Contacts of the helix formed by residues 570 - 584 (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 LEU 570 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398B GLU* 3.3 24.5 - - - +
569B GLU* 1.3 73.5 - - - +
571B ALA* 1.3 67.6 + - - +
573B LYS* 2.9 10.4 + - + +
574B LEU* 2.9 22.3 + - - +
594B THR 4.4 0.9 - - - +
595B VAL* 3.9 39.7 - - + +
598B THR* 4.1 20.6 - - + -
599B ASN* 3.8 33.0 - - + +
602B VAL* 4.8 3.6 - - + -
753B GOL 2.7 27.4 + - - +
754B GOL 4.2 11.7 - - - +
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Residues in contact with ALA 571 (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* 3.6 33.9 - - + -
453B LEU* 5.1 2.2 - - + +
454B SER* 3.7 26.0 - - - +
540B TRP* 4.0 7.2 - - + -
569B GLU* 3.5 0.6 + - - +
570B LEU* 1.3 75.7 - - - +
572B PRO* 1.4 70.8 - - + +
574B LEU* 3.0 10.0 + - - +
575B ALA* 3.0 22.2 + - - +
753B GOL 4.6 0.6 + - - -
754B GOL 4.5 5.9 + - - +
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Residues in contact with PRO 572 (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* 3.7 23.3 - - + -
540B TRP* 3.7 17.9 - - + -
559B PHE* 4.1 9.0 - - + +
562B VAL* 4.1 9.4 - - + +
563B LEU* 4.0 28.3 - - + +
566B PHE 5.0 0.7 - - - +
569B GLU* 3.7 21.8 - - + +
570B LEU 3.6 3.4 - - - -
571B ALA* 1.4 94.4 - - + +
573B LYS* 1.3 56.2 + - - +
575B ALA* 3.6 1.8 + - + +
576B LEU* 2.9 35.4 + - - +
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Residues in contact with LYS 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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364B ASP* 5.4 2.9 - - - -
365B SER* 4.1 7.4 - - - +
368B ARG* 5.9 0.2 - - - +
398B GLU* 2.7 38.5 + - - +
563B LEU* 3.9 15.1 - - + +
567B PRO 2.8 27.5 + - - -
569B GLU 2.9 23.0 + - - +
570B LEU* 2.9 11.9 + - + +
572B PRO* 1.3 73.8 - - - +
574B LEU* 1.3 61.1 + - - +
576B LEU* 3.1 3.4 + - - -
577B ALA 2.8 25.5 + - - -
591B PHE* 3.4 43.0 - - + +
594B THR* 4.0 18.2 - - + -
595B VAL* 3.7 10.8 - - + -
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Residues in contact with LEU 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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418B SER* 4.3 11.7 - - - +
422B PHE* 3.9 27.1 - - + -
452B ALA 6.0 1.6 - - - +
453B LEU* 5.1 8.7 - - + -
454B SER 6.3 0.2 - - - +
570B LEU 2.9 11.8 + - - +
571B ALA* 3.0 10.3 + - - +
573B LYS* 1.3 77.4 - - - +
575B ALA* 1.3 57.2 + - - +
577B ALA* 3.2 5.9 + - - +
578B ALA* 2.9 27.8 + - - +
592B TYR* 3.8 28.3 - - + -
595B VAL* 3.9 11.3 - - + +
602B VAL* 3.7 23.3 - - + -
604B SER* 4.5 4.3 - - - -
605B ALA* 4.1 19.1 - - + +
754B GOL 5.7 2.0 - - - +
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Residues in contact with ALA 575 (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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449B ILE* 5.6 0.7 - - - -
453B LEU* 3.8 21.9 - - + +
540B TRP* 4.0 3.4 - - + -
547B LEU* 5.3 0.7 - - + +
559B PHE* 3.7 37.6 - - + -
571B ALA 3.0 15.3 + - - +
572B PRO 3.8 4.5 - - - +
574B LEU* 1.3 76.0 - - - +
576B LEU* 1.3 53.1 + - - +
578B ALA* 3.4 5.7 + - - +
579B THR* 2.7 37.6 + - - -
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Residues in contact with LEU 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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556B THR* 3.7 30.5 + - + +
559B PHE* 3.7 26.0 - - + +
560B THR* 3.4 27.8 - - + +
563B LEU* 3.7 28.9 - - + -
572B PRO 2.9 25.9 + - - +
573B LYS 3.1 4.5 + - - +
575B ALA* 1.3 75.2 - - - +
577B ALA* 1.3 64.0 + - - +
579B THR* 3.5 4.4 + - - -
580B ALA* 3.1 23.7 + - - +
587B ASP* 5.3 0.3 - - - +
