Contacts of the helix formed by residues 561 - 576 (chain C) in PDB entry 5AO4
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 SER 561 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559C ARG* 2.8 27.0 - - - +
560C LYS* 1.3 63.0 + - - -
562C LEU* 1.3 56.1 + - - +
563C TYR* 2.9 18.9 - - - +
564C ALA* 3.2 29.1 - - - +
565C ALA 4.1 1.0 + - - -
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Residues in contact with LEU 562 (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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455C LYS* 5.4 12.3 - - + -
457C VAL* 4.9 1.6 - - + +
554C CYS* 5.8 3.8 - - + -
556C LYS 5.5 5.6 - - - +
557C VAL 4.6 5.4 - - - +
560C LYS* 2.9 19.8 - - + +
561C SER* 1.3 76.4 - - - +
563C TYR* 1.3 56.5 + - - +
564C ALA 3.1 0.9 - - - -
565C ALA* 2.8 30.0 + - + +
566C ARG* 2.9 11.6 + - - +
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Residues in contact with TYR 563 (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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561C SER* 4.3 9.9 - - - +
562C LEU* 1.3 79.8 - - - +
564C ALA* 1.3 57.8 + - - +
566C ARG* 3.7 17.3 - - + -
567C GLN* 2.4 62.2 + - + +
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Residues in contact with ALA 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C PHE* 5.0 1.3 - - + -
561C SER* 3.2 26.7 + - - +
562C LEU 3.1 0.8 - - - -
563C TYR* 1.3 80.4 - - - +
565C ALA* 1.3 61.5 + - - +
567C GLN* 3.9 4.2 - - - -
568C TYR* 2.7 45.3 + - + -
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Residues in contact with ALA 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C VAL* 3.6 29.7 - - + +
498C PHE* 3.9 24.5 - - + -
552C VAL* 5.5 0.8 - - + +
554C CYS* 4.1 20.0 - - + -
561C SER 4.1 0.8 + - - +
562C LEU* 2.8 15.0 + - + +
564C ALA* 1.3 80.1 - - - +
566C ARG* 1.3 59.8 + - - +
568C TYR* 3.5 2.3 + - - +
569C PHE* 3.1 24.9 + - - +
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Residues in contact with ARG 566 (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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457C VAL* 3.7 31.7 + - + +
458C GLY* 4.1 11.9 - - - -
459C GLU 5.2 0.8 + - - +
562C LEU 2.9 7.4 + - - +
563C TYR* 2.9 27.9 + - + +
565C ALA* 1.3 77.7 - - - +
567C GLN* 1.3 60.8 + - - +
569C PHE* 3.4 15.3 + - - +
570C VAL* 3.1 45.0 + - + +
580C LYS 5.2 6.3 + - - -
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Residues in contact with GLN 567 (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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563C TYR* 2.4 59.7 + - + +
564C ALA* 3.9 5.4 - - - +
566C ARG* 1.3 65.8 - - - +
568C TYR* 1.3 68.4 + - + +
570C VAL* 3.7 6.1 + - - +
571C GLN* 3.5 20.4 + - - +
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Residues in contact with TYR 568 (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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496C GLU* 6.0 5.8 - - + -
498C PHE* 4.0 28.3 - + + -
564C ALA* 2.7 43.5 + - + +
565C ALA 3.8 4.7 - - - +
567C GLN* 1.3 79.6 - - + +
569C PHE* 1.3 57.4 + - - +
571C GLN* 3.4 6.5 + - - +
572C TRP* 2.9 27.7 + - - +
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Residues in contact with PHE 569 (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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457C VAL* 4.3 10.1 - - + -
458C GLY* 4.1 11.9 - - - -
459C GLU 3.7 15.7 - - - -
460C THR* 3.6 24.9 - - + -
498C PHE* 5.6 0.9 - - + -
550C ILE 4.9 0.2 - - - -
552C VAL* 3.5 37.9 - - + -
565C ALA 3.1 17.8 + - - +
566C ARG* 3.6 27.1 - - - +
567C GLN 3.3 0.4 - - - -
568C TYR* 1.3 74.0 - - - +
570C VAL* 1.3 73.9 - - + +
571C GLN 3.0 1.6 - - - -
572C TRP* 2.9 23.9 + + - +
573C CYS* 2.9 41.1 + - + -
580C LYS 5.0 9.2 - - - -
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Residues in contact with VAL 570 (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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566C ARG* 3.1 44.0 + - + +
567C GLN* 4.2 5.8 - - - +
568C TYR 3.5 0.2 - - - -
569C PHE* 1.3 82.7 - - + +
571C GLN* 1.3 61.2 + - - +
573C CYS* 3.8 3.5 + - - +
574C ALA* 3.2 23.7 + - + +
580C LYS 5.6 8.3 - - - +
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Residues in contact with GLN 571 (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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567C GLN 3.5 11.3 + - - +
568C TYR* 3.4 10.9 + - - +
569C PHE 3.0 0.2 - - - -
570C VAL* 1.3 80.9 - - - +
572C TRP* 1.3 55.1 + - - +
574C ALA* 3.7 9.6 - - - +
575C ASP* 2.7 54.2 + - + +
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Residues in contact with TRP 572 (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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460C THR* 4.8 0.7 - - + -
468C ILE* 5.2 0.2 - - + -
476C LEU* 3.8 45.1 - - + -
479C GLU* 3.3 40.4 - - + +
500C VAL* 4.3 7.9 - - + -
550C ILE* 4.1 22.0 - - + -
552C VAL* 4.7 3.6 - - + -
568C TYR 2.9 14.4 + - - +
569C PHE* 2.9 27.2 + + - +
571C GLN* 1.3 76.0 - - - +
573C CYS* 1.3 73.9 + - - +
575C ASP* 3.7 6.3 - - + +
576C ARG* 2.8 58.7 + - + +
578C PHE* 4.3 19.1 - + - -
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Residues in contact with CYS 573 (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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460C THR* 3.5 22.9 - - - -
569C PHE* 2.9 52.9 + - + +
570C VAL* 4.2 4.3 - - - +
572C TRP* 1.3 80.2 - - - +
574C ALA* 1.3 56.9 + - - +
576C ARG* 4.7 1.1 - - - -
577C ASN* 2.7 28.4 + - - -
578C PHE* 2.9 22.2 + - + +
579C THR 3.4 18.4 - - - +
580C LYS* 5.2 4.5 - - - +
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Residues in contact with ALA 574 (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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570C VAL* 3.2 19.3 + - + +
571C GLN* 3.3 12.1 + - - +
573C CYS* 1.3 78.3 - - - +
575C ASP* 1.3 61.8 + - - +
577C ASN* 3.3 22.9 + - - +
578C PHE 5.5 0.7 - - - -
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Residues in contact with ASP 575 (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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571C GLN* 2.7 37.4 + - + +
572C TRP* 3.8 7.4 - - + +
574C ALA* 1.3 74.8 - - - +
576C ARG* 1.3 57.2 + - + +
577C ASN* 3.2 4.6 + - - +
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Residues in contact with ARG 576 (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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468C ILE* 4.6 10.1 - - - +
472C ASP* 6.0 3.6 - - - +
476C LEU* 4.7 17.2 - - - +
479C GLU* 5.4 3.8 - - - +
572C TRP* 2.8 47.1 + - + +
575C ASP* 1.3 75.5 - - + +
577C ASN* 1.3 72.0 + - - +
578C PHE* 3.0 54.0 + - + -
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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