Contacts of the helix formed by residues 535 - 550 (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 ARG 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A VAL* 3.9 24.3 - - - +
532A VAL* 3.6 51.7 + - + +
533A GLY 3.0 5.2 + - - +
534A TRP* 1.3 77.9 - - - +
536A TRP* 1.3 68.8 + - + +
537A ARG* 3.3 3.6 - - + +
538A LEU* 3.0 23.3 + - + +
539A VAL* 3.2 7.3 + - - +
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Residues in contact with TRP 536 (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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414A ILE* 3.7 24.9 - - + -
415A PHE* 4.0 17.5 - + - -
456A PRO* 3.5 37.9 - - + -
534A TRP 3.9 0.4 + - - -
535A ARG* 1.3 76.3 - - + +
537A ARG* 1.3 93.2 + - + +
539A VAL* 3.2 11.2 + - - +
540A TRP* 2.8 27.4 + - + +
562A VAL* 3.9 17.7 - - + +
565A THR* 5.0 12.6 - - + +
566A PHE* 3.4 40.2 - + + -
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Residues in contact with ARG 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PRO* 3.7 25.8 - - + +
457A LEU 2.9 27.3 + - - -
459A ASP* 3.7 19.8 + - - +
503A GLU* 3.0 23.6 + - - -
506A LEU* 3.6 31.2 - - + -
535A ARG* 3.2 3.6 + - + +
536A TRP* 1.3 116.7 - - + +
538A LEU* 1.3 60.6 + - + +
540A TRP* 3.3 4.6 + - - +
541A TYR* 3.0 36.8 + - + -
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 4.4 11.0 - - + -
506A LEU* 3.8 18.4 - - + -
525A LEU* 3.9 25.9 - - + +
528A LEU* 4.0 16.2 - - + -
529A ALA* 3.5 33.4 - - + +
532A VAL* 4.4 2.7 - - + -
533A GLY 3.3 20.6 - - - +
534A TRP* 3.5 18.2 - - + -
535A ARG* 3.0 26.7 + - + +
537A ARG* 1.3 79.4 - - + +
539A VAL* 1.3 56.6 + - - +
541A TYR 3.5 1.0 + - - -
542A ARG* 2.9 29.1 + - - +
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A TRP* 3.8 27.6 - - + +
535A ARG 3.5 12.3 - - - +
536A TRP* 3.2 12.9 + - - +
538A LEU* 1.3 71.9 - - - +
540A TRP* 1.3 65.8 + - - +
542A ARG* 3.5 7.8 - - - +
543A ALA* 3.0 23.2 + - - +
558A HIS* 3.4 41.6 - - + +
561A GLU* 3.8 25.4 - - + +
562A VAL* 4.1 5.6 - - + -
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Residues in contact with TRP 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE* 3.8 22.7 - + - -
453A LEU* 4.7 10.7 - - + +
454A SER 3.7 25.3 + - - -
455A VAL* 5.4 0.6 - - - +
456A PRO* 3.8 27.1 - - + +
536A TRP* 2.8 16.7 + - + +
537A ARG* 3.4 12.1 - - - +
538A LEU 3.3 0.2 - - - -
539A VAL* 1.3 75.6 - - - +
541A TYR* 1.3 73.3 + + - +
543A ALA* 3.1 8.9 + - - +
544A VAL* 3.0 37.7 + - + +
559A PHE* 3.5 38.0 - + - -
562A VAL* 3.8 24.2 - - + +
571A ALA* 3.9 24.9 - - + -
572A PRO* 3.8 19.1 - - + -
575A ALA* 3.9 6.5 - - + -
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Residues in contact with TYR 541 (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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455A VAL* 4.8 4.3 - - + -
456A PRO* 3.4 29.8 + - + +
506A LEU* 3.7 40.2 + - + -
509A VAL* 3.8 19.7 - - + -
510A ARG* 3.0 53.8 + - + +
513A LEU* 3.6 21.4 - - + +
525A LEU* 4.0 8.4 - - + +
537A ARG* 3.0 26.1 + - + +
538A LEU 4.1 2.2 - - - +
540A TRP* 1.3 91.2 - + - +
542A ARG* 1.3 56.3 + - - +
544A VAL* 3.8 7.6 - - + -
545A ALA* 3.1 26.5 + - - +
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Residues in contact with ARG 542 (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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522A THR* 5.9 3.6 - - + -
525A LEU* 3.7 13.0 - - + +
526A ASP* 5.2 2.6 + - - -
534A TRP* 3.8 48.8 - - + +
538A LEU 2.9 18.8 + - - +
539A VAL* 3.5 7.5 - - - +
541A TYR* 1.3 74.5 - - - +
543A ALA* 1.3 60.1 + - - +
545A ALA* 3.0 7.4 + - + +
546A GLU* 2.9 48.8 + - + +
558A HIS* 3.6 34.4 + - - -
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Residues in contact with ALA 543 (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 3.0 13.2 + - - +
