Contacts of the helix formed by residues 551 - 566 (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 ASP 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A GLU* 3.0 21.3 + - + +
549A THR* 3.3 21.5 - - + +
550A GLY* 1.3 73.3 - - - +
552A TYR* 1.3 61.5 + - - +
553A ASP* 3.7 6.9 + - - +
554A SER* 2.6 35.6 + - - -
555A ALA* 3.3 13.5 + - - +
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Residues in contact with TYR 552 (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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446A ALA* 5.2 2.1 - - - +
546A GLU 4.5 0.7 - - - -
547A LEU* 3.6 37.9 + - + -
550A GLY* 3.2 31.0 + - - -
551A ASP* 1.3 71.7 - - - +
553A ASP* 1.3 68.3 + - - +
555A ALA* 3.5 4.5 - - - +
556A THR* 3.0 29.8 + - - -
579A THR* 3.7 7.3 - - + +
582A LEU* 3.6 45.6 + - + +
583A ALA* 3.7 34.3 - - + -
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Residues in contact with ASP 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ASP* 3.3 7.2 + - - +
552A TYR* 1.3 79.6 - - - +
554A SER* 1.3 57.7 + - - +
556A THR* 3.5 6.3 + - - +
557A LYS* 3.0 27.1 + - - +
585A ASN* 5.4 5.9 + - - -
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Residues in contact with SER 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLU* 3.3 23.6 - - - -
551A ASP* 2.6 32.3 + - - -
552A TYR 3.3 0.4 - - - -
553A ASP* 1.3 75.7 - - - +
555A ALA* 1.3 56.6 - - - +
557A LYS* 3.3 10.2 + - - +
558A HIS* 2.8 46.4 + - - -
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Residues in contact with ALA 555 (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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543A ALA* 3.6 24.1 - - - +
546A GLU* 3.4 11.3 + - + -
547A LEU* 4.2 11.9 - - + +
551A ASP 3.3 12.4 + - - +
552A TYR* 3.5 10.1 - - - +
554A SER* 1.3 75.2 - - - +
556A THR* 1.3 59.9 + - - +
558A HIS 3.3 0.7 + - - -
559A PHE* 2.8 39.9 + - + -
579A THR* 4.0 13.7 - - + -
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Residues in contact with THR 556 (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* 3.0 18.1 + - - +
553A ASP* 3.6 6.5 - - - +
555A ALA* 1.3 75.0 - - - +
557A LYS* 1.3 61.1 + - - +
560A THR* 2.8 40.6 + - - +
576A LEU* 3.5 16.0 + - + +
579A THR* 3.4 17.5 - - - +
580A ALA* 5.0 2.6 + - - -
585A ASN* 5.8 1.4 + - - -
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Residues in contact with LYS 557 (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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553A ASP 3.0 15.7 + - - +
554A SER* 3.3 11.2 + - - +
556A THR* 1.3 76.0 - - - +
558A HIS* 1.3 76.6 + - + +
560A THR* 3.5 6.1 + - - -
561A GLU* 3.2 43.9 + - + +
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Residues in contact with HIS 558 (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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539A VAL* 3.4 24.3 - - + +
542A ARG* 3.6 34.0 + - - -
543A ALA* 3.7 16.8 - - + -
546A GLU* 2.6 38.7 + - - -
554A SER* 2.8 25.6 + - - +
557A LYS* 1.3 87.1 + - + +
559A PHE* 1.3 64.5 + - - +
560A THR 3.2 1.3 - - - -
561A GLU* 3.4 24.8 + - - +
562A VAL* 3.3 25.2 + - - +
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Residues in contact with PHE 559 (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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453A LEU* 4.5 2.7 - - + -
540A TRP* 3.5 47.3 - + - -
543A ALA* 3.5 30.7 - - + +
544A VAL* 3.8 20.0 - - + -
547A LEU* 4.0 15.0 - - + -
