Contacts of the helix formed by residues 534 - 549 (chain C) in PDB entry 4CFE
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 534 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533C GLY* 1.3 76.3 - - - +
535C HIS* 1.3 60.1 + - - +
536C THR* 3.9 5.7 + - - -
537C MET* 3.6 33.7 + - - +
538C ASP* 2.8 37.2 + - - +
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Residues in contact with HIS 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C TYR 5.5 7.3 + - - -
451C VAL* 5.5 7.3 - - + +
452C LYS* 5.0 7.5 + - - +
471C SER* 4.5 15.9 - - - -
472C ILE 3.1 31.6 + - - -
473C ASP* 4.2 16.1 + - - -
534C SER* 1.3 72.5 + - - +
536C THR* 1.3 60.6 + - - +
538C ASP* 3.2 13.2 + - + +
539C PHE* 2.9 29.3 + - + +
255D HIS* 5.6 5.2 + + - -
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Residues in contact with THR 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C SER* 3.3 6.1 + - - -
535C HIS* 1.3 80.4 + - - +
537C MET* 1.3 66.7 + - + +
539C PHE* 3.3 7.2 + - - +
540C PHE* 3.1 35.3 + - + -
255D HIS* 3.8 34.4 + - + +
264D THR* 3.3 32.4 - - + +
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Residues in contact with MET 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C SER* 3.2 28.8 + - - +
536C THR* 1.3 80.5 - - + +
538C ASP* 1.3 60.0 + - - +
540C PHE* 3.3 29.0 + - + +
541C GLU* 2.9 45.4 + - - +
264D THR* 5.0 7.2 - - + +
265D LEU 5.6 1.3 - - - +
266D LEU* 4.1 30.5 - - + -
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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
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442C ARG* 4.4 4.4 + - - +
444C ASN* 3.3 24.4 + - - +
447C THR* 4.9 8.0 + - - +
449C ASN* 5.4 4.5 - - - +
451C VAL* 3.6 34.1 - - + +
533C GLY* 5.5 1.2 - - - -
534C SER 2.8 25.4 + - - +
535C HIS* 3.4 15.5 - - + +
537C MET* 1.3 76.5 - - - +
539C PHE* 1.3 57.5 + - - +
541C GLU* 4.0 10.2 - - - +
542C MET* 3.0 30.8 + - - +
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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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451C VAL* 4.4 5.6 - - + +
452C LYS 5.2 1.8 - - - -
453C MET* 3.9 15.9 - - + -
469C PHE 4.0 10.1 - - - -
470C LYS 3.5 11.4 - - - -
471C SER* 3.5 45.1 - - - -
535C HIS* 2.9 16.9 + - + +
536C THR* 3.6 8.3 - - - +
537C MET 3.2 0.2 - - - -
538C ASP* 1.3 78.4 - - - +
540C PHE* 1.3 82.6 + + - +
542C MET* 3.5 4.0 + - - +
543C CYS* 3.0 57.4 + - - -
237D ASN 3.9 11.9 - - - -
239D LEU* 4.1 12.6 - - + -
253D ALA* 4.3 5.8 - - + -
255D HIS* 4.3 7.9 - + - +
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Residues in contact with PHE 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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536C THR* 3.1 26.6 + - + +
537C MET* 3.3 20.6 + - + +
539C PHE* 1.3 95.0 - + - +
541C GLU* 1.3 57.1 + - - +
543C CYS* 3.3 1.0 + - - -
544C ALA* 2.9 26.6 + - - +
239D LEU* 4.0 7.0 - - + -
251D LEU* 3.3 30.3 - - + +
252D SER* 3.7 8.7 - - - -
253D ALA* 3.4 44.9 - - + -
264D THR* 3.2 28.9 - - - -
266D LEU* 3.7 31.6 - - + -
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Residues in contact with GLU 541 (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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442C ARG* 4.7 12.0 + - - +
444C ASN* 5.2 4.3 + - - -
537C MET* 2.9 27.4 + - - +
538C ASP* 4.1 12.6 - - - +
540C PHE* 1.3 75.7 - - - +
542C MET* 1.3 61.1 + - - +
544C ALA* 3.5 7.1 + - - +
545C SER* 3.3 23.0 + - - -
266D LEU* 4.8 6.8 - - + +
268D LYS* 3.5 36.1 + - + +
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Residues in contact with MET 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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428C PHE* 4.0 23.5 - - + -
