Contacts of the helix formed by residues 572 - 582 (chain B) in PDB entry 2PKG
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 ASP 572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534B ALA* 3.6 24.0 - - + +
537B ARG* 4.8 5.4 - - - +
538B PHE* 5.9 0.2 - - - -
570B ASP* 3.7 2.1 - - - +
571B GLN* 1.3 90.9 + - - +
573B VAL* 1.3 66.2 + - - +
574B ASP* 2.7 45.0 + - - +
575B VAL* 2.9 41.9 + - + +
576B LYS 3.4 3.1 + - - -
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Residues in contact with VAL 573 (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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571B GLN* 2.9 15.9 + - - +
572B ASP* 1.3 71.0 + - - +
574B ASP* 1.3 66.3 + - - +
576B LYS* 2.9 14.8 + - + +
577B TYR* 2.7 34.5 + - + +
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Residues in contact with ASP 574 (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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538B PHE* 3.8 24.5 - - + -
572B ASP* 2.7 24.4 + - - +
573B VAL* 1.3 75.1 - - - +
575B VAL* 1.3 61.8 + - - +
577B TYR* 3.2 27.5 - - - +
578B PHE* 3.2 22.7 - - + -
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Residues in contact with VAL 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ALA* 4.6 5.8 - - + -
537B ARG* 4.4 11.9 - - + +
538B PHE* 3.5 34.1 - - + +
541B ALA* 5.0 1.2 - - + +
567B LEU* 4.3 14.6 - - + +
570B ASP* 3.4 38.1 - - + +
572B ASP* 2.9 30.6 + - + +
574B ASP* 1.3 78.1 - - - +
576B LYS* 1.3 53.7 + - - +
578B PHE* 3.2 1.6 + - - +
579B ALA* 2.5 39.3 + - + +
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Residues in contact with LYS 576 (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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567B LEU 4.7 2.9 - - - -
568B THR* 3.3 27.8 - - - +
569B GLN* 5.0 2.2 - - - +
570B ASP 4.4 14.9 + - - +
571B GLN 5.3 2.0 - - - -
572B ASP 3.4 4.2 + - - +
573B VAL* 2.9 16.9 + - + +
575B VAL* 1.3 77.5 - - - +
577B TYR* 1.3 70.5 + - - +
579B ALA* 2.6 25.2 + - + +
580B GLN* 3.0 17.9 + - + +
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Residues in contact with TYR 577 (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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573B VAL* 2.7 23.0 + - + +
574B ASP* 3.2 25.6 - - - +
576B LYS* 1.3 76.8 - - - +
578B PHE* 1.3 84.4 + + + +
580B GLN* 3.7 2.1 + - - +
581B GLU* 3.4 29.3 + - + +
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Residues in contact with PHE 578 (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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538B PHE* 3.7 34.3 - + - +
541B ALA* 4.3 5.2 - - + +
542B LYS* 3.6 44.6 - - + +
545B GLN* 4.9 4.9 - - - +
574B ASP* 3.2 28.9 + - - -
575B VAL 3.2 4.2 + - - +
576B LYS 3.0 0.2 + - - -
577B TYR* 1.3 99.2 - + + +
579B ALA* 1.3 68.6 + - - +
581B GLU* 2.9 25.5 + - + +
582B ALA* 3.2 13.2 + - - +
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Residues in contact with ALA 579 (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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541B ALA* 4.0 13.4 - - + +
564B LEU* 3.0 29.2 - - - +
567B LEU* 4.0 30.1 - - + +
568B THR* 4.1 5.8 - - - -
575B VAL* 2.5 26.9 + - + +
576B LYS* 2.6 19.3 + - - +
578B PHE* 1.3 72.0 - - - +
580B GLN* 1.3 57.1 + - - +
582B ALA* 3.9 3.8 + - - +
583B LEU* 3.9 0.3 - - - +
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Residues in contact with GLN 580 (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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568B THR* 4.0 21.7 + - + +
576B LYS* 3.0 19.4 + - + +
577B TYR 4.5 1.6 - - - +
579B ALA* 1.3 73.7 - - - +
581B GLU* 1.3 55.3 + - - +
582B ALA 2.9 5.6 - - - -
583B LEU* 2.8 44.5 + - + +
584B THR* 3.1 18.3 + - - +
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Residues in contact with GLU 581 (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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545B GLN* 4.0 15.9 + - - +
577B TYR* 3.4 28.5 + - + +
578B PHE* 2.9 21.5 + - + +
580B GLN* 1.3 78.1 - - - +
582B ALA* 1.3 59.6 + - - +
583B LEU 3.4 0.2 - - - -
584B THR* 3.7 17.7 - - - -
585B VAL* 3.4 21.0 - - + +
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Residues in contact with ALA 582 (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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541B ALA* 4.5 8.3 - - + +
545B GLN* 3.8 37.8 + - + +
564B LEU* 4.4 15.9 - - + -
578B PHE 3.2 7.9 + - - +
579B ALA 4.0 11.7 - - - +
580B GLN 2.9 0.4 - - - -
581B GLU* 1.3 77.6 - - - +
583B LEU* 1.3 62.7 + - - +
584B THR 3.4 0.2 - - - -
585B VAL* 3.4 3.8 + - - +
586B LEU* 3.0 32.5 + - + +
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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