Contacts of the helix formed by residues 524 - 538 (chain A) in PDB entry 5JZU
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 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A GLY 4.3 7.3 - - - +
522A THR 2.9 6.9 + - - -
523A ASP* 1.3 73.5 - - - +
525A GLY* 1.3 69.2 + - - +
526A ARG* 2.8 66.7 + - - +
527A PHE* 3.1 37.9 + - + +
528A TYR* 3.1 15.4 + - - -
555A HIS* 4.1 1.1 - - - -
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Residues in contact with GLY 525 (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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524A ASP* 1.3 75.8 + - - +
526A ARG* 1.3 56.6 + - - +
528A TYR* 3.3 5.7 + - - +
529A PHE* 2.8 31.7 + - - +
555A HIS* 3.5 37.6 + - - -
556A PHE* 3.8 3.2 - - - -
564A LEU* 3.9 16.4 - - - -
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Residues in contact with ARG 526 (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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496A PHE* 4.4 15.9 - - + -
524A ASP* 2.8 40.6 + - - +
525A GLY* 1.3 77.2 - - - +
527A PHE* 1.3 65.3 + - + +
529A PHE* 3.4 2.4 + - - +
530A HIS* 3.1 38.4 + - + +
564A LEU* 3.8 21.6 - - + +
565A TYR* 5.6 2.8 + - + -
105B LEU* 6.4 0.4 - - + -
107B GLU 5.0 2.5 - - - +
108B TYR* 2.8 84.4 + - - -
109B THR* 3.9 9.1 - - - +
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Residues in contact with PHE 527 (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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492A VAL* 3.6 41.5 - - + -
493A HIS* 3.6 28.3 - + - -
496A PHE* 4.0 24.7 - + + -
511A LEU* 4.1 16.4 - - + +
515A ILE* 3.7 20.7 - - + +
521A GLY 3.7 11.4 - - - -
522A THR 3.6 12.8 - - - -
524A ASP* 3.1 36.2 + - + +
526A ARG* 1.3 80.1 - - + +
528A TYR* 1.3 61.6 + - - +
530A HIS* 4.4 0.8 - - - +
531A LEU* 3.0 32.6 + - - +
108B TYR* 4.6 9.0 - + - -
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Residues in contact with TYR 528 (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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515A ILE* 3.5 34.5 - - + +
522A THR 4.6 0.7 - - - -
523A ASP* 2.8 32.5 + - - -
524A ASP 3.1 26.5 - - - -
525A GLY* 3.3 5.8 + - - +
527A PHE* 1.3 80.2 - - - +
529A PHE* 1.3 63.4 + - - +
531A LEU* 3.9 2.6 - - - +
532A GLY* 3.2 20.8 + - - -
546A TRP* 3.7 33.1 - + - +
547A TYR* 4.1 5.9 - - - -
549A LEU* 4.3 7.2 - - + -
550A GLY* 3.6 24.2 - - - -
553A ARG* 3.3 16.8 - - - -
555A HIS* 3.6 19.5 - + - -
556A PHE* 3.9 17.0 - - + -
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Residues in contact with PHE 529 (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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525A GLY 2.8 17.9 + - - +
526A ARG* 3.5 7.4 - - - +
527A PHE 3.3 0.2 - - - -
528A TYR* 1.3 76.8 - - - +
530A HIS* 1.3 82.1 + + - +
533A ASP* 3.3 32.4 + - + +
547A TYR* 3.8 9.2 + - - -
556A PHE* 3.6 10.7 - + + -
562A ARG* 3.5 39.7 - - + -
564A LEU* 4.5 2.5 - - + -
679A HIS* 5.7 2.9 - - + -
680A THR* 3.7 33.7 - - - -
105B LEU* 3.7 44.6 - - + -
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Residues in contact with HIS 530 (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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496A PHE* 3.3 36.1 - + + -
499A LYS* 3.3 45.9 + - + +
511A LEU* 4.0 11.2 - - + +
526A ARG* 3.1 28.1 + - - +
527A PHE* 4.4 2.2 - - - +
529A PHE* 1.3 94.3 - + - +
531A LEU* 1.3 67.2 + - - +
533A ASP* 4.3 0.6 - - - +
534A ALA* 3.0 20.8 + - - +
105B LEU* 2.9 32.3 + - - +
106B GLY* 4.3 7.4 - - - -
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Residues in contact with LEU 531 (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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508A ILE* 3.8 42.4 - - + +
511A LEU* 3.7 16.9 - - + +
512A LYS* 3.8 20.4 - - + +
