Contacts of the helix formed by residues 543 - 557 (chain C) in PDB entry 5A31
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 ARG 543 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510C SER* 5.7 1.0 + - - -
511C THR* 5.5 2.8 - - - +
514C ARG* 3.2 39.3 - - - +
536C CYS* 4.0 20.2 - - - -
537C CYS* 4.7 2.8 - - - -
540C ASN* 3.2 39.3 + - + +
541C ASP 3.2 3.1 - - - +
542C THR* 1.3 71.9 - - - +
544C GLU* 1.3 62.4 + - - +
545C GLU* 2.8 37.8 + - - +
546C GLY* 4.0 11.4 - - - +
547C LYS* 3.4 23.6 + - - +
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Residues in contact with GLU 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220A MET* 3.6 26.8 - - + +
1264A THR* 3.9 13.1 - - - +
1266A HIS* 2.8 39.5 + - + +
1267A ARG 4.9 0.5 + - - -
1314A ILE* 4.9 7.4 - - - +
542C THR 2.8 14.1 + - - +
543C ARG* 1.3 70.1 - - - +
545C GLU* 1.3 65.2 + - - +
546C GLY 3.2 0.2 - - - -
547C LYS* 3.2 15.5 + - + +
548C ALA* 2.9 24.9 + - - +
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Residues in contact with GLU 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C ARG* 3.5 17.8 + - - -
543C ARG* 2.8 33.2 + - - +
544C GLU* 1.3 77.0 - - - +
546C GLY* 1.3 56.1 + - - +
548C ALA* 3.8 4.9 - - - +
549C LEU* 3.0 33.2 + - - +
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Residues in contact with GLY 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C ARG* 5.1 5.7 - - - +
533C ALA* 4.6 9.4 - - - +
536C CYS* 5.0 9.2 - - - -
537C CYS* 4.3 12.9 - - - -
543C ARG* 3.6 15.6 + - - +
544C GLU 3.2 0.6 - - - -
545C GLU* 1.3 78.1 - - - +
547C LYS* 1.3 62.4 + - - +
549C LEU* 3.7 9.6 + - - +
550C LEU* 3.1 21.8 + - - +
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Residues in contact with LYS 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C CYS* 4.3 13.2 - - - -
541C ASP* 3.4 32.9 + - - +
542C THR 5.1 1.6 - - - +
543C ARG 3.4 15.9 + - - +
544C GLU* 3.2 19.6 + - + +
546C GLY* 1.3 72.0 - - - +
548C ALA* 1.3 65.1 + - - +
550C LEU* 3.3 9.0 + - - +
551C ARG* 3.2 19.8 + - - +
351K ASP* 4.3 20.6 - - - +
354K MET* 4.0 27.1 - - - +
378K TYR* 5.0 10.4 + - + +
381K THR* 5.5 5.1 + - - +
383K ASN* 4.6 11.6 + - - +
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Residues in contact with ALA 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C GLU 2.9 17.2 + - - +
545C GLU* 3.8 5.4 - - - +
547C LYS* 1.3 74.9 - - - +
549C LEU* 1.3 59.9 + - - +
551C ARG* 2.9 24.9 + - - +
552C GLN* 3.1 20.9 + - + +
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Residues in contact with LEU 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C ARG* 4.2 13.7 - - + +
517C ALA* 4.2 13.7 - - + -
518C GLN* 3.9 35.2 - - + +
521C PHE* 3.9 36.3 - - + -
533C ALA* 5.3 5.8 - - + -
545C GLU 3.0 18.4 + - - +
546C GLY* 3.8 7.9 - - - +
548C ALA* 1.3 72.5 - - - +
550C LEU* 1.3 65.8 + - - +
552C GLN* 3.4 12.2 + - - +
553C ILE* 3.1 34.9 + - + +
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Residues in contact with LEU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530C SER* 4.0 13.0 - - - +
