Contacts of the helix formed by residues 570 - 584 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A GLU* 3.3 33.9 - - + +
568A GLY 4.1 2.0 + - - +
569A GLU* 1.3 75.1 + - - +
571A ALA* 1.3 66.7 + - - +
572A PRO 3.4 0.7 - - - -
573A LYS* 3.1 9.5 + - + +
574A LEU* 3.0 23.1 + - - +
594A THR 4.5 0.7 - - - +
595A VAL* 4.0 38.7 - - + +
598A THR* 4.2 14.1 - - + +
599A ASN* 3.9 33.0 - - + +
602A VAL* 4.9 5.2 - - + -
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Residues in contact with ALA 571 (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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415A PHE* 3.6 33.7 - - + -
453A LEU* 4.8 3.2 - - + +
454A SER* 3.6 27.1 - - - +
540A TRP* 3.9 7.4 - - + -
569A GLU* 4.5 0.6 + - - +
570A LEU* 1.3 74.8 - - - +
572A PRO* 1.4 69.7 - - + +
574A LEU* 3.2 9.3 + - - +
575A ALA* 3.0 21.5 + - - +
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Residues in contact with PRO 572 (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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415A PHE* 3.7 22.7 - - + -
540A TRP* 3.8 17.0 - - + -
559A PHE* 4.2 4.4 - - + +
562A VAL* 4.3 4.7 - - + +
563A LEU* 3.9 35.9 - - + +
566A PHE 4.7 1.1 - - - +
569A GLU* 3.5 26.2 - - + +
571A ALA* 1.4 94.8 - - + +
573A LYS* 1.3 56.1 + - - +
575A ALA* 3.7 2.1 - - + +
576A LEU* 3.1 35.8 + - - +
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Residues in contact with LYS 573 (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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365A SER* 3.9 1.8 - - - -
368A ARG* 6.2 0.2 - - - +
398A GLU* 2.5 39.5 + - - +
563A LEU* 3.8 15.9 - - + +
567A PRO 2.9 21.6 + - - -
569A GLU 2.8 27.2 + - - +
570A LEU* 3.1 9.7 + - + +
572A PRO* 1.3 74.3 - - - +
574A LEU* 1.3 60.3 + - - +
576A LEU* 3.4 2.8 + - - +
577A ALA* 2.9 23.2 + - - +
591A PHE* 3.3 34.1 - - + +
594A THR* 3.8 12.3 - - + -
595A VAL* 3.7 10.8 - - + -
756A GOL 3.3 28.7 - - - +
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Residues in contact with LEU 574 (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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418A SER* 4.6 10.8 - - - +
422A PHE* 3.9 26.7 - - + -
452A ALA 6.0 1.1 - - - +
453A LEU* 4.9 11.4 - - + -
454A SER* 6.2 0.4 - - - +
570A LEU 3.0 11.9 + - - +
571A ALA* 3.6 10.8 - - - +
573A LYS* 1.3 77.6 - - - +
575A ALA* 1.3 56.4 + - - +
577A ALA* 3.2 4.5 + - - +
578A ALA* 3.0 28.8 + - - +
592A TYR* 3.7 32.5 - - + -
595A VAL* 3.9 12.5 - - + +
602A VAL* 3.9 19.1 - - + -
604A SER* 4.5 3.4 - - - -
605A ALA* 4.1 20.0 - - + +
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Residues in contact with ALA 575 (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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449A ILE* 5.7 0.7 - - - -
453A LEU* 4.0 17.1 - - + +
540A TRP* 3.9 7.9 - - + -
547A LEU* 5.2 1.4 - - - +
559A PHE* 3.7 39.1 - - + -
571A ALA 3.0 15.2 + - - +
572A PRO 3.7 5.6 - - - +
574A LEU* 1.3 76.3 - - - +
576A LEU* 1.3 52.4 + - - +
578A ALA* 3.4 5.0 + - - +
579A THR* 2.7 37.3 + - - -
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Residues in contact with LEU 576 (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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556A THR* 3.5 26.0 + - + +
559A PHE* 3.4 24.7 - - + -
560A THR* 3.5 30.5 - - - +
563A LEU* 3.6 30.5 - - + -
572A PRO 3.1 22.3 + - - +
573A LYS* 3.8 0.7 - - - +
575A ALA* 1.3 73.8 - - - +
577A ALA* 1.3 64.8 + - - +
579A THR* 3.8 3.7 - - - +
580A ALA* 3.0 24.4 + - - +
587A ASP* 5.4 0.2 - - - -
591A PHE* 3.7 28.5 - - + -
