Contacts of the helix formed by residues 574 - 585 (chain C) 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 ASP 574 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B PRO* 4.2 10.6 - - - +
572C THR* 3.1 9.8 - - - +
573C PRO* 1.3 82.1 - - + +
575C ALA* 1.3 61.0 + - - +
576C PHE 3.6 1.3 - - - -
577C ASP* 3.5 28.3 - - - +
578C LYS* 3.2 38.9 + - + +
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Residues in contact with ALA 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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554C LEU* 3.7 24.5 - - + -
569C LEU* 3.4 30.1 - - + +
570C ALA* 4.0 9.9 - - - +
572C THR* 3.4 15.7 + - - +
573C PRO 3.3 3.6 + - - -
574C ASP* 1.3 75.7 - - - +
576C PHE* 1.3 61.1 + - - +
578C LYS* 3.3 2.6 + - - +
579C VAL* 2.9 34.1 + - - +
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Residues in contact with PHE 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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545C ARG* 3.6 44.2 - - + -
548C LEU* 4.1 14.4 - - + -
549C PRO 3.9 0.4 - - - -
550C LYS* 3.6 62.6 - - + +
553C ILE* 3.9 33.2 - - + -
554C LEU* 3.8 17.4 - - + +
573C PRO 5.0 2.0 + - - +
575C ALA* 1.3 80.2 - - - +
577C ASP* 1.3 68.8 + - - +
579C VAL* 4.6 2.2 - - - +
580C ALA* 3.1 29.4 + - + +
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Residues in contact with ASP 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PRO* 3.5 18.9 - - + +
541C TYR* 2.8 26.4 + - - +
545C ARG* 3.3 30.4 + - - +
573C PRO 5.1 2.7 + - - +
574C ASP* 3.5 26.0 + - - +
575C ALA 3.3 0.6 - - - -
576C PHE* 1.3 86.2 - - - +
578C LYS* 1.3 60.4 + - - +
580C ALA* 4.1 1.6 - - - -
581C LEU* 3.6 7.3 + - - +
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Residues in contact with LYS 578 (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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267B PRO* 3.7 24.9 - - + -
268B ASP 4.9 5.1 + - - +
269B VAL* 4.3 12.5 - - + +
273B GLU* 2.9 42.1 + - - -
569C LEU* 4.7 15.7 - - + +
572C THR* 5.2 9.0 + - - +
574C ASP* 3.2 35.1 + - + +
575C ALA* 3.3 5.5 + - - +
576C PHE 3.2 0.2 - - - -
577C ASP* 1.3 75.8 - - - +
579C VAL* 1.3 64.2 + - - +
580C ALA 3.3 1.3 - - - -
581C LEU* 3.4 2.4 + - - +
582C ILE* 3.1 33.6 + - + +
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Residues in contact with VAL 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.9 20.8 - - + +
281B PHE* 3.6 30.3 - - + -
553C ILE* 3.8 22.9 - - + -
554C LEU* 5.1 5.6 - - + -
557C ILE* 4.8 11.7 - - + -
569C LEU* 3.8 21.1 - - + -
575C ALA 2.9 22.4 + - - +
576C PHE* 4.3 3.1 - - - +
578C LYS* 1.3 75.0 - - - +
580C ALA* 1.3 58.6 + - - +
582C ILE* 3.5 2.1 + - - +
583C LEU* 3.0 32.2 + - + +
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Residues in contact with ALA 580 (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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541C TYR* 4.0 4.9 - - + -
544C PHE* 3.7 6.1 - - + -
545C ARG* 3.9 30.1 - - + -
548C LEU* 4.2 19.7 - - + -
553C ILE* 6.4 0.2 - - - -
576C PHE* 3.1 23.7 + - + +
577C ASP 4.3 2.0 - - - +
579C VAL* 1.3 79.4 - - - +
581C LEU* 1.3 56.7 + - - +
583C LEU* 3.6 4.0 + - - -
584C PHE* 2.9 29.3 + - - +
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Residues in contact with LEU 581 (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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263B MET* 3.7 26.5 - - + -
266B ALA* 4.1 15.9 - - + -
267B PRO* 3.3 30.5 - - + +
269B VAL* 4.0 11.4 - - + -
498B MET* 4.5 1.8 - - + -
541C TYR* 3.6 23.3 - - + +
577C ASP 3.6 12.3 + - - +
578C LYS* 3.4 5.6 + - - +
579C VAL 3.3 0.6 - - - -
580C ALA* 1.3 77.5 - - - +
582C ILE* 1.3 59.9 + - - +
584C PHE* 4.1 7.4 - - + -
585C MET* 3.0 54.0 + - + +
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Residues in contact with ILE 582 (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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269B VAL* 3.7 30.5 - - + -
273B GLU* 3.3 26.2 - - + +
274B PHE* 3.6 45.9 - - + +
277B VAL* 3.7 27.6 - - + -
278B SER* 4.0 10.5 - - - +
569C LEU* 5.3 1.6 - - + -
578C LYS* 3.1 22.9 + - + +
579C VAL 3.9 3.6 - - - +
581C LEU* 1.3 76.4 - - - +
583C LEU* 1.3 62.0 + - + +
584C PHE 3.6 0.2 + - - -
585C MET* 4.4 1.3 - - + -
586C GLN* 3.6 20.3 + - - +
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Residues in contact with LEU 583 (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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277B VAL* 5.8 1.1 - - + +
278B SER* 6.0 1.1 - - - -
281B PHE* 3.9 46.2 - - + -
517C MET* 3.7 29.6 - - + -
520C VAL* 3.3 38.9 - - + +
544C PHE* 4.6 3.6 - - + -
548C LEU* 5.0 9.9 - - + -
553C ILE* 5.4 2.5 - - + -
579C VAL* 3.0 20.5 + - + +
580C ALA* 4.0 3.8 - - - +
582C ILE* 1.3 77.1 - - + +
584C PHE* 1.3 65.4 + - - +
586C GLN* 3.8 33.2 - - - +
587C ALA 4.0 0.3 + - - -
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Residues in contact with PHE 584 (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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263B MET* 5.2 0.2 - - + -
498B MET* 4.7 2.9 - - + -
520C VAL* 5.0 0.2 - - - -
524C LEU* 3.6 22.0 - - + -
537C ILE* 4.1 23.6 - - + -
540C PHE* 3.5 44.9 - + - -
541C TYR* 3.9 27.6 - + + -
544C PHE* 3.8 22.4 - + + -
580C ALA 2.9 19.9 + - - +
581C LEU* 3.3 12.8 + - + +
583C LEU* 1.3 78.0 - - - +
585C MET* 1.3 65.3 + - + +
586C GLN 3.2 0.9 - - - -
587C ALA* 2.9 10.1 + - - +
588C ILE* 2.9 44.3 + - + +
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Residues in contact with MET 585 (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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269B VAL* 4.7 10.5 - - + -
274B PHE* 3.6 35.7 - - + -
495B VAL* 3.7 13.6 - - - +
496B MET* 3.7 38.8 - - + +
498B MET* 3.7 38.6 - - + +
581C LEU* 3.0 36.0 + - + +
582C ILE* 4.6 2.5 - - - -
584C PHE* 1.3 78.0 - - + +
586C GLN* 1.3 57.3 + - - +
588C ILE* 3.7 12.8 - - - +
589C PHE* 3.5 16.8 + - - +
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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