Contacts of the helix formed by residues 535 - 548 (chain C) in PDB entry 4L28
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 THR 535 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ARG* 5.6 1.8 + - - +
445C GLN* 5.7 2.5 - - - +
503C LEU* 3.9 7.1 - - - +
507C HIS* 3.4 42.3 + - + +
508C PHE* 3.8 22.9 - - + -
533C VAL* 5.0 2.5 - - + -
534C VAL* 1.3 82.0 - - - +
536C ALA* 1.3 65.8 + - - +
537C ILE* 3.4 16.4 + - - +
538C ASP* 3.0 28.6 + - - +
539C LEU* 3.3 10.4 + - - +
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Residues in contact with ALA 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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189A VAL* 3.9 37.5 - - + -
206A VAL* 6.0 0.4 - - + -
210A LEU* 5.0 5.1 - - + +
503C LEU* 3.6 27.7 - - + +
507C HIS* 4.4 2.9 + - + -
535C THR* 1.3 76.2 - - - +
537C ILE* 1.3 60.6 + - + +
539C LEU* 3.2 5.6 + - + +
540C LEU* 2.9 29.0 + - - +
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Residues in contact with ILE 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 4.2 16.8 - - + +
209A ARG* 3.3 68.0 - - + +
210A LEU* 3.9 19.5 - - + -
213A GLU* 5.5 4.5 - - + -
507C HIS* 5.9 1.6 - - - +
535C THR* 3.1 9.3 + - - +
536C ALA* 1.3 79.5 - - + +
538C ASP* 1.3 59.0 + - - +
540C LEU* 3.3 8.4 + - + +
541C ASN* 2.9 43.2 + - - +
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Residues in contact with ASP 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 4.8 3.3 - - + +
445C GLN* 5.8 1.4 + - - -
533C VAL 3.8 7.0 - - - +
534C VAL* 3.6 15.8 - - + -
535C THR* 3.0 37.3 + - - +
537C ILE* 1.3 78.6 - - - +
539C LEU* 1.3 65.1 + - - +
541C ASN* 3.1 13.8 + - - +
542C PHE* 2.9 23.4 + - - +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C TRP* 4.1 34.3 - - + -
417C LEU* 4.4 8.1 - - + -
496C LEU* 4.0 33.0 - - + +
499C LEU* 4.0 21.3 - - + -
500C SER* 4.4 12.8 - - - +
503C LEU* 4.2 13.0 - - + -
534C VAL* 4.6 0.8 - - - +
535C THR 3.3 8.7 + - - +
536C ALA* 3.2 8.9 + - - +
538C ASP* 1.3 78.8 - - - +
540C LEU* 1.3 63.5 + - - +
542C PHE* 3.3 4.1 + - + +
543C VAL* 3.0 28.0 + - + +
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 5.7 5.2 - - - +
210A LEU* 3.8 27.1 - - + +
213A GLU* 3.8 29.6 - - + +
214A ILE* 3.9 27.8 - - + -
536C ALA 2.9 17.3 + - - +
537C ILE* 3.5 7.6 - - + +
539C LEU* 1.3 79.9 - - - +
541C ASN* 1.3 57.4 + - - +
543C VAL* 3.3 8.7 + - + -
544C ALA* 2.8 39.9 + - + +
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Residues in contact with ASN 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU* 3.5 33.1 - - - +
537C ILE* 2.9 35.6 + - - +
538C ASP* 3.1 16.1 + - - +
540C LEU* 1.3 78.3 - - - +
542C PHE* 1.3 57.2 + - - +
544C ALA* 3.8 4.3 - - - +
545C ALA* 2.9 31.2 + - - +
548C ARG* 4.7 1.7 + - - -
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Residues in contact with PHE 542 (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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408C TRP* 4.6 6.1 - + - -
409C TRP* 5.1 0.2 - - + -
412C LEU* 4.1 20.9 - - + -
416C GLU* 3.1 34.8 - - + -
417C LEU* 3.5 37.7 - - + +
496C LEU* 3.8 23.3 - - + -
538C ASP 2.9 9.2 + - - +
539C LEU* 3.6 4.7 - - + +
541C ASN* 1.3 75.3 - - - +
543C VAL* 1.3 75.1 + - + +
545C ALA* 3.2 6.5 + - + +
546C GLN* 2.9 60.0 + - + +
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Residues in contact with VAL 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TRP* 4.2 10.9 - - + +
409C TRP* 3.5 54.7 - - + +
539C LEU* 3.0 24.2 + - + +
540C LEU* 3.8 10.3 - - + +
542C PHE* 1.3 85.1 - - + +
544C ALA* 1.3 60.3 + - + +
546C GLN* 3.0 8.7 + - - +
547C GLU* 2.9 26.0 + - + +
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Residues in contact with ALA 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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213A GLU* 4.9 18.6 - - + +
540C LEU* 2.8 27.8 + - + +
541C ASN* 4.0 4.7 - - - +
543C VAL* 1.3 76.6 - - - +
545C ALA* 1.3 64.7 + - - +
547C GLU* 3.1 22.6 - - + +
548C ARG* 3.4 24.3 + - - +
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Residues in contact with ALA 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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541C ASN 2.9 19.4 + - - +
542C PHE* 3.2 6.3 + - + +
544C ALA* 1.3 75.2 - - - +
546C GLN* 1.3 62.7 + - + +
547C GLU 3.0 0.2 - - - -
548C ARG* 2.9 49.4 + - - +
549C ASP* 5.0 0.3 - - - +
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Residues in contact with GLN 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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408C TRP* 3.4 34.6 - - + -
542C PHE* 2.9 48.4 + - + +
543C VAL 3.3 8.1 - - - +
545C ALA* 1.3 78.8 - - - +
547C GLU* 1.3 61.7 + - - +
548C ARG 3.3 0.5 + - - -
549C ASP* 3.9 16.6 + - - +
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Residues in contact with GLU 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TRP* 5.8 1.3 - - - -
543C VAL* 2.9 10.3 + - + +
544C ALA* 3.1 22.4 - - - +
545C ALA 3.0 0.2 - - - -
546C GLN* 1.3 78.8 - - - +
548C ARG* 1.3 56.9 + - + +
549C ASP 3.1 10.9 + - - +
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Residues in contact with ARG 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU* 5.6 4.9 + - - -
541C ASN 4.7 1.6 + - - -
544C ALA* 3.4 25.1 + - - +
545C ALA* 2.9 40.1 + - - +
547C GLU* 1.3 76.0 - - + +
549C ASP* 1.3 64.0 + - - +
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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