555A ALA* 2.8 27.4 + - + +
558A HIS* 1.3 72.3 - - - +
560A THR* 1.3 57.2 + - - +
562A VAL* 3.1 7.2 + - - +
563A LEU* 2.8 27.4 + - - +
572A PRO* 4.2 5.5 - - - +
575A ALA* 3.7 24.9 - - + -
576A LEU* 3.4 21.5 - - + -
579A THR* 3.7 23.6 - - - -
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Residues in contact with THR 560 (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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368A ARG* 3.8 17.5 - - - +
556A THR* 2.8 28.8 + - - +
557A LYS* 3.6 6.5 - - - -
558A HIS 3.2 0.2 - - - -
559A PHE* 1.3 72.5 - - - +
561A GLU* 1.3 55.9 + - - +
563A LEU* 3.0 7.7 + - - +
564A ASP* 2.7 49.0 + - - +
576A LEU* 3.5 15.9 - - + +
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Residues in contact with GLU 561 (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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539A VAL* 3.8 27.9 - - + +
557A LYS* 3.2 32.6 + - + +
558A HIS* 3.4 24.9 - - - +
560A THR* 1.3 75.6 - - - +
562A VAL* 1.3 55.2 + - - +
564A ASP* 3.6 7.0 + - - +
565A THR* 2.8 33.3 + - - -
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Residues in contact with VAL 562 (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* 3.8 18.4 - - + -
536A TRP* 3.9 38.8 - - + +
539A VAL* 4.1 6.5 - - + -
540A TRP* 3.8 39.9 - - + +
558A HIS 3.4 14.6 - - - +
559A PHE 3.1 7.0 + - - +
561A GLU* 1.3 74.7 - - - +
563A LEU* 1.3 66.4 + - - +
565A THR* 3.1 8.2 + - - -
566A PHE* 2.9 26.5 + - + +
572A PRO* 4.3 3.1 - - + -
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Residues in contact with LEU 563 (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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364A ASP* 4.9 0.4 - - - +
368A ARG* 3.7 28.5 - - - +
559A PHE 2.8 13.8 + - - +
560A THR* 3.4 9.2 - - - +
562A VAL* 1.3 76.9 - - - +
564A ASP* 1.3 57.1 + - - +
566A PHE 2.9 13.9 + - - +
567A PRO* 2.9 38.7 - - + +
569A GLU 4.1 0.9 - - - +
572A PRO* 3.9 17.7 - - + +
573A LYS* 3.8 31.9 - - + +
576A LEU* 3.6 23.6 - - + -
591A PHE* 3.7 25.1 - - + -
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Residues in contact with ASP 564 (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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368A ARG* 2.6 50.7 + - - +
371A ARG* 4.6 6.8 + - - -
372A ARG* 3.6 21.7 - - - +
560A THR* 2.7 32.2 + - - +
561A GLU* 3.9 6.6 - - - +
562A VAL 3.2 0.2 - - - -
563A LEU* 1.3 71.7 - - - +
565A THR* 1.3 59.2 + - - +
567A PRO* 4.0 6.7 - - - +
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Residues in contact with THR 565 (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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372A ARG* 2.9 54.0 + - - +
382A PHE* 4.1 2.8 - - - -
536A TRP* 5.0 12.8 - - + +
561A GLU 2.8 18.4 + - - -
562A VAL* 3.1 11.6 + - - -
564A ASP* 1.3 79.7 - - - +
566A PHE* 1.3 84.9 + - + +
567A PRO* 3.5 4.3 - - - +
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Residues in contact with PHE 566 (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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372A ARG* 4.4 6.5 - - - -
387A GLU* 4.8 11.0 - - + -
391A GLN* 3.2 27.1 - - + +
414A ILE* 4.0 26.7 - - + -
415A PHE* 4.7 2.0 - + + -
536A TRP* 3.4 54.5 - + - -
562A VAL* 2.9 25.7 + - + +
563A LEU* 2.9 11.9 - - - +
565A THR* 1.3 103.9 - - + +
567A PRO* 1.3 57.8 - - - +
568A GLY 3.1 5.8 - - - -
569A GLU* 3.1 32.2 + - + +
572A PRO* 4.7 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