Contacts of the helix formed by residues 538 - 552 (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 538 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ARG* 5.8 0.2 - - - +
370A LYS* 3.9 17.9 - - + +
371A LYS 3.2 11.9 + - - +
372A TYR* 4.0 18.9 - - + -
526A GLU* 4.0 6.5 - - - -
537A LEU* 1.3 74.3 - - - +
539A TRP* 1.3 56.9 + - - +
540A ALA* 4.0 2.0 + - - -
541A ALA* 3.3 18.4 + - - +
542A SER* 2.6 36.1 + - - -
10G T 4.0 24.7 + - - +
11G A 3.8 17.9 - - - +
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Residues in contact with TRP 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LYS* 5.5 5.7 - - + +
522A THR* 3.3 49.1 + - + +
525A TYR* 4.0 15.7 - + + +
526A GLU* 3.6 19.1 + - + +
538A THR* 1.3 77.0 - - - +
540A ALA* 1.3 75.7 + - + +
542A SER* 3.7 4.5 - - - -
543A MET* 3.1 48.8 + - - +
555B GLU* 5.9 1.3 - - - -
595B SER* 3.2 38.2 + - - +
596B GLY 4.6 1.8 - - - -
597B MET* 3.5 41.1 - - + -
11G A 3.3 31.0 + - - -
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A THR* 3.4 3.0 + - - +
539A TRP* 1.3 105.7 - - + +
541A ALA* 1.3 56.7 + - - +
543A MET* 4.0 6.7 - - - +
544A GLU* 3.2 25.6 - - - +
557B LYS* 5.9 0.3 - - - -
595B SER 5.8 0.7 - - - +
596B GLY* 6.1 2.5 - - - +
10G T 4.1 24.7 - - - +
11G A 5.7 1.3 - - - +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LYS 4.2 0.2 - - - +
372A TYR 3.3 28.5 - - - +
374A PRO* 3.7 11.7 - - + +
537A LEU* 3.5 21.2 - - + +
538A THR* 3.3 18.5 + - - +
539A TRP 3.2 0.4 - - - -
540A ALA* 1.3 77.8 - - - +
542A SER* 1.3 51.8 + - - +
543A MET 3.5 0.7 - - - -
544A GLU* 4.1 1.6 - - - -
545A SER* 2.5 36.6 + - - -
10G T 4.7 2.2 + - - +
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Residues in contact with SER 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A TYR* 3.3 28.7 - - - -
526A GLU* 3.7 8.8 - - - -
529A TRP* 4.0 11.5 - - - +
537A LEU* 3.5 18.0 + - - +
538A THR 2.6 23.9 + - - -
539A TRP 3.2 4.4 + - - -
541A ALA* 1.3 78.1 - - - +
543A MET* 1.3 59.5 + - - +
545A SER* 3.3 6.0 + - - -
546A LEU* 2.9 34.5 + - - +
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Residues in contact with MET 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A TYR* 3.6 31.8 - - + +
539A TRP* 3.1 38.5 + - - +
540A ALA* 4.0 7.2 - - - +
542A SER* 1.3 74.6 - - - +
544A GLU* 1.3 82.9 + - - +
545A SER 3.3 0.2 - - - -
546A LEU* 3.9 3.8 - - - +
547A GLU* 3.0 38.1 + - - +
581A ASN* 3.7 28.9 - - - +
585A TRP* 4.0 6.9 - - + -
555B GLU* 4.8 11.9 - - - +
557B LYS* 5.0 13.2 - - + -
561B HIS* 6.1 2.0 - - + -
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Residues in contact with GLU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PRO* 3.9 24.8 - - + +
376A SER* 5.0 3.2 - - - +
540A ALA 3.2 19.0 - - - +
541A ALA* 3.9 1.7 + - - +
542A SER 3.3 0.4 - - - -
543A MET* 1.3 97.4 - - - +
545A SER* 1.3 64.3 + - - +
547A GLU* 3.9 16.3 - - - +
548A PHE* 3.1 25.1 + - - +
557B LYS* 3.2 42.5 + - - +
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Residues in contact with SER 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PRO* 4.2 0.2 - - - +
375A PHE* 3.0 32.2 + - - +
529A TRP* 3.5 34.2 - - - -
537A LEU* 3.4 10.4 - - - +
541A ALA 2.5 24.6 + - - -
542A SER 3.5 5.6 - - - -
543A MET 3.3 0.2 - - - -
544A GLU* 1.3 77.6 - - - +
