Contacts of the helix formed by residues 522 - 534 (chain A) in PDB entry 5ZR1
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 THR 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A LYS* 3.8 18.5 - - - +
521A PRO* 1.3 82.9 - - + +
523A ASP* 1.3 63.8 + - - +
524A CYS 3.2 3.4 + - - -
525A TYR* 3.6 20.6 + - + +
526A GLU 4.0 0.3 + - - -
539A TRP* 3.3 58.7 + - + +
578A ILE* 5.0 1.1 - - + -
595B SER* 5.2 6.2 - - - -
597B MET* 3.8 29.2 - - + -
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Residues in contact with ASP 523 (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 MET* 3.8 16.4 - - - -
519A VAL 3.5 6.2 + - - -
520A LYS* 3.0 45.2 + - - +
521A PRO 3.2 1.8 - - - -
522A THR* 1.3 77.2 + - - +
524A CYS* 1.3 59.7 + - - +
525A TYR 3.3 0.4 - - - -
526A GLU* 3.4 27.7 + - - +
527A THR* 3.0 33.4 + - + +
178D THR* 3.3 29.8 - - - +
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Residues in contact with CYS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 3.9 24.8 - - + +
518A MET* 4.3 6.9 - - + +
521A PRO 3.7 3.4 + - - +
522A THR 3.2 1.6 - - - -
523A ASP* 1.3 76.3 - - - +
525A TYR* 1.3 71.4 + - - +
527A THR* 3.3 8.1 + - - -
528A LEU* 3.0 32.2 + - - +
571A MET* 4.1 11.2 - - - -
578A ILE* 3.5 24.7 - - - -
582A PHE* 3.5 31.5 - - + -
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Residues in contact with TYR 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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522A THR* 3.6 23.3 + - + +
523A ASP 3.3 0.2 - - - -
524A CYS* 1.3 93.2 - - - +
526A GLU* 1.3 61.6 + - - +
529A TRP* 3.2 19.2 + - - +
539A TRP* 4.0 28.0 - + + +
542A SER* 3.3 24.7 - - - -
543A MET* 3.6 26.9 - - + +
546A LEU* 4.1 7.6 - - + +
577A ASP* 3.3 8.3 + - - +
578A ILE* 3.4 22.2 - - + -
581A ASN* 2.5 33.2 + - + +
582A PHE* 4.3 9.9 - + - -
585A TRP* 3.7 28.0 - + - -
597B MET* 5.9 1.8 - - + -
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Residues in contact with GLU 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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370A LYS* 3.7 27.8 + - - +
520A LYS* 5.8 1.7 + - - +
522A THR 4.2 2.2 - - - +
523A ASP* 3.4 30.0 + - - +
524A CYS 3.3 0.4 - - - -
525A TYR* 1.3 77.4 - - - +
527A THR* 1.3 60.8 + - + +
529A TRP* 3.9 1.4 - - - +
530A ASN* 3.0 29.9 + - - +
535A GLU 5.0 0.9 - - - +
537A LEU 3.7 20.8 + - - +
538A THR* 4.1 4.0 - - - -
539A TRP* 3.6 34.4 + - + +
542A SER* 3.7 7.8 + - - -
178D THR* 4.5 6.2 + - - -
11G A 4.3 7.8 + - - -
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Residues in contact with THR 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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513A ILE* 3.3 18.7 - - - +
518A MET* 3.4 19.4 - - + +
523A ASP* 3.0 20.5 + - + +
524A CYS* 3.3 7.8 + - - -
526A GLU* 1.3 76.3 - - + +
528A LEU* 1.3 65.6 + - - +
530A ASN* 3.8 6.3 - - - +
531A LYS* 3.2 32.0 + - - +
182D GLU* 4.8 12.8 - - - +
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Residues in contact with LEU 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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511A VAL* 3.7 33.9 - - + -
513A ILE* 4.3 7.4 - - + +
524A CYS 3.0 20.0 + - - +
527A THR* 1.3 78.1 + - - +
529A TRP* 1.3 57.9 + - - +
531A LYS* 3.1 2.9 + - - -
532A VAL* 2.9 39.7 + - + +
546A LEU* 3.8 28.7 - - + -
550A PHE* 4.9 9.6 - - + -
561A ILE* 4.8 5.2 - - + -
563A VAL* 3.9 17.3 - - + -
582A PHE* 3.6 29.8 - - + -
585A TRP* 4.5 3.4 - - + -
593A LEU* 5.5 1.3 - - + -
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Residues in contact with TRP 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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375A PHE* 3.4 48.5 - + + -
394A PHE* 4.7 2.0 - + - -
525A TYR 3.2 17.3 + - - +
526A GLU 4.2 0.7 - - - +
528A LEU* 1.3 79.0 - - - +
530A ASN* 1.3 54.9 + - - +
532A VAL* 4.3 13.7 - - + -
533A SER* 2.6 66.7 + - - -
535A GLU* 3.6 28.8 + - - +
537A LEU* 3.8 17.3 - - + +
542A SER* 4.0 19.1 - - - +
545A SER* 3.5 29.9 - - - -
546A LEU* 3.6 25.1 - - + -
549A TYR* 4.1 13.9 - + + -
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Residues in contact with ASN 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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370A LYS* 6.0 1.4 - - - +
526A GLU 3.0 20.5 + - - +
527A THR* 3.8 8.2 - - - +
529A TRP* 1.3 77.7 - - - +
531A LYS* 1.3 62.2 + - + +
534A GLY* 2.8 42.8 + - - +
535A GLU 3.6 15.6 + - - +
536A ARG* 4.2 17.9 - - - +
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Residues in contact with LYS 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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395A TYR* 3.8 14.7 - - - -
396A GLY* 4.0 8.1 + - - -
399A SER* 5.6 6.2 + - - +
509A LEU* 4.0 9.7 - - + +
510A TYR 6.1 0.7 - - - +
511A VAL* 3.7 32.8 - - + +
512A GLU 6.0 1.3 - - - -
527A THR* 3.2 20.7 + - - +
528A LEU 3.1 5.2 + - - +
530A ASN* 1.3 78.3 - - + +
532A VAL* 1.3 66.5 + - - +
534A GLY 4.7 0.2 + - - -
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Residues in contact with VAL 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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394A PHE* 3.5 8.2 - - + +
395A TYR* 2.7 39.0 + - + -
509A LEU* 4.8 4.0 - - + -
528A LEU* 2.9 36.7 + - + +
529A TRP* 4.0 19.1 - - + +
531A LYS* 1.3 77.5 - - - +
533A SER* 1.3 57.6 + - - +
546A LEU* 4.5 7.6 - - + -
549A TYR* 3.9 33.9 - - + +
550A PHE* 5.6 0.4 - - + -
561A ILE* 3.7 24.0 - - + -
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Residues in contact with SER 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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393A GLU* 2.9 20.4 - - - +
394A PHE* 3.3 33.6 - - - -
529A TRP* 2.6 59.8 + - - -
532A VAL* 1.3 76.2 - - - +
534A GLY* 1.3 62.8 + - - +
535A GLU* 3.3 15.7 + - - +
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Residues in contact with GLY 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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393A GLU* 3.6 15.1 + - - +
395A TYR 5.2 0.4 - - - +
396A GLY* 5.8 1.5 - - - +
530A ASN* 2.8 26.6 + - - +
531A LYS 4.6 0.6 + - - -
532A VAL 3.8 0.8 - - - -
533A SER* 1.3 78.3 + - - +
535A GLU* 1.3 59.6 + - - +
536A ARG* 4.2 2.6 + - - +
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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