540A TRP 3.3 9.2 - - - +
542A ARG* 1.3 75.5 - - - +
544A VAL* 1.3 62.2 + - - +
546A GLU* 3.4 15.1 + - - +
547A LEU* 3.0 19.9 + - - +
555A ALA* 3.6 12.4 - - - +
558A HIS* 3.7 14.6 - - + +
559A PHE* 3.5 34.5 - - + +
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Residues in contact with VAL 544 (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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450A VAL* 3.8 30.5 - - + +
453A LEU* 4.2 12.3 - - + -
513A LEU* 3.8 21.8 - - + -
540A TRP* 3.0 35.0 + - + +
541A TYR* 3.6 11.9 - - + +
542A ARG 3.2 0.2 - - - -
543A ALA* 1.3 75.8 - - - +
545A ALA* 1.3 62.6 + - - +
547A LEU* 3.1 20.2 - - - +
548A LEU* 3.3 8.8 + - - +
559A PHE* 3.9 17.5 - - + -
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Residues in contact with ALA 545 (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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513A LEU* 3.8 22.4 - - + -
518A VAL* 3.6 7.7 - - + +
521A ALA* 5.6 0.7 - - + -
522A THR* 3.7 29.2 - - + -
525A LEU* 5.4 0.7 - - + -
541A TYR 3.1 13.5 + - - +
542A ARG* 3.0 10.9 + - - +
544A VAL* 1.3 73.5 - - - +
546A GLU* 1.3 62.2 + - + +
548A LEU* 3.1 7.3 + - - +
549A THR* 2.9 29.1 + - - -
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Residues in contact with GLU 546 (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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522A THR* 6.5 0.2 - - + -
542A ARG* 2.9 33.1 + - + +
543A ALA* 3.6 8.0 - - - +
544A VAL 3.3 0.2 - - - -
545A ALA* 1.3 76.5 - - + +
547A LEU* 1.3 56.3 + - - +
549A THR* 3.8 9.6 - - + -
550A GLY 3.1 5.5 + - - -
551A ASP* 3.0 52.9 + - + +
554A SER* 3.3 23.8 - - - -
555A ALA* 3.4 4.3 + - - +
558A HIS* 2.6 40.5 + - - -
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Residues in contact with LEU 547 (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* 3.4 18.3 - - + +
449A ILE* 4.1 28.3 - - + -
450A VAL* 4.7 7.6 - - + -
453A LEU* 4.6 6.7 - - + -
543A ALA 3.0 16.4 + - - +
544A VAL* 3.1 12.1 - - - +
545A ALA 3.2 0.2 - - - -
546A GLU* 1.3 77.4 - - - +
548A LEU* 1.3 63.3 + - - +
550A GLY* 3.2 9.4 + - - -
552A TYR* 3.6 15.9 + - + -
555A ALA* 4.3 1.8 - - + -
559A PHE* 4.0 23.3 - - + -
575A ALA 5.2 1.8 - - - +
579A THR* 3.5 32.8 - - + +
582A LEU* 3.7 25.6 - - + -
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Residues in contact with LEU 548 (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* 4.0 16.8 - - + +
447A ASN* 4.0 17.9 - - + +
450A VAL* 3.7 24.5 - - + -
513A LEU* 3.5 51.6 - - + +
516A GLY* 4.8 9.9 - - - +
518A VAL* 4.3 20.0 - - + +
544A VAL 3.3 8.7 + - - +
545A ALA 3.1 6.5 + - - +
547A LEU* 1.3 77.2 - - - +
549A THR* 1.3 59.9 + - - +
550A GLY* 3.5 0.5 + - - -
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Residues in contact with THR 549 (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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518A VAL* 4.1 16.5 - - - +
545A ALA 2.9 15.5 + - - -
546A GLU* 3.8 8.3 - - + +
548A LEU* 1.3 77.5 - - - +
550A GLY* 1.3 57.4 + - - +
551A ASP* 3.5 27.6 - - + +
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Residues in contact with GLY 550 (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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546A GLU 3.1 4.0 + - - -
547A LEU 3.2 4.2 + - - -
548A LEU 3.2 1.4 + - - -
549A THR* 1.3 79.5 - - - +
551A ASP* 1.3 58.9 + - - +
552A TYR* 3.2 45.2 + - - -
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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
------------------------------------------------------------
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