Contacts of the helix formed by residues 463 - 472 (chain B) in PDB entry 2PZG
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 463 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ATP 3.1 25.2 + - - -
440B VAL 4.3 4.3 - - - -
441B LEU* 3.6 12.0 - - - +
461B GLY 3.2 3.4 - - - -
462B ALA* 1.3 79.5 - - - +
464B LYS* 1.3 59.8 + - - +
466B SER* 3.3 5.2 + - - -
467B LEU* 2.9 29.6 + - - +
619B LEU* 3.6 6.7 - - - -
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Residues in contact with LYS 464 (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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2B ATP 2.7 51.3 + - - +
456B VAL* 3.9 16.8 - - + +
457B ALA* 3.5 31.6 - - - +
458B GLY 2.9 20.6 + - - +
459B SER 3.2 6.9 + - - -
462B ALA* 4.6 3.6 - - + -
463B GLY* 1.3 75.0 - - - +
465B THR* 1.3 66.5 + - - +
467B LEU* 3.3 13.2 + - - +
468B LEU* 3.3 16.8 + - - +
573B SER* 5.5 0.9 - - - -
603B VAL* 3.6 38.2 - - + +
604B THR 5.7 2.0 - - - -
619B LEU* 3.9 13.5 - - + -
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Residues in contact with THR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ATP 3.0 18.9 + - - +
4B MG 2.1 31.1 - - - -
464B LYS* 1.3 75.4 - - - +
466B SER* 1.3 63.4 + - - +
468B LEU* 3.0 8.5 + - + +
469B MET* 2.9 46.0 + - + +
490B PHE* 5.4 1.1 - - + -
493B GLN* 2.9 3.3 + - - +
572B ASP* 2.6 28.0 + - - +
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ATP 2.6 30.1 + - - -
401B TRP* 2.9 27.4 + - - -
440B VAL* 3.4 22.1 - - - +
441B LEU* 4.0 4.9 - - - -
463B GLY 3.6 5.8 - - - -
464B LYS 3.3 0.2 - - - -
465B THR* 1.3 76.0 - - - +
467B LEU* 1.3 62.5 + - - +
469B MET* 3.1 12.7 + - - +
470B MET* 3.0 24.9 + - - +
475B LEU* 3.9 7.8 - - - +
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Residues in contact with LEU 467 (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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394B MET* 3.6 34.0 - - + +
441B LEU* 3.6 21.9 - - + +
444B ILE* 4.0 16.2 - - + -
446B PHE* 4.1 9.2 - - + -
456B VAL* 3.9 27.6 - - + -
463B GLY 2.9 14.4 + - - +
464B LYS* 3.3 9.9 - - - +
465B THR 3.2 0.4 - - - -
466B SER* 1.3 75.5 - - - +
468B LEU* 1.3 68.4 + - + +
470B MET* 3.2 12.7 + - - +
471B ILE* 3.2 21.3 + - + +
601B ILE* 5.4 1.1 - - + -
617B LEU* 3.9 22.4 - - + -
619B LEU* 4.6 1.8 - - + -
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Residues in contact with LEU 468 (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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464B LYS 3.3 11.9 + - - +
465B THR* 3.0 8.5 + - + +
467B LEU* 1.3 81.8 - - + +
469B MET* 1.3 56.9 + - - +
471B ILE* 3.1 12.3 + - + +
472B MET* 3.0 43.5 + - + +
490B PHE* 4.1 10.8 - - + -
570B LEU* 4.0 24.6 - - + +
571B LEU 4.6 1.3 - - - -
572B ASP* 3.6 42.6 - - + +
601B ILE* 3.9 28.3 - - + -
603B VAL* 3.9 13.0 - - + -
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Residues in contact with MET 469 (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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401B TRP* 4.1 29.8 - - + -
465B THR* 2.9 37.5 + - + +
466B SER 3.1 9.4 + - - +
468B LEU* 1.3 74.3 - - + +
470B MET* 1.3 59.3 + - - +
472B MET* 3.3 25.4 + - + -
473B GLY 3.0 7.4 + - - -
474B GLU* 2.9 49.8 + - + +
475B LEU* 3.9 3.1 - - + -
490B PHE* 4.0 16.4 - - + -
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Residues in contact with MET 470 (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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394B MET* 4.1 11.4 - - + -
397B VAL* 3.7 16.4 - - + -
399B ALA* 3.6 20.9 - - + -
441B LEU* 3.7 17.0 - - + -
466B SER 3.0 19.8 + - - +
467B LEU 3.2 7.1 + - - +
469B MET* 1.3 73.2 - - - +
471B ILE* 1.3 67.2 + - - +
473B GLY* 3.1 13.0 + - - -
475B LEU* 3.3 30.1 - - + +
477B PRO* 3.4 47.1 - - + -
482B ILE* 3.6 22.8 - - + +
484B HIS* 5.1 0.3 + - - -
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Residues in contact with ILE 471 (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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392B VAL* 4.4 7.2 - - + -
394B MET* 3.7 14.1 - - + -
446B PHE* 4.2 13.7 - - + -
467B LEU* 3.4 17.5 - - + +
468B LEU* 3.1 16.2 + - + +
470B MET* 1.3 75.8 - - - +
472B MET* 1.3 60.3 + - - +
473B GLY 3.5 0.5 + - - -
482B ILE* 4.7 4.9 - - + -
484B HIS* 3.0 46.5 + - + +
488B ILE* 3.8 3.5 - - + +
568B LEU* 3.8 26.2 - - + -
570B LEU* 4.1 15.5 - - + -
601B ILE* 3.5 30.5 - - + -
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Residues in contact with MET 472 (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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468B LEU* 3.0 23.6 + - + +
469B MET* 3.9 28.0 - - + +
470B MET 3.1 0.4 - - - -
471B ILE* 1.3 77.7 - - - +
473B GLY* 1.3 58.6 + - - +
474B GLU* 3.3 16.4 + - + +
488B ILE* 4.2 18.2 - - + -
490B PHE* 3.6 59.0 - - + -
570B LEU* 3.6 15.3 - - + -
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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