Contacts of the helix formed by residues 534 - 551 (chain A) in PDB entry 1Z6T
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 534 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A HIS* 5.6 3.2 + - - +
532A ILE 4.1 0.8 + - - -
533A LEU* 1.3 77.5 - - - +
535A GLU* 1.3 65.1 + - - +
536A LYS* 3.3 31.3 + - - +
537A ASP* 2.9 37.8 + - - +
538A CYS* 2.9 27.4 + - - +
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Residues in contact with GLU 535 (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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534A ASP* 1.3 82.7 - - - +
536A LYS* 1.3 74.1 + - + +
538A CYS* 3.5 7.3 - - - +
539A ALA* 3.2 20.8 + - - +
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Residues in contact with LYS 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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534A ASP* 3.6 32.8 + - - +
535A GLU* 1.3 88.6 + - + +
537A ASP* 1.3 65.9 + - - +
539A ALA* 3.4 8.6 + - - +
540A VAL* 3.3 22.9 + - - +
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Residues in contact with ASP 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A HIS* 5.1 4.5 - - - +
498A LYS* 6.0 0.5 - - - -
501A CYS* 3.6 32.4 - - - +
505A PHE* 3.2 20.3 - - + -
533A LEU* 4.1 13.2 - - + +
534A ASP* 2.9 25.3 + - - +
536A LYS* 1.3 79.4 - - - +
538A CYS* 1.3 56.2 - - - +
540A VAL* 3.3 3.9 + - - +
541A SER* 2.8 31.9 + - - -
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Residues in contact with CYS 538 (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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530A ARG* 3.5 30.1 - - + -
533A LEU* 4.0 11.3 - - + +
534A ASP 2.9 21.1 + - - +
535A GLU* 3.5 8.7 - - - +
536A LYS 3.3 0.2 - - - -
537A ASP* 1.3 76.7 - - - +
539A ALA* 1.3 60.5 + - - +
541A SER* 3.2 9.8 - - - -
542A GLU* 3.2 34.9 + - - +
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Residues in contact with ALA 539 (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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535A GLU 3.2 9.6 + - - +
536A LYS* 3.6 11.0 - - - +
537A ASP 3.3 0.2 - - - -
538A CYS* 1.3 76.0 - - - +
540A VAL* 1.3 60.7 + - + +
542A GLU* 2.9 29.8 + - - +
543A ASN* 3.0 18.6 + - - +
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PHE* 3.4 40.6 - - + -
536A LYS 3.3 12.0 + - - +
537A ASP* 3.3 6.1 + - - +
539A ALA* 1.3 73.9 - - + +
541A SER* 1.3 67.4 + - - +
543A ASN* 3.1 19.0 + - - +
544A PHE* 3.1 27.4 + - + -
575A GLU* 4.0 27.6 - - + +
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Residues in contact with SER 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PHE* 3.4 15.1 - - - -
526A PHE* 3.4 24.6 + - - -
530A ARG* 3.3 20.9 + - - +
533A LEU* 4.0 16.4 - - - +
537A ASP 2.8 18.1 + - - -
538A CYS* 3.2 13.0 - - - -
540A VAL* 1.3 73.4 - - - +
542A GLU* 1.3 57.1 + - - +
544A PHE* 3.2 3.6 + - - +
545A GLN* 2.9 27.5 + - - +
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Residues in contact with GLU 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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530A ARG* 3.5 36.9 + - - +
538A CYS* 3.2 19.9 + - - +
539A ALA* 2.9 15.6 + - - +
541A SER* 1.3 76.1 - - - +
543A ASN* 1.3 67.1 + - - +
545A GLN* 3.3 1.4 + - - +
546A GLU* 3.1 33.4 + - - +
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Residues in contact with ASN 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 ALA 3.0 15.2 + - - -
540A VAL* 3.2 14.9 - - + +
542A GLU* 1.3 76.5 - - - +
544A PHE* 1.3 65.2 + - + +
546A GLU* 3.2 19.9 + - - +
547A PHE* 3.1 23.2 + - - +
570A GLU* 4.9 0.3 - - - +
573A THR 4.4 1.4 - - - +
574A SER* 3.2 25.0 + - - +
575A GLU* 3.0 27.7 + - - +
576A VAL* 4.1 8.7 - - + +
