Contacts of the helix formed by residues 551 - 566 (chain B) in PDB entry 2PZI
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 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546B GLU* 2.9 23.1 + - + +
549B THR* 3.4 11.6 - - - +
550B GLY* 1.3 74.9 - - - +
552B TYR* 1.3 60.2 + - - +
553B ASP* 3.8 7.6 + - - +
554B SER* 2.7 35.7 + - - -
555B ALA* 3.1 15.6 + - - +
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Residues in contact with TYR 552 (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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446B ALA* 5.5 1.0 - - - +
547B LEU* 3.6 39.4 + - + -
550B GLY* 3.2 27.6 + - - -
551B ASP* 1.3 69.6 + - - +
553B ASP* 1.3 58.5 + - - +
555B ALA* 3.6 4.2 - - - +
556B THR* 2.8 40.3 + - - +
579B THR* 3.7 12.7 - - + +
582B LEU* 3.6 49.4 + - + +
583B ALA* 3.7 28.5 - - + -
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Residues in contact with ASP 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ASP* 3.3 8.3 - - - +
552B TYR* 1.3 79.8 - - - +
554B SER* 1.3 56.9 + - - +
556B THR* 3.4 5.2 + - - -
557B LYS* 3.0 27.6 + - - +
585B ASN* 5.5 4.3 + - - -
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Residues in contact with SER 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B GLU* 3.1 29.2 + - - -
551B ASP* 2.7 30.1 + - - -
553B ASP* 1.3 75.7 - - - +
555B ALA* 1.3 60.3 + - - +
557B LYS* 3.1 9.1 + - - +
558B HIS* 2.9 40.8 + - - -
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Residues in contact with ALA 555 (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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543B ALA* 3.5 24.5 - - - +
546B GLU* 3.3 11.3 + - + -
547B LEU* 3.9 13.7 - - + +
551B ASP 3.1 13.4 + - - +
552B TYR* 3.6 8.1 - - - +
554B SER* 1.3 75.1 - - - +
556B THR* 1.3 54.8 + - - +
558B HIS 3.3 0.5 + - - -
559B PHE* 2.8 43.6 + - + -
579B THR* 3.9 14.6 - - + -
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Residues in contact with THR 556 (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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552B TYR* 2.8 17.4 + - - +
553B ASP* 3.8 4.5 - - - -
555B ALA* 1.3 70.4 - - - +
557B LYS* 1.3 63.3 + - - +
560B THR* 2.6 37.6 + - - +
576B LEU* 3.7 22.0 + - + +
579B THR* 3.1 24.8 - - - +
580B ALA* 4.9 3.3 + - - +
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Residues in contact with LYS 557 (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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553B ASP 3.0 15.0 + - - +
554B SER* 3.1 13.0 + - - +
556B THR* 1.3 76.6 - - - +
558B HIS* 1.3 76.4 + - + +
560B THR* 3.6 4.9 - - - -
561B GLU* 3.2 48.3 + - + +
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Residues in contact with HIS 558 (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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539B VAL* 3.6 27.1 - - + +
542B ARG* 3.9 32.4 + - - +
543B ALA* 3.7 16.4 - - + -
546B GLU* 2.6 40.5 + - - -
554B SER* 2.9 19.5 + - - +
557B LYS* 1.3 90.6 + - + +
559B PHE* 1.3 65.7 + - - +
560B THR 3.0 1.3 - - - -
561B GLU* 3.2 31.1 + - - +
562B VAL* 3.3 16.9 + - - +
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Residues in contact with PHE 559 (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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453B LEU* 4.4 5.6 - - + -
540B TRP* 3.5 46.4 - + - -
543B ALA* 3.5 31.1 - - + +
544B VAL* 3.6 22.2 - - + -
547B LEU* 4.1 10.8 - - + -
555B ALA* 2.8 27.2 + - + +
556B THR* 4.6 0.4 - - - -