440C VAL* 3.6 29.2 - - + -
441C ARG* 3.9 2.2 - - - -
442C ARG* 3.6 38.1 - - + +
451C VAL* 3.3 41.1 - - + +
452C LYS* 4.7 0.9 - - - -
453C MET* 4.4 19.7 - - + +
538C ASP 3.0 18.4 + - - +
539C PHE* 3.8 5.2 - - - +
541C GLU* 1.3 76.0 - - - +
543C CYS* 1.3 62.4 + - - +
545C SER* 2.8 21.3 + - - -
546C LEU* 3.4 10.9 + - - +
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Residues in contact with CYS 543 (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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453C MET* 3.6 17.0 - - - -
469C PHE* 3.6 20.0 - - + -
539C PHE* 3.0 55.6 + - - +
540C PHE* 3.7 5.2 - - - +
542C MET* 1.3 75.8 - - - +
544C ALA* 1.3 60.1 + - - +
546C LEU* 3.2 3.5 + - - +
547C ILE* 2.9 35.9 + - - +
239D LEU* 3.7 21.8 - - + -
251D LEU* 4.3 4.0 - - + -
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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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540C PHE 2.9 16.8 + - - +
541C GLU 3.8 5.4 - - - +
542C MET 3.3 0.2 - - - -
543C CYS* 1.3 78.2 - - - +
545C SER* 1.3 56.9 + - - +
547C ILE* 3.9 1.1 - - - +
548C THR* 2.9 36.8 + - - +
249D MET* 4.2 16.3 - - + +
251D LEU* 4.0 13.9 - - + +
268D LYS* 4.3 23.3 - - + -
270D ILE* 5.4 5.6 - - + -
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Residues in contact with SER 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C LEU* 3.5 23.9 - - - +
428C PHE* 4.1 5.2 - - - -
442C ARG* 4.4 8.6 + - - -
541C GLU 3.3 11.6 + - - -
542C MET* 2.8 23.9 + - - -
544C ALA* 1.3 78.6 - - - +
546C LEU* 1.3 59.0 + - - +
548C THR* 3.7 4.0 + - - -
549C THR* 2.9 31.2 + - - +
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Residues in contact with LEU 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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419C VAL* 4.7 4.5 - - + +
422C ALA* 3.8 33.9 - - + +
423C MET* 4.4 9.2 - - + -
426C LEU* 3.8 4.0 - - + -
428C PHE* 4.2 22.2 - - + -
440C VAL* 5.9 0.2 - - + -
453C MET* 3.6 26.7 - - + -
455C LEU* 3.9 16.8 - - + -
467C LEU* 5.5 2.5 - - + -
469C PHE* 3.9 16.2 - - + -
542C MET 3.4 8.7 + - - +
543C CYS* 3.2 8.6 + - - +
545C SER* 1.3 79.6 + - - +
547C ILE* 1.3 63.5 + - - +
549C THR 3.6 2.4 - - - -
550C LEU* 3.1 30.0 + - + +
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Residues in contact with ILE 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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405C GLY 5.8 2.5 - - - -
406C ILE* 4.9 25.8 - - + -
469C PHE* 3.9 24.2 - - + -
543C CYS 2.9 21.7 + - - +
544C ALA 3.9 4.0 - - - +
546C LEU* 1.3 74.8 - - - +
548C THR* 1.3 67.2 + - - +
550C LEU* 3.3 25.0 + - + +
551C ALA 4.5 1.9 - - - +
239D LEU* 4.2 24.9 - - + -
241D ALA* 5.5 4.7 - - + -
244D ILE* 5.7 2.7 - - + -
249D MET* 3.8 22.0 - - + -
251D LEU* 4.4 14.6 - - + -
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Residues in contact with THR 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 ALA 2.9 21.8 + - - -
545C SER* 3.9 6.1 - - - -
546C LEU 3.4 0.2 - - - -
547C ILE* 1.3 78.2 - - - +
549C THR* 1.3 63.6 + - + +
550C LEU 3.0 5.9 + - - -
551C ALA 4.0 9.7 + - - +
249D MET* 3.9 14.0 - - - +
270D ILE* 3.9 27.4 - - + +
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Residues in contact with THR 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLU* 4.8 2.8 - - - +
421C ARG* 5.6 2.8 + - - -
422C ALA* 3.5 23.5 + - - +
425C GLN* 4.4 19.4 - - - +
426C LEU* 3.7 26.5 - - + +
545C SER* 2.9 19.2 + - - +
546C LEU* 3.6 3.8 + - - -
547C ILE 3.4 0.2 - - - -
548C THR* 1.3 81.4 - - + +
550C LEU* 1.3 58.8 + - - +
551C ALA 4.0 1.8 - - - -
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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