Contacts of the strand formed by residues 618 - 625 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607A THR* 3.2 7.8 - - - +
608A ALA 3.0 34.4 + - - +
611A LEU* 3.4 24.5 - - + -
612A ILE* 3.9 19.1 - - + -
616A ALA* 3.2 10.4 - - + -
617A ALA* 1.3 78.0 - - - +
619A THR* 1.3 67.5 + - - +
620A VAL* 4.3 8.7 - - + -
657A LEU* 3.7 33.4 - - + -
671A GLU* 5.3 5.6 - - + -
672A TYR 5.8 0.2 - - - +
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Residues in contact with THR 619 (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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605A GLU* 4.2 16.6 - - + +
606A ALA 3.3 10.1 - - - +
607A THR* 4.7 6.4 + - - +
617A ALA 3.9 2.8 + - - -
618A MET* 1.3 79.1 - - - +
620A VAL* 1.3 70.1 + - - +
672A TYR* 3.4 42.4 + - + +
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Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 4.5 1.1 - - + -
605A GLU* 3.5 8.7 - - - +
606A ALA* 2.7 58.6 + - + +
608A ALA* 4.1 26.0 - - + +
611A LEU* 4.2 7.2 - - + -
618A MET* 4.3 8.1 - - + -
619A THR* 1.3 83.1 - - - +
621A ALA* 1.3 59.1 + - - +
622A VAL* 3.9 6.1 - - + -
657A LEU* 4.1 20.2 - - + -
669A ILE* 3.9 19.7 - - + -
670A THR 3.5 8.7 - - - +
672A TYR* 3.6 10.6 - - - +
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Residues in contact with ALA 621 (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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595A LEU* 4.0 6.1 - - + -
603A VAL* 3.9 13.7 - - + -
604A VAL 3.4 4.0 - - - -
620A VAL* 1.3 72.6 - - - +
622A VAL* 1.3 64.2 + - - +
669A ILE* 3.7 1.9 - - - +
670A THR* 2.8 39.9 + - + +
672A TYR* 4.0 2.3 - - - +
1480A ADP 3.4 42.4 - - + +
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Residues in contact with VAL 622 (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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589A LEU* 3.8 21.1 - - + -
591A PHE* 3.6 31.9 - - + -
602A LYS 3.8 0.7 - - - +
603A VAL* 3.2 3.0 - - - -
604A VAL* 2.7 39.1 + - + +
606A ALA* 3.8 17.3 - - + -
620A VAL* 3.9 9.6 - - + -
621A ALA* 1.3 78.6 - - - +
623A LYS* 1.3 63.6 + - - +
624A MET* 4.7 2.4 - - - +
667A LEU* 3.7 28.9 - - + -
668A VAL 3.5 4.9 - - - +
669A ILE* 4.1 8.3 - - + -
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Residues in contact with LYS 623 (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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600A PHE* 5.4 2.7 - - - -
601A GLY* 4.1 10.6 - - - +
602A LYS 3.4 5.4 - - - +
603A VAL* 3.5 21.8 - - + -
621A ALA 4.1 0.2 - - - -
622A VAL* 1.3 73.9 - - - +
624A MET* 1.3 66.0 + - - +
637A LEU* 4.0 19.2 - - + +
640A GLU* 3.2 37.3 + - - +
666A THR 3.8 0.7 - - - +
667A LEU* 3.5 2.3 - - - -
668A VAL* 2.6 51.5 + - + +
670A THR* 5.8 3.4 - - - +
1480A ADP 2.7 57.6 + - + +
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Residues in contact with MET 624 (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* 4.0 26.0 - - + -
601A GLY* 3.5 3.3 - - - -
602A LYS* 2.6 78.1 + - + +
604A VAL* 3.6 27.8 - - + +
622A VAL* 4.7 2.9 - - - +
623A LYS* 1.3 76.9 - - - +
625A LEU* 1.3 69.7 + - - +
637A LEU* 4.4 5.6 - - - -
665A PRO* 5.6 3.6 - - + -
666A THR 3.7 14.1 - - - +
667A LEU* 4.3 14.1 - - + -
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Residues in contact with LEU 625 (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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600A PHE 4.4 4.9 - - - +
601A GLY* 4.7 3.1 - - - -
602A LYS* 4.8 0.5 - - - +
624A MET* 1.3 87.5 - - - +
626A LYS* 1.3 66.9 + - - +
627A PRO* 3.9 2.3 - - - +
629A ALA* 4.0 7.2 - - + -
633A GLU* 3.4 43.3 - - + +
634A ARG* 3.3 51.4 - - + +
637A LEU* 4.0 24.1 - - + +
665A PRO* 5.9 7.4 - - + +
666A THR* 4.4 3.5 + - - +
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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