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Residues in contact with ALA 577 (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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573A LYS 2.9 17.2 + - - +
574A LEU* 3.2 3.6 + - - +
576A LEU* 1.3 76.3 - - - +
578A ALA* 1.3 63.2 + - - +
580A ALA* 3.5 4.6 + - - +
581A GLU* 3.2 21.5 + - - +
587A ASP* 4.2 11.8 - - - +
591A PHE* 3.8 13.6 - - + +
592A TYR* 3.6 47.5 - - + +
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Residues in contact with ALA 578 (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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422A PHE* 3.7 20.9 - - + -
444A LEU* 4.8 0.4 - - - -
449A ILE* 3.7 35.1 - - + +
547A LEU* 5.8 0.4 - - + -
574A LEU 3.0 16.8 + - - +
575A ALA 3.8 4.5 - - - +
577A ALA* 1.3 72.9 - - - +
579A THR* 1.3 65.1 + - - +
581A GLU* 3.4 5.1 + - - +
582A LEU* 3.1 26.3 + - - +
592A TYR* 3.5 10.0 + - - +
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Residues in contact with THR 579 (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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547A LEU* 3.5 30.1 - - + +
552A TYR* 3.7 25.8 - - + +
555A ALA* 4.0 5.4 - - + -
556A THR* 3.4 24.9 - - - +
559A PHE* 3.7 13.3 - - - -
575A ALA 2.7 22.5 + - - -
576A LEU* 3.8 6.7 - - - -
577A ALA 3.3 0.2 - - - -
578A ALA* 1.3 74.1 - - - +
580A ALA* 1.3 66.3 + - - +
582A LEU* 3.0 5.8 + - - +
583A ALA* 2.9 22.0 + - + +
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Residues in contact with ALA 580 (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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556A THR* 5.0 2.8 + - - -
576A LEU 3.0 17.6 + - - +
577A ALA 3.6 4.9 - - - +
578A ALA 3.4 0.2 - - - -
579A THR* 1.3 75.5 - - - +
581A GLU* 1.3 56.6 + - - +
583A ALA* 3.2 7.1 + - - -
584A GLY 3.0 23.7 + - - -
585A ASN* 3.0 33.6 + - + +
587A ASP* 4.1 23.1 - - + -
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Residues in contact with GLU 581 (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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426A LEU* 5.4 0.9 - - - +
444A LEU* 3.4 17.9 - - + +
577A ALA 3.2 12.1 + - - +
578A ALA 3.5 9.4 - - - +
580A ALA* 1.3 75.6 - - - +
582A LEU* 1.3 66.7 + - - +
584A GLY* 3.2 12.1 + - - -
585A ASN 4.4 3.3 + - - +
592A TYR* 2.9 31.3 + - + -
608A GLY 5.1 0.9 - - - -
611A ARG* 2.3 43.8 + - - +
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Residues in contact with LEU 582 (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 LEU* 3.2 35.7 - - + +
445A THR* 4.2 1.3 - - - -
446A ALA* 4.0 22.7 - - + +
449A ILE* 3.8 18.8 - - + -
547A LEU* 3.7 19.5 - - + -
552A TYR* 3.6 44.8 - - + +
578A ALA 3.1 11.8 + - - +
579A THR 3.0 7.4 + - - +
581A GLU* 1.3 79.0 - - - +
583A ALA* 1.3 62.3 + - - +
584A GLY* 3.3 0.9 + - - -
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Residues in contact with ALA 583 (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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552A TYR* 3.7 30.7 - - + -
553A ASP* 5.9 1.1 - - - +
556A THR* 6.1 0.2 - - - +
579A THR* 2.9 16.4 + - + +
580A ALA* 3.6 2.2 - - - +
582A LEU* 1.3 76.2 - - - +
584A GLY* 1.3 60.6 + - - +
585A ASN* 3.3 29.9 + - - +
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Residues in contact with GLY 584 (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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580A ALA 3.0 4.7 + - - -
581A GLU* 3.2 7.7 + - - -
582A LEU 3.2 5.2 + - - -
583A ALA* 1.3 79.0 - - - +
585A ASN* 1.3 63.6 + - - +
586A THR 4.2 0.2 + - - -
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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