533C ALA* 3.3 32.0 - - + +
534C GLN* 4.1 13.5 - - + +
537C CYS* 5.9 2.0 - - - -
546C GLY 3.1 12.9 + - - +
547C LYS* 3.3 13.5 - - - +
549C LEU* 1.3 72.2 - - - +
551C ARG* 1.3 67.0 + - - +
553C ILE* 2.9 29.4 - - + +
554C LEU* 3.2 35.9 + - + +
378K TYR* 5.5 3.1 - - - +
383K ASN* 5.9 0.2 - - - +
386K LEU* 3.8 22.4 - - + -
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Residues in contact with ARG 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C LYS 3.2 7.4 + - - +
548C ALA* 2.9 14.1 + - - +
550C LEU* 1.3 80.1 - - - +
552C GLN* 1.3 58.9 + - + +
554C LEU* 3.4 1.6 + - - +
555C GLN* 2.9 56.9 + - + +
382K ASN* 2.6 42.9 + - - +
383K ASN* 3.2 24.0 + - - +
384K SER* 3.9 20.2 + - - +
385K LYS* 5.4 1.0 - - - +
386K LEU* 4.7 13.7 - - + +
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Residues in contact with GLN 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C PHE* 3.9 30.3 - - + -
548C ALA* 3.1 16.4 + - + +
549C LEU* 3.8 16.8 - - - +
550C LEU 3.2 0.2 - - - -
551C ARG* 1.3 77.0 - - + +
553C ILE* 1.3 65.2 + - - +
555C GLN* 3.4 12.8 + - - +
556C LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C ALA* 6.3 0.2 - - + -
521C PHE* 3.3 37.5 - - + -
526C TRP* 3.3 37.7 - - + +
529C ALA* 3.9 10.1 - - + +
530C SER* 3.3 46.4 - - - +
533C ALA* 4.4 2.7 - - + -
549C LEU* 3.2 15.3 - - + +
550C LEU* 2.9 38.8 - - + +
552C GLN* 1.3 76.4 - - - +
554C LEU* 1.3 64.3 + - + +
556C LEU 3.6 5.0 + - - -
557C ARG* 3.8 6.2 + - - +
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Residues in contact with LEU 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C TRP* 5.8 1.3 - - + -
527C ASP* 5.5 0.9 - - - +
530C SER* 3.2 29.2 - - - +
550C LEU* 3.2 36.3 + - + +
551C ARG 4.2 2.2 - - - +
553C ILE* 1.3 78.3 - - + +
555C GLN* 1.3 63.3 + - - +
557C ARG* 3.0 62.7 + - - +
385K LYS* 4.8 15.1 - - + +
386K LEU* 3.9 26.5 - - + +
389K ARG* 4.5 13.2 - - - +
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Residues in contact with GLN 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C ARG* 2.9 45.1 + - + +
552C GLN* 3.8 11.9 - - - +
554C LEU* 1.3 78.4 - - - +
556C LEU* 1.3 61.1 + - - +
557C ARG 3.5 5.0 + - - -
385K LYS* 4.8 24.8 + - + +
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Residues in contact with LEU 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C PHE* 4.3 17.0 - - + +
526C TRP* 3.4 44.5 - - + +
552C GLN 2.9 16.3 + - - +
553C ILE 3.9 0.7 - - - +
554C LEU 3.3 0.2 - - - -
555C GLN* 1.3 76.8 - - - +
557C ARG* 1.3 62.5 + - - +
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Residues in contact with ARG 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C TRP* 5.2 19.4 - - + -
527C ASP* 3.8 21.4 + - - -
553C ILE 3.8 5.6 + - - +
554C LEU* 3.0 64.8 + - - +
555C GLN 4.2 6.5 - - - -
556C LEU* 1.3 82.2 - - - +
385K LYS* 6.0 2.6 + - - +
389K ARG* 4.2 23.4 - - - +
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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