Contacts of the helix formed by residues 525 - 540 (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 LEU 525 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520C TYR* 3.0 32.8 + - + +
523C CYS* 4.4 17.7 - - + +
524C LYS* 1.3 88.5 - - - +
526C TRP* 1.3 63.5 + - - +
527C ASP 3.4 2.6 + - - -
528C GLU* 3.2 32.8 + - + +
529C ALA* 3.3 17.0 + - - +
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Residues in contact with TRP 526 (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* 4.1 18.1 + + - +
524C LYS* 3.0 59.0 + - + -
525C LEU* 1.3 72.2 - - - +
527C ASP* 1.3 61.3 + - - +
529C ALA* 3.2 9.0 + - - +
530C SER* 2.9 32.3 + - - +
553C ILE* 3.3 42.5 - - + +
554C LEU* 5.8 0.9 - - + -
556C LEU* 3.4 45.3 - - + +
557C ARG* 5.2 17.7 - - + -
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Residues in contact with ASP 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C LEU 3.4 0.8 - - - -
526C TRP* 1.3 80.9 - - - +
528C GLU* 1.3 66.4 + - + +
530C SER* 3.2 18.3 + - - -
531C THR* 3.2 14.0 + - - +
554C LEU* 5.5 0.3 - - - +
557C ARG* 3.8 26.4 + - - -
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Residues in contact with GLU 528 (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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520C TYR* 3.2 33.7 - - + -
525C LEU* 3.2 38.8 + - + +
526C TRP 3.4 0.4 - - - -
527C ASP* 1.3 76.0 - - + +
529C ALA* 1.3 64.4 + - - +
531C THR* 3.2 27.1 - - + +
532C CYS* 3.4 12.5 + - - -
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Residues in contact with ALA 529 (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* 3.3 34.0 - - + +
520C TYR* 3.9 6.4 - - + +
521C PHE* 3.8 14.4 - - - +
525C LEU 3.3 8.3 + - - +
526C TRP 3.2 10.6 + - - +
528C GLU* 1.3 77.2 - - - +
530C SER* 1.3 56.9 + - - +
532C CYS 3.3 1.2 + - - -
533C ALA* 2.8 31.4 + - - +
553C ILE* 3.9 18.8 - - + -
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Residues in contact with SER 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C TRP 2.9 17.1 + - - -
527C ASP* 3.2 11.8 + - - -
529C ALA* 1.3 76.5 - - - +
531C THR* 1.3 62.7 + - - +
533C ALA* 3.3 2.4 + - - +
534C GLN* 3.1 31.4 + - - +
550C LEU* 4.0 4.6 - - - +
553C ILE* 3.3 15.4 - - - +
554C LEU* 3.2 30.9 - - - +
389K ARG* 5.4 7.0 - - - -
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Residues in contact with THR 531 (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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527C ASP 3.2 6.7 + - - +
528C GLU* 3.2 28.9 - - + +
530C SER* 1.3 77.1 - - - +
532C CYS* 1.3 65.7 + - - +
534C GLN* 3.2 18.6 + - - +
535C LYS* 3.1 51.4 + - + +
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Residues in contact with CYS 532 (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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513C PHE* 3.7 32.0 - - + +
516C LEU* 3.6 27.1 - - - -
517C ALA* 3.9 8.3 - - + +
520C TYR* 4.3 11.2 - - - -
528C GLU 3.7 13.0 - - - +
529C ALA 3.3 6.8 + - - +
530C SER 3.3 0.4 - - - -
531C THR* 1.3 86.0 - - - +
533C ALA* 1.3 65.6 + - - +
535C LYS* 3.3 9.3 + - - +
536C CYS* 3.0 22.7 + - - +
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Residues in contact with ALA 533 (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* 5.9 0.9 - - - +
517C ALA* 3.9 11.6 - - + +
529C ALA 2.8 18.4 + - - +
530C SER* 3.3 0.9 + - - +
532C CYS* 1.3 77.4 - - - +
534C GLN* 1.3 62.0 + - - +