515A ILE* 4.1 8.1 - - + -
527A PHE 3.0 19.0 + - - +
528A TYR 3.9 3.1 - - - +
530A HIS* 1.3 77.8 - - - +
532A GLY* 1.3 57.7 + - - +
534A ALA* 3.3 1.8 + - - +
535A MET* 2.9 44.5 + - + +
546A TRP* 3.5 43.7 - - + +
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Residues in contact with GLY 532 (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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528A TYR 3.2 9.2 + - - -
531A LEU* 1.3 80.9 - - - +
533A ASP* 1.3 55.3 + - - +
535A MET* 3.2 5.9 + - - -
536A GLN* 2.8 32.9 + - - +
543A ALA* 3.4 17.4 - - - +
546A TRP* 4.9 2.0 - - - +
547A TYR* 3.1 24.9 - - - -
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Residues in contact with ASP 533 (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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499A LYS* 2.8 33.0 + - - +
529A PHE* 3.3 25.7 + - + +
530A HIS* 4.3 1.8 - - - +
531A LEU 3.3 0.2 - - - -
532A GLY* 1.3 70.6 - - - +
534A ALA* 1.3 66.1 + - - +
536A GLN* 3.0 10.1 + - - +
537A ARG* 3.0 56.0 + - - +
547A TYR* 3.0 12.0 + - - +
562A ARG* 5.8 0.5 + - - -
677A TRP* 5.1 0.2 - - - +
678A PRO 3.3 23.4 - - - +
679A HIS* 5.0 3.5 - - - +
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Residues in contact with ALA 534 (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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499A LYS* 3.7 11.8 - - + +
504A ILE* 3.4 29.1 - - + +
507A SER* 3.9 12.3 - - - +
508A ILE* 3.9 18.2 - - + -
511A LEU* 5.0 0.7 - - + -
530A HIS 3.0 18.4 + - - +
531A LEU* 3.6 5.2 - - - +
533A ASP* 1.3 76.8 - - - +
535A MET* 1.3 61.9 + - - +
537A ARG* 3.4 1.9 + - - -
538A VAL* 3.3 22.5 + - - +
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Residues in contact with MET 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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508A ILE* 4.2 16.6 - - + -
512A LYS* 4.5 11.0 - - + -
531A LEU* 2.9 38.5 + - + +
532A GLY 3.4 5.4 - - - +
534A ALA* 1.3 74.9 - - - +
536A GLN* 1.3 66.2 + - - +
538A VAL* 3.2 13.1 - - - +
540A ASN* 2.9 53.3 + - + +
542A GLU* 3.9 11.2 - - + -
543A ALA* 3.6 20.4 - - + -
546A TRP* 3.5 40.2 - - + +
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Residues in contact with GLN 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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532A GLY 2.8 14.6 + - - +
533A ASP* 3.0 16.3 + - - +
535A MET* 1.3 76.6 - - - +
537A ARG* 1.3 62.9 + - + +
539A GLY* 3.1 13.7 + - - -
540A ASN 4.6 2.5 - - - +
543A ALA* 3.7 15.5 - - + -
544A TYR* 3.5 17.1 - - + -
547A TYR* 2.8 25.7 + - - -
562A ARG* 3.8 2.4 + - - -
677A TRP* 4.7 5.6 - - - -
678A PRO* 4.2 24.4 - - + +
724A GLU* 3.0 32.7 + - - +
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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
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499A LYS* 4.2 8.1 - - - +
502A ASN* 4.1 4.9 + - - -
504A ILE* 4.2 25.8 - - + +
533A ASP* 3.0 47.2 + - - +
534A ALA 3.8 5.2 - - - +
535A MET 3.2 0.2 - - - -
536A GLN* 1.3 76.9 - - + +
538A VAL* 1.3 59.4 + - - +
539A GLY 3.3 0.6 + - - -
617A GLU 5.0 1.0 + - - -
618A ASN* 2.9 53.1 + - - +
619A LEU* 4.3 11.5 - - - +
677A TRP* 3.5 72.9 - - + +
678A PRO 5.6 0.2 + - - -
679A HIS* 6.0 0.8 - - - +
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Residues in contact with VAL 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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504A ILE* 3.7 21.3 - - + -
505A ALA* 4.6 12.3 - - + +
508A ILE* 3.7 21.8 - - + -
534A ALA 3.3 15.0 - - - +
535A MET* 3.2 15.9 - - - +
537A ARG* 1.3 78.3 - - - +
539A GLY* 1.3 60.3 + - - +
540A ASN* 3.3 11.6 + - + +
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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