Contacts of the helix formed by residues 531 - 543 (chain B) in PDB entry 5ZCS
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 LEU 531 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498B GLN* 3.4 26.5 - - - +
501B ILE* 5.4 7.9 - - + -
528B ILE* 4.0 23.1 + - + +
530B GLN* 1.3 95.5 - - + +
532B LYS* 1.3 61.9 - - - +
533B LYS* 3.4 6.3 - - + +
534B ASP* 4.1 30.6 + - + +
535B ILE* 4.2 14.6 - - - +
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Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B GLN 3.9 2.6 + - - +
531B LEU* 1.3 72.1 - - - +
533B LYS* 1.3 69.6 + - + +
534B ASP 3.2 2.5 - - - -
535B ILE* 3.3 12.1 + - + +
536B GLN* 3.0 54.5 + - + +
592B PHE* 4.9 15.5 - - + -
593B GLU 5.3 4.7 - - - +
595B GLU* 4.6 11.9 + - - -
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Residues in contact with LYS 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B LEU* 3.4 5.5 - - + +
532B LYS* 1.3 84.8 - - + +
534B ASP* 1.3 60.0 + - - +
536B GLN* 3.4 26.1 + - + +
537B ASP* 2.8 44.2 + - - +
595B GLU* 3.7 27.8 + - - +
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Residues in contact with ASP 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ILE* 4.1 16.8 - - - +
505B LEU* 3.5 32.6 - - - +
509B LEU* 5.7 2.9 - - - +
528B ILE* 6.6 0.4 - - + -
531B LEU* 4.1 29.2 + - + +
532B LYS 3.2 0.8 - - - -
533B LYS* 1.3 78.8 - - - +
535B ILE* 1.3 59.1 + - + +
537B ASP* 3.4 6.1 + - - +
538B GLY* 2.9 25.5 + - - -
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Residues in contact with ILE 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B LEU* 4.1 35.9 - - + +
524B LEU* 5.1 10.3 - - + -
525B SER* 3.8 34.5 - - - +
528B ILE* 5.5 6.1 - - + +
531B LEU 4.2 15.0 - - - +
532B LYS* 3.3 11.9 + - + +
534B ASP* 1.3 77.8 - - + +
536B GLN* 1.3 57.5 + - - +
538B GLY* 3.4 1.4 + - - -
539B LEU* 2.9 32.9 + - + +
592B PHE* 4.3 25.1 - - + -
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Residues in contact with GLN 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B LYS* 3.0 51.6 + - + +
533B LYS* 3.4 32.8 + - + +
534B ASP 3.3 0.2 - - - -
535B ILE* 1.3 77.9 - - - +
537B ASP* 1.3 58.5 + - - +
539B LEU* 3.4 5.1 + - - +
540B LEU* 2.9 40.4 + - + +
592B PHE* 4.7 6.7 - - + -
593B GLU 4.9 0.2 + - - -
594B PHE* 4.3 36.9 - - + +
595B GLU* 4.5 17.0 + - - +
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Residues in contact with ASP 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B LYS* 2.8 29.4 + - - +
534B ASP* 3.9 6.8 - - - +
536B GLN* 1.3 75.9 - - - +
538B GLY* 1.3 61.3 + - - +
540B LEU* 3.8 11.8 - - - +
541B LYS* 2.9 30.5 + - - +
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Residues in contact with GLY 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B LEU* 4.1 27.7 - - - +
534B ASP 2.9 17.2 + - - -
535B ILE* 3.8 1.6 - - - -
537B ASP* 1.3 77.0 - - - +
539B LEU* 1.3 55.6 + - - +
541B LYS* 3.4 4.9 + - - +
542B MET* 2.9 32.5 + - - +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B ILE* 2.9 19.7 + - + +
536B GLN* 3.7 4.9 - - - +
537B ASP 3.3 0.2 - - - -
538B GLY* 1.3 76.0 - - - +
540B LEU* 1.3 72.1 + - + +
542B MET* 4.9 1.6 - - - -
543B LEU* 2.9 59.1 + - + +
588B THR* 4.4 21.3 - - + +
589B LEU* 3.8 26.2 - - + -
592B PHE* 4.5 12.6 - - + -
594B PHE* 3.7 31.9 - - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B GLN* 2.9 27.1 + - + +
537B ASP* 4.1 12.1 - - - +
539B LEU* 1.3 88.7 - - + +
541B LYS* 1.3 53.7 + - - +
543B LEU* 5.5 0.2 - - - -
544B SER* 2.6 34.2 + - - +
589B LEU* 6.3 0.2 - - + -
594B PHE* 6.5 0.9 - - + -
602B PHE* 3.7 35.9 - - + -
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B LEU* 5.8 12.3 - - + -
537B ASP 2.9 18.9 + - - +
538B GLY* 3.8 5.6 - - - +
539B LEU 3.2 0.2 - - - -
540B LEU* 1.3 79.0 - - - +
542B MET* 1.3 63.0 + - - +
544B SER* 3.9 0.6 + - - -
545B LEU* 3.3 46.4 - - + +
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Residues in contact with MET 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B LEU* 5.9 5.8 - - + -
512B GLY 3.5 24.2 - - - +
513B LEU* 4.1 22.0 - - + -
517B LEU* 3.8 33.0 - - + -
538B GLY 2.9 16.6 + - - +
539B LEU* 4.3 1.8 - - - +
541B LYS* 1.3 79.9 - - - +
543B LEU* 1.3 85.1 + - + +
544B SER 3.5 0.3 + - - -
545B LEU* 3.6 2.8 + - - +
546B VAL* 3.3 27.5 + - + +
588B THR* 5.2 4.0 - - + -
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Residues in contact with LEU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B LEU* 6.5 0.9 - - + -
539B LEU* 2.9 39.0 + - + +
540B LEU* 5.5 0.4 - - - -
542B MET* 1.3 100.1 - - + +
544B SER* 1.3 59.9 + - - +
546B VAL* 3.3 4.8 + - - +
547B LEU* 2.9 47.7 + - + +
585B ALA* 3.5 38.8 - - + +
588B THR* 4.6 10.3 - - + -
589B LEU* 3.8 31.2 - - + +
602B PHE* 5.4 5.2 - - + -
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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