591B PHE* 3.7 26.3 - - + -
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Residues in contact with ALA 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 LYS 2.8 12.9 + - - +
574B LEU* 3.6 5.6 - - - +
576B LEU* 1.3 77.3 - - - +
578B ALA* 1.3 60.4 + - - +
580B ALA* 3.6 4.3 + - - +
581B GLU* 3.2 16.6 + - - +
587B ASP* 4.5 9.3 - - + +
591B PHE* 3.9 6.2 - - + -
592B TYR* 3.5 63.8 - - + +
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Residues in contact with ALA 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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422B PHE* 4.0 14.4 - - + -
444B LEU* 4.9 0.2 - - - -
449B ILE* 3.8 38.8 - - + +
547B LEU* 5.4 0.9 - - + -
574B LEU 2.9 15.4 + - - +
575B ALA* 3.7 5.8 - - - +
576B LEU 3.3 0.4 - - - -
577B ALA* 1.3 74.8 - - - +
579B THR* 1.3 59.0 + - - +
581B GLU* 3.2 4.5 + - - +
582B LEU* 2.9 34.1 + - - +
592B TYR* 3.5 10.2 + - - +
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Residues in contact with THR 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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547B LEU* 3.1 33.1 - - + +
552B TYR* 3.7 23.9 - - + +
555B ALA* 3.9 6.1 - - + -
556B THR* 3.1 26.0 - - - +
559B PHE* 3.6 10.4 - - - -
575B ALA 2.7 21.6 + - - -
576B LEU* 3.8 7.0 - - - -
577B ALA 3.4 0.2 - - - -
578B ALA* 1.3 76.3 - - - +
580B ALA* 1.3 56.7 + - - +
582B LEU* 3.4 5.0 + - - +
583B ALA* 2.8 30.8 + - + +
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Residues in contact with ALA 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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556B THR* 4.9 2.6 + - - +
576B LEU 3.1 17.2 + - - +
577B ALA 3.8 4.5 - - - +
578B ALA 3.4 0.2 - - - -
579B THR* 1.3 75.0 - - - +
581B GLU* 1.3 61.6 + - - +
583B ALA* 3.4 6.3 + - - +
584B GLY 3.0 2.8 + - - -
585B ASN* 2.8 49.8 + - + +
586B THR 5.0 0.2 - - - -
587B ASP* 4.2 21.5 - - + -
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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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426B LEU* 4.8 0.3 - - - +
444B LEU* 3.5 19.6 - - + +
577B ALA 3.2 9.2 + - - +
578B ALA 3.2 10.2 + - - +
580B ALA* 1.3 72.5 - - - +
582B LEU* 1.3 57.6 + - - +
584B GLY* 2.6 28.3 + - - -
585B ASN 4.8 2.0 - - - -
592B TYR* 2.7 37.3 + - + +
608B GLY* 5.0 2.5 - - - +
611B ARG* 2.7 46.0 + - - +
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Residues in contact with LEU 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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444B LEU* 3.1 39.7 - - + +
446B ALA* 3.9 24.2 - - + +
449B ILE* 3.7 24.5 - - + -
547B LEU* 4.2 11.4 - - + -
552B TYR* 3.6 43.0 + - + +
578B ALA 2.9 19.0 + - - +
579B THR 3.6 5.4 - - - +
581B GLU* 1.3 76.8 - - - +
583B ALA* 1.3 59.9 + - - +
584B GLY* 3.4 0.5 + - - -
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Residues in contact with ALA 583 (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* 3.7 28.0 - - + -
579B THR* 2.8 19.2 + - + +
580B ALA* 3.6 5.6 - - - +
581B GLU 3.0 0.2 - - - -
582B LEU* 1.3 75.7 - - - +
584B GLY* 1.3 60.5 + - - +
585B ASN* 3.3 29.1 + - - +
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Residues in contact with GLY 584 (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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580B ALA 3.7 0.2 - - - -
581B GLU* 2.6 24.5 + - - -
582B LEU 3.2 0.6 + - - -
583B ALA* 1.3 73.1 - - - +
585B ASN* 1.3 62.8 + - - +
586B THR 4.3 0.3 + - - -
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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