Contacts of the helix formed by residues 435 - 443 (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 GLY 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A ALA 3.0 10.5 + - - +
432A GLY 3.2 10.1 + - - -
433A GLN 3.2 0.8 - - - -
434A LEU* 1.3 80.2 - - - +
436A VAL* 1.3 62.4 + - - -
437A GLU* 2.7 23.7 - - - +
438A PHE 3.2 0.2 + - - -
439A PHE* 3.2 18.2 + - - +
473A PHE* 4.3 1.6 - - - -
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Residues in contact with VAL 436 (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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435A GLY* 1.3 71.2 - - - -
437A GLU* 1.3 83.5 + - + +
439A PHE* 3.0 3.3 + - - +
440A ASP* 2.9 28.4 + - - +
473A PHE* 3.6 37.5 - - + +
477A TRP* 3.5 36.6 - - + +
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Residues in contact with GLU 437 (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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434A LEU 3.4 2.5 - - - +
435A GLY* 2.7 24.5 - - - +
436A VAL* 1.3 94.4 + - + +
438A PHE* 1.3 86.7 + - + +
440A ASP* 3.2 21.8 - - - +
441A GLU* 3.6 5.2 + - - +
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Residues in contact with PHE 438 (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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401A SER* 4.5 11.7 - - - -
405A LEU* 4.8 17.0 - - + -
434A LEU* 3.6 43.1 - - + +
435A GLY 3.5 4.7 - - - +
437A GLU* 1.3 95.4 + - + +
439A PHE* 1.3 71.8 + - - +
441A GLU* 2.8 31.6 + - + +
442A LYS* 3.8 9.3 + - + -
443A LEU* 4.8 13.2 - - + -
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Residues in contact with PHE 439 (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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427A MET* 4.5 3.1 - - + -
431A ALA* 3.4 22.2 - - + -
434A LEU* 5.3 0.4 - - - +
435A GLY 3.2 8.9 + - - +
436A VAL 3.0 9.4 + - - +
438A PHE* 1.3 78.0 - - - +
440A ASP* 1.3 60.4 + - - +
441A GLU 2.6 13.7 + - - -
443A LEU* 3.0 50.5 + - + +
444A ASN* 3.2 25.9 + - + -
447A CYS* 3.3 35.7 - - + -
469A LEU* 3.3 26.2 - - + -
473A PHE* 4.0 10.1 - + + -
477A TRP* 3.4 33.0 - + - -
482A ILE* 5.3 1.3 - - + -
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Residues in contact with ASP 440 (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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436A VAL* 2.9 19.7 + - - +
437A GLU* 3.2 15.5 - - - +
439A PHE* 1.3 81.9 - - - +
441A GLU* 1.3 64.6 + - - +
444A ASN* 4.0 13.5 - - - +
477A TRP* 2.8 35.2 + - - -
481A THR* 4.3 12.6 + - - +
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Residues in contact with GLU 441 (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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437A GLU 3.6 4.8 + - - +
438A PHE* 2.8 25.4 + - + +
439A PHE 2.6 6.5 + - - -
440A ASP* 1.3 82.6 - - - +
442A LYS* 1.3 76.3 + - + +
443A LEU 3.6 2.1 + - - -
444A ASN* 4.4 4.0 + - - +
445A SER* 4.8 4.3 + - - -
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Residues in contact with LYS 442 (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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405A LEU* 5.8 0.2 - - - +
409A VAL* 5.2 5.0 - - - +
438A PHE* 3.8 8.3 + - + -
439A PHE 3.5 0.4 + - - -
441A GLU* 1.3 94.2 - - + +
443A LEU* 1.3 70.2 + - + +
445A SER* 4.1 23.7 + - - +
446A LEU* 4.6 9.2 - - - +
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Residues in contact with LEU 443 (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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405A LEU* 4.3 27.4 - - + -
408A ILE* 6.6 0.4 - - + -
409A VAL* 4.9 1.1 - - + -
427A MET* 3.6 31.0 - - + -
430A LEU* 4.9 0.4 - - + -
431A ALA* 4.5 3.8 - - - -
434A LEU* 4.0 21.5 - - + -
438A PHE* 4.8 8.1 - - + +
439A PHE* 3.0 45.4 + - + +
442A LYS* 1.3 88.2 - - + +
444A ASN* 1.3 72.9 + - - +
445A SER 3.4 1.1 - - - -
446A LEU* 3.0 30.2 + - + +
447A CYS* 3.1 9.5 + - - -
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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