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Residues in contact with PHE 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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504A MET 3.9 5.6 - - - -
505A PHE* 3.5 28.3 - + + -
506A SER 3.5 19.3 - - - -
507A LEU* 4.5 7.2 - - + -
510A ILE* 3.4 28.3 - - + -
526A PHE* 3.5 25.4 - + + -
540A VAL* 3.1 34.2 + - + -
541A SER 3.7 1.3 - - - +
543A ASN* 1.3 80.9 - - + +
545A GLN* 1.3 63.6 + - - +
547A PHE* 3.4 3.7 + + - +
548A LEU* 3.1 28.7 + - - +
575A GLU* 4.3 8.7 - - + -
576A VAL* 3.8 28.9 - - + -
579A GLN* 3.8 15.3 - - - -
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Residues in contact with GLN 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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523A ILE* 4.2 20.8 - - + +
526A PHE* 4.1 15.2 - - + -
527A VAL* 3.1 36.1 + - - +
530A ARG* 2.7 43.8 + - - +
541A SER 2.9 8.4 + - - +
542A GLU* 3.8 3.6 - - - +
543A ASN 3.3 0.2 - - - -
544A PHE* 1.3 77.5 - - - +
546A GLU* 1.3 59.1 + - + +
548A LEU* 3.4 5.2 + - - +
549A SER* 3.0 29.4 + - - -
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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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542A GLU* 3.1 21.0 + - - +
543A ASN* 3.2 23.4 + - - +
545A GLN* 1.3 77.9 - - + +
547A PHE* 1.3 64.3 - - - +
549A SER* 3.0 9.1 + - - +
550A LEU* 2.9 33.9 + - + +
570A GLU* 4.1 13.6 - - - +
571A PRO* 4.6 13.5 - - - +
574A SER* 5.0 2.4 + - - -
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Residues in contact with PHE 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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507A LEU* 4.3 6.1 - - + -
510A ILE* 4.2 35.0 - - + -
543A ASN 3.1 17.5 + - - +
544A PHE 3.5 8.1 - - - +
546A GLU* 1.3 78.5 - - - +
548A LEU* 1.3 64.5 + - + +
550A LEU* 4.6 0.2 - - - -
551A ASN* 3.0 55.1 + - + +
555A LEU* 5.6 3.8 - - + -
563A ILE* 4.1 25.1 - - + -
566A LEU* 3.7 9.4 - - + -
567A GLY* 3.6 24.5 - - - -
570A GLU* 3.6 32.3 - - + -
576A VAL* 3.7 22.2 - - + -
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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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510A ILE* 3.6 38.1 - - + -
514A THR* 4.5 6.7 - - + -
519A PRO* 4.9 2.2 - - + -
522A LEU* 4.2 13.2 - - + -
523A ILE* 3.5 28.5 - - + +
526A PHE* 3.4 39.5 - - + -
544A PHE 3.1 13.9 + - - +
545A GLN* 3.7 3.1 - - - +
546A GLU 3.2 0.2 - - - -
547A PHE* 1.3 81.0 - - + +
549A SER* 1.3 60.1 + - - +
551A ASN 3.6 0.7 - - - -
552A GLY* 2.9 30.3 + - - -
555A LEU* 3.6 20.5 - - + +
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Residues in contact with SER 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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523A ILE* 4.0 14.6 - - - -
545A GLN* 3.0 19.5 + - - -
546A GLU* 3.0 16.7 + - - +
548A LEU* 1.3 76.6 - - - +
550A LEU* 1.3 74.2 + - - +
551A ASN 3.3 0.3 + - - -
552A GLY* 3.3 10.5 + - - -
553A HIS* 5.0 1.6 + - - -
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Residues in contact with LEU 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* 2.9 15.9 + - + +
547A PHE 3.9 3.6 - - - +
549A SER* 1.3 83.2 + - - +
551A ASN* 1.3 87.5 + - - +
553A HIS* 3.3 21.5 + - - +
569A CYS* 5.9 2.9 - - + +
570A GLU* 3.9 19.7 - - - +
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Residues in contact with ASN 551 (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 PHE* 3.0 48.5 + - + +
548A LEU 3.6 1.8 - - - -
549A SER 3.2 0.6 - - - -
550A LEU* 1.3 100.1 - - - +
552A GLY* 1.3 58.3 + - - +
553A HIS* 3.3 8.8 + - - -
554A LEU* 2.9 27.5 + - + +
555A LEU* 3.3 21.8 + - + +
566A LEU* 3.5 38.3 + - + +
570A GLU* 4.0 4.2 + - - -
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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