536C CYS* 3.3 9.1 + - - +
537C CYS* 3.1 26.4 + - - +
546C GLY* 4.6 12.4 - - - +
549C LEU* 5.3 5.8 - - + -
550C LEU* 3.3 28.0 - - + +
553C ILE* 4.4 5.2 - - + -
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Residues in contact with GLN 534 (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* 3.1 20.7 + - - +
531C THR* 3.2 29.9 + - - +
533C ALA* 1.3 72.5 - - - +
535C LYS* 1.3 76.9 + - + +
537C CYS* 3.4 9.3 + - + +
538C ALA* 3.0 22.0 + - - +
550C LEU* 4.1 9.5 - - + +
358K PHE* 6.1 5.6 - - + -
389K ARG* 4.9 13.8 + - - +
390K PHE* 6.1 1.2 - - - -
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Residues in contact with LYS 535 (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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513C PHE* 4.1 23.3 - - + -
531C THR* 3.1 46.2 + - + +
532C CYS* 3.5 9.9 - - - +
533C ALA 3.3 0.2 - - - -
534C GLN* 1.3 88.0 - - + +
536C CYS* 1.3 60.0 + - - +
538C ALA* 3.1 17.8 + - + +
539C PHE* 2.9 29.8 + - + -
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Residues in contact with CYS 536 (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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510C SER* 3.8 25.6 - - - +
513C PHE* 4.2 4.0 - - + +
514C ARG* 4.0 26.5 - - - +
532C CYS 3.0 13.1 + - - +
533C ALA* 3.3 10.3 + - - +
535C LYS* 1.3 74.3 - - - +
537C CYS* 1.3 58.4 + - - +
539C PHE* 3.0 14.9 + - - +
540C ASN 2.8 25.6 + - - +
543C ARG* 4.0 27.1 - - - -
546C GLY* 5.0 8.1 - - - -
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Residues in contact with CYS 537 (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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533C ALA 3.1 16.6 + - - +
534C GLN* 3.6 11.9 - - - +
535C LYS 3.3 0.2 - - - -
536C CYS* 1.3 74.2 - - - +
538C ALA* 1.3 62.2 + - - +
540C ASN 3.6 9.0 - - - -
541C ASP* 2.8 48.2 + - - +
543C ARG 4.7 4.0 - - - -
546C GLY* 4.3 26.2 - - - -
547C LYS* 4.3 17.3 - - - -
550C LEU* 5.9 3.1 - - - -
358K PHE* 6.1 5.6 - - + -
378K TYR* 6.0 2.2 - - - -
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Residues in contact with ALA 538 (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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534C GLN 3.0 13.2 + - - +
535C LYS* 3.1 14.1 + - - +
537C CYS* 1.3 77.3 - - - +
539C PHE* 1.3 63.2 + - + +
541C ASP* 4.8 2.5 + - - +
362K GLN* 5.5 10.1 - - - +
147R PRO* 5.5 5.2 - - - +
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Residues in contact with PHE 539 (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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498C TYR* 5.4 5.8 - - - -
509C GLU* 4.8 8.3 - - - -
510C SER* 3.5 27.8 - - - +
513C PHE* 3.6 35.4 - + - -
535C LYS* 2.9 35.6 + - + -
536C CYS* 3.0 11.6 + - - +
538C ALA* 1.3 80.7 - - + +
540C ASN* 1.3 65.3 + - - +
541C ASP 4.0 0.4 + - - -
147R PRO* 5.1 9.7 - - - +
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Residues in contact with ASN 540 (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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510C SER* 3.1 28.1 + - - -
536C CYS 2.8 9.4 + - - +
537C CYS* 3.1 11.2 - - - +
539C PHE* 1.3 78.2 + - - +
541C ASP* 1.3 64.0 + - - +
542C THR* 3.2 6.7 - - - +
543C ARG* 3.2 42.8 + - + +
146R SER* 6.0 2.8 - - - -
147R PRO* 6.1 1.6 - - - -
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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