Contacts of the helix formed by residues 482 - 489 (chain A) 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 ILE 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A PHE* 5.3 2.0 - - + -
444A ASN* 4.1 8.3 - - - +
447A CYS* 6.5 0.4 - - + -
448A MET* 4.6 15.5 - - + -
466A LEU* 3.6 35.2 - - + -
469A LEU* 5.6 1.8 - - + -
470A VAL* 5.0 1.8 - - + -
477A TRP* 3.7 33.4 - - + -
478A ALA* 2.8 25.3 + - + +
481A THR* 1.3 90.7 - - + +
483A ILE* 1.3 69.0 + - - +
484A PRO* 2.7 4.7 - - - -
485A LYS* 3.0 18.1 + - - +
486A VAL* 3.3 14.5 + - + +
508A LEU* 4.1 14.1 - - + -
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Residues in contact with ILE 483 (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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478A ALA* 3.4 16.6 - - + +
479A HIS* 3.6 17.5 - - - +
482A ILE* 1.3 78.1 - - - +
484A PRO* 1.3 75.6 - - + +
486A VAL* 3.2 9.1 + - + +
487A LEU* 2.9 24.8 + - + +
508A LEU* 4.7 11.0 - - + -
512A CYS* 4.2 19.5 - - - -
516A ILE* 4.8 8.3 - - + -
520A HIS* 3.9 37.0 - - + +
521A MET* 3.6 29.8 - - + -
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Residues in contact with PRO 484 (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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479A HIS 3.6 17.9 - - - +
480A ALA* 4.1 13.9 - - - +
481A THR 4.1 1.6 - - - +
482A ILE 3.0 10.8 - - - +
483A ILE* 1.3 95.4 - - + +
485A LYS* 1.3 59.8 + - + +
486A VAL 2.7 12.5 + - - -
487A LEU* 2.7 19.8 + - + +
488A ALA* 2.8 13.9 + - - +
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Residues in contact with LYS 485 (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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444A ASN* 3.5 30.1 - - - +
445A SER* 4.4 13.9 - - - +
448A MET* 4.2 23.1 - - + +
481A THR 4.1 15.9 - - - +
482A ILE 3.0 6.7 + - - +
484A PRO* 1.3 79.1 - - + +
486A VAL* 1.3 61.1 + - - +
488A ALA* 3.8 9.6 - - - +
489A MET* 3.1 26.1 + - + +
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A MET* 4.8 8.3 - - + -
451A LEU* 6.0 0.7 - - + -
466A LEU* 4.4 4.0 - - + -
482A ILE* 3.3 23.5 + - + +
483A ILE* 3.2 13.4 + - + +
484A PRO 2.7 5.1 + - - -
485A LYS* 1.3 72.6 - - - +
487A LEU* 1.3 70.2 + - + +
489A MET* 2.9 26.4 + - - +
501A THR* 3.1 28.7 - - + +
504A CYS* 3.9 38.4 - - + -
505A ILE* 4.4 11.9 - - + -
508A LEU* 5.4 3.8 - - + -
521A MET* 6.4 0.7 - - - -
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Residues in contact with LEU 487 (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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483A ILE* 2.9 23.8 + - + +
484A PRO* 2.7 12.8 + - + +
486A VAL* 1.3 74.0 - - + +
488A ALA* 1.3 55.5 + - - +
490A SER* 2.4 34.7 + - - -
491A GLY 4.2 0.2 + - - -
501A THR* 4.3 2.0 - - + -
505A ILE* 4.0 22.7 - - + -
520A HIS* 2.6 33.7 - - + +
521A MET* 4.5 2.7 - - + -
524A THR* 3.1 38.4 - - + +
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Residues in contact with ALA 488 (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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484A PRO 2.8 14.8 + - - +
485A LYS* 3.8 11.4 - - - +
487A LEU* 1.3 76.6 - - - +
489A MET* 1.3 56.5 + - - +
491A GLY* 3.1 20.6 + - - -
492A ASP 4.2 1.4 + - - -
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Residues in contact with MET 489 (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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448A MET* 4.6 12.1 - - + +
451A LEU* 4.3 15.0 - - + -
452A VAL* 4.1 24.9 - - + -
485A LYS 3.1 18.7 + - - +
486A VAL* 2.9 18.3 + - + +
488A ALA* 1.3 72.1 - - - +
490A SER* 1.3 55.6 + - - +
491A GLY 2.9 10.0 + - - -
492A ASP* 3.4 20.8 + - + +
497A HIS* 4.1 18.5 - - + +
498A ARG* 4.2 5.9 - - - -
500A THR* 4.4 17.5 - - - -
501A THR* 3.4 17.3 + - - +
504A CYS* 5.9 2.0 - - - -
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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