546A LEU* 1.3 57.7 + - - +
548A PHE* 3.9 2.1 - - - +
549A TYR* 3.1 27.2 + - - +
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A TYR* 4.1 24.7 - - + +
528A LEU* 3.8 29.2 - - + -
529A TRP* 3.6 31.0 - - + -
532A VAL* 4.5 6.5 - - + -
542A SER 2.9 19.7 + - - +
545A SER* 1.3 75.1 - - - +
547A GLU* 1.3 59.0 + - - +
549A TYR* 3.0 5.9 + - + +
550A PHE* 2.9 54.4 + - + -
585A TRP* 3.6 33.4 - - + -
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Residues in contact with GLU 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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543A MET* 3.0 24.4 + - - +
544A GLU* 3.9 21.6 - - - +
546A LEU* 1.3 76.9 - - - +
548A PHE* 1.3 60.7 + - - +
550A PHE* 4.3 0.3 - - - +
551A LYS* 3.3 43.3 + - + +
581A ASN* 5.7 0.2 - - - +
585A TRP* 3.8 27.2 + - + +
588A TYR* 4.2 6.2 + - - +
557B LYS* 6.1 0.5 - - - +
561B HIS* 2.4 41.2 + - - -
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Residues in contact with PHE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 3.7 24.2 - + - -
376A SER* 3.5 44.6 - - - +
379A PHE* 6.1 1.1 - + - -
381A SER 5.9 1.1 - - - -
382A ILE* 4.5 14.8 - - + -
385A ILE* 4.1 27.1 - - + -
544A GLU 3.1 19.8 + - - +
545A SER 4.1 2.5 - - - +
547A GLU* 1.3 76.5 - - - +
549A TYR* 1.3 62.6 + - - +
551A LYS* 4.9 0.2 - - - -
552A ARG* 3.4 52.8 + - + +
553A VAL* 3.5 6.4 - - + +
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Residues in contact with TYR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 4.7 6.3 - + + -
388A LEU* 3.7 29.6 - - + -
394A PHE* 4.8 2.7 - + - -
395A TYR* 2.3 36.4 + - - -
529A TRP* 4.1 15.5 - + + -
532A VAL* 3.9 15.7 - - + -
545A SER 3.1 20.0 + - - +
546A LEU* 3.0 11.0 + - + +
548A PHE* 1.3 78.4 - - - +
550A PHE* 1.3 83.9 + + - +
553A VAL* 3.4 17.6 - - + +
558A LYS* 3.1 43.8 + - + +
559A LYS 3.9 1.7 + - - -
561A ILE* 3.6 24.2 - - + +
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Residues in contact with PHE 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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528A LEU* 4.9 5.4 - - + -
532A VAL* 5.6 0.4 - - + -
546A LEU* 2.9 43.1 + - + +
547A GLU 3.6 1.1 + - - +
548A PHE 3.4 0.2 - - - -
549A TYR* 1.3 106.1 - + - +
551A LYS* 1.3 57.9 + - - +
558A LYS* 3.1 8.5 + - + +
561A ILE* 4.2 10.8 - - + -
585A TRP* 3.8 38.8 - + + +
588A TYR* 4.1 12.3 - - + -
590A ASN 3.3 1.7 - - - -
591A ALA* 3.0 52.8 + - + +
592A LYS 4.6 4.5 - - - -
593A LEU* 3.8 34.3 - - + -
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Residues in contact with LYS 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 GLU* 3.3 32.6 + - + +
548A PHE* 4.9 0.2 - - - -
550A PHE* 1.3 79.6 - - - +
552A ARG* 1.3 104.3 + - + +
553A VAL 3.8 0.2 - - - -
588A TYR* 3.6 47.4 + - + +
590A ASN* 3.0 24.7 + - - +
561B HIS* 5.4 3.8 - - - -
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Residues in contact with ARG 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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382A ILE* 3.9 27.8 - - + +
548A PHE* 3.4 47.0 + - + +
551A LYS* 1.3 127.7 + - + +
553A VAL* 1.3 66.5 + - - +
554A PRO* 3.5 8.0 - - - +
590A ASN* 4.5 4.3 + - - +
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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