558B HIS* 1.3 71.6 - - - +
560B THR* 1.3 56.5 + - - +
562B VAL* 3.3 7.2 + - - +
563B LEU* 2.9 26.5 + - - +
572B PRO* 4.1 6.0 - - - +
575B ALA* 3.7 22.4 - - + -
576B LEU* 3.7 21.9 - - + +
579B THR* 3.6 25.8 - - - -
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Residues in contact with THR 560 (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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368B ARG* 3.5 25.4 - - - +
556B THR* 2.6 28.4 + - - +
557B LYS* 3.6 6.5 - - - -
558B HIS 3.0 1.0 - - - -
559B PHE* 1.3 74.7 - - - +
561B GLU* 1.3 54.9 + - - +
563B LEU* 3.6 5.7 - - - +
564B ASP* 2.8 43.1 + - - +
576B LEU* 3.4 16.3 - - + +
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Residues in contact with GLU 561 (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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539B VAL* 3.5 25.8 - - + +
557B LYS* 3.2 43.8 + - + +
558B HIS* 3.2 17.0 + - - +
560B THR* 1.3 75.4 - - - +
562B VAL* 1.3 53.7 + - - +
564B ASP* 3.6 7.0 + - - +
565B THR* 2.7 36.4 + - - -
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Residues in contact with VAL 562 (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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415B PHE* 3.9 22.0 - - + -
536B TRP* 3.8 47.1 - - + +
539B VAL* 4.1 6.3 - - + -
540B TRP* 4.0 28.3 - - + +
558B HIS 3.5 13.5 - - - +
559B PHE 3.3 7.3 + - - +
560B THR 3.2 0.6 - - - -
561B GLU* 1.3 75.0 - - + +
563B LEU* 1.3 61.0 + - - +
565B THR* 3.1 6.9 + - - -
566B PHE* 2.8 32.2 + - + +
572B PRO* 4.1 4.5 - - + -
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Residues in contact with LEU 563 (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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368B ARG* 3.6 34.3 - - - +
559B PHE 2.9 17.5 + - - +
560B THR* 3.2 6.5 + - - +
562B VAL* 1.3 77.6 - - - +
564B ASP* 1.3 58.4 + - - +
566B PHE 3.0 6.4 - - - +
567B PRO* 2.9 50.4 - - + +
569B GLU 4.1 3.6 - - - +
572B PRO* 4.0 14.3 - - + +
573B LYS* 3.9 29.6 - - + +
576B LEU* 3.7 20.9 - - + -
591B PHE* 3.7 18.8 - - + -
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Residues in contact with ASP 564 (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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368B ARG* 2.9 39.8 + - - +
371B ARG* 3.6 21.8 + - - +
372B ARG* 3.6 19.7 - - - +
560B THR* 2.8 35.1 + - - +
561B GLU* 4.0 7.6 + - - +
563B LEU* 1.3 73.7 - - - +
565B THR* 1.3 60.8 + - - +
567B PRO* 3.9 7.6 - - - +
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Residues in contact with THR 565 (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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372B ARG* 2.7 53.0 + - - +
382B PHE* 4.2 1.2 - - - -
536B TRP* 5.0 10.6 - - + +
561B GLU 2.7 22.7 + - - -
562B VAL* 3.1 7.2 + - - -
564B ASP* 1.3 78.6 - - - +
566B PHE* 1.3 84.0 + - + +
567B PRO* 3.5 5.9 - - - +
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Residues in contact with PHE 566 (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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372B ARG* 4.8 4.7 - - - -
387B GLU* 4.9 14.8 - - + -
391B GLN* 3.0 33.2 - - + +
414B ILE* 3.8 27.1 - - + -
415B PHE* 4.7 2.7 - + + -
536B TRP* 3.4 56.8 - + - -
562B VAL* 2.8 31.1 + - + +
563B LEU* 3.0 10.3 - - - +
565B THR* 1.3 94.3 - - + +
567B PRO* 1.3 59.1 - - - +
568B GLY 3.0 5.9 + - - -
569B GLU* 3.1 27.2 + - + +
572B PRO* 5.0 0.6 - - + +
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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