 4.9 - - - -
604B VAL 2.9 37.9 + - - +
606B ALA* 4.4 2.9 - - + -
620B VAL* 3.8 13.0 - - + -
621B ALA* 1.3 80.5 - - - +
623B LYS* 1.3 61.3 + - - +
624B MET* 3.9 5.9 + - - +
667B LEU* 3.5 44.2 - - + -
668B VAL 3.4 3.8 - - - +
669B ILE* 3.7 18.8 - - + -
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Residues in contact with LYS 623 (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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600B PHE* 4.5 10.3 - - - -
601B GLY* 5.0 3.8 - - - -
602B LYS 3.3 5.2 - - - +
603B VAL* 3.4 26.2 - - + +
621B ALA 4.3 0.4 - - - -
622B VAL* 1.3 71.9 - - - +
624B MET* 1.3 65.1 + - - +
636B ALA 6.1 0.2 - - - -
637B LEU* 3.7 22.6 - - + +
640B GLU* 2.9 33.3 + - - -
666B THR 3.7 1.6 - - - +
667B LEU* 3.6 7.8 - - - -
668B VAL* 2.9 43.2 + - + +
670B THR* 5.8 2.9 - - + -
810B ASP* 4.1 3.4 + - - +
1486B ADP 2.7 46.5 + - - +
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Residues in contact with MET 624 (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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591B PHE* 4.9 10.5 - - + -
600B PHE 4.3 0.6 - - - +
601B GLY* 2.9 7.8 - - - -
602B LYS* 2.6 74.1 + - + +
604B VAL* 4.4 10.3 - - + -
622B VAL* 4.2 15.7 - - - +
623B LYS* 1.3 73.5 - - - +
625B LEU* 1.3 67.5 + - - +
637B LEU* 4.4 4.9 - - - -
665B PRO* 5.7 5.6 - - + -
666B THR 4.2 4.9 - - - +
667B LEU* 3.6 28.3 - - + -
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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