Contacts of the helix formed by residues 407 - 424 (chain C) in PDB entry 4RPP
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 407 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A CYS* 6.4 0.2 - - - -
508A VAL* 5.7 0.2 - - - -
405C THR* 3.8 9.6 - - + +
406C SER* 1.3 80.1 + - - +
408C PRO* 1.3 74.9 - - - +
409C THR* 3.3 19.3 + - - -
410C GLU* 3.3 25.7 + - + +
411C ALA* 3.1 22.7 + - - +
440C GLN* 4.7 7.3 + - - -
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Residues in contact with PRO 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A VAL* 4.7 10.5 - - + -
527A VAL* 3.7 35.7 - - + +
529A PRO* 5.3 12.1 - - + -
406C SER 3.3 10.5 - - - +
407C ASP* 1.3 91.1 - - - +
409C THR* 1.3 53.6 + - - +
411C ALA* 3.3 3.6 + - - +
412C THR* 2.6 37.5 + - - -
523C ASN* 4.6 7.4 - - + -
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Residues in contact with THR 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ASP* 3.3 11.7 + - - -
408C PRO* 1.3 78.9 - - - +
410C GLU* 1.3 57.7 + - - +
412C THR* 3.3 9.3 + - - -
413C ALA* 2.9 27.5 + - + +
437C SER* 4.3 22.9 - - - +
440C GLN* 3.4 20.2 - - + +
523C ASN* 4.9 13.8 + - - +
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Residues in contact with GLU 410 (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 THR* 4.1 19.5 - - + +
407C ASP* 3.3 26.9 + - + +
408C PRO 3.2 0.2 - - - -
409C THR* 1.3 76.9 - - - +
411C ALA* 1.3 60.8 + - - +
413C ALA* 3.0 6.0 + - - +
414C VAL* 2.9 31.6 + - + +
440C GLN* 3.1 44.3 + - - +
443C ARG* 4.6 9.0 + - - +
444C TYR* 3.0 34.4 + - - +
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Residues in contact with ALA 411 (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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419A ALA* 3.9 17.8 - - + +
422A ARG* 5.3 4.3 - - + -
423A CYS* 4.3 27.6 - - + -
525A MET* 4.5 0.2 - - - +
527A VAL* 4.3 17.9 - - + -
405C THR* 5.2 4.8 + - - +
407C ASP 3.1 10.6 + - - +
408C PRO 3.7 7.4 - - - +
410C GLU* 1.3 79.6 - - - +
412C THR* 1.3 61.5 + - - +
414C VAL* 3.4 10.3 + - - +
415C GLY* 3.1 17.8 + - - -
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Residues in contact with THR 412 (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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525A MET* 4.2 11.6 - - + +
527A VAL* 3.4 6.7 - - - +
408C PRO 2.6 20.3 + - - -
409C THR* 3.3 12.6 - - + -
411C ALA* 1.3 74.1 - - - +
413C ALA* 1.3 62.8 + - - +
415C GLY* 3.4 1.9 + - - -
416C ALA* 3.1 21.7 + - - +
512C LEU* 4.4 10.3 - - + -
513C THR 5.3 0.2 - - - +
523C ASN* 3.2 41.6 + - - +
524C THR 3.9 16.4 - - - +
525C MET* 4.1 10.0 - - + +
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Residues in contact with ALA 413 (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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409C THR* 2.9 13.9 + - + +
410C GLU* 3.0 11.9 + - - +
412C THR* 1.3 76.3 - - - +
414C VAL* 1.3 62.6 + - - +
416C ALA* 3.3 7.4 + - - +
417C VAL* 3.1 28.9 + - - +
437C SER 5.0 0.4 - - - +
440C GLN* 4.0 22.7 - - + +
441C VAL* 3.8 26.6 - - + +
444C TYR* 4.4 3.4 - - + -
512C LEU* 4.7 2.7 - - - +
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Residues in contact with VAL 414 (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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418A GLU* 3.9 14.4 - - + +
419A ALA 5.1 0.4 - - - +
422A ARG* 3.2 62.8 - - + +
395C PHE* 5.6 2.5 - - + -
399C ARG* 5.9 2.5 - - + -
405C THR* 5.9 1.8 - - - +
410C GLU* 2.9 20.6 + - + +
411C ALA* 3.6 10.3 - - - +
413C ALA* 1.3 74.0 - - - +
415C GLY* 1.3 65.6 + - - +
417C VAL* 3.2 4.5 + - - +
418C GLU* 3.0 22.2 + - + +
444C TYR* 3.5 22.0 - - + +
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Residues in contact with GLY 415 (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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415A GLY* 3.8 27.5 - - - -
418A GLU* 5.0 0.7 - - - -
419A ALA* 4.8 1.5 - - - +
525A MET* 4.2 6.7 - - - -
411C ALA 3.1 11.2 + - - -
412C THR 3.9 2.7 - - - -
413C ALA 3.4 0.2 - - - -
414C VAL* 1.3 80.2 - - - +
416C ALA* 1.3 56.1 + - - +
418C GLU* 3.7 3.7 - - - +
419C ALA* 2.9 31.7 + - - +
525C MET* 3.6 8.3 - - - +
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Residues in contact with ALA 416 (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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412C THR 3.1 13.9 + - - +
413C ALA 3.4 9.4 - - - +
414C VAL 3.1 0.2 - - - -
415C GLY* 1.3 77.6 - - - +
417C VAL* 1.3 58.4 + - + +
420C SER* 3.0 24.9 + - - -
428C ILE* 4.3 9.6 - - + -
441C VAL* 5.3 0.9 - - + -
510C ILE* 3.3 18.0 - - + +
512C LEU* 3.8 34.5 - - + -
525C MET* 3.6 10.7 - - - -
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Residues in contact with VAL 417 (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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395C PHE* 3.5 28.7 - - + -
413C ALA 3.1 17.9 + - - +
414C VAL 3.8 3.6 - - - +
416C ALA* 1.3 71.7 - - - +
418C GLU* 1.3 65.9 + - - +
420C SER* 2.5 22.9 + - - -
421C PHE* 3.2 21.1 - - + -
428C ILE* 4.3 1.6 - - - -
441C VAL* 3.6 37.0 - - + +
444C TYR* 4.1 16.2 - - + -
446C PRO* 3.9 16.4 - - + -
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Residues in contact with GLU 418 (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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399A ARG* 2.7 36.4 + - - -
414A VAL* 3.8 15.8 - - + +
415A GLY* 4.7 0.9 - - - -
418A GLU* 3.5 41.8 - - + +
395C PHE* 3.4 23.3 - - + -
399C ARG* 3.9 0.5 + - - -
414C VAL* 3.0 17.0 + - + +
415C GLY 3.7 4.0 - - - +
417C VAL* 1.3 76.7 - - - +
419C ALA* 1.3 63.0 + - - +
421C PHE* 3.2 15.1 + - - +
422C ARG* 3.2 27.9 + - - +
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Residues in contact with ALA 419 (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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411A ALA* 3.8 30.1 - - + +
414A VAL* 5.1 2.0 - - - -
415A GLY* 4.8 1.1 - - - -
415C GLY 2.9 18.8 + - - +
418C GLU* 1.3 77.6 - - - +
420C SER* 1.3 63.0 + - - +
422C ARG* 3.1 16.9 + - - +
423C CYS* 3.1 19.1 + - - +
510C ILE* 3.7 18.4 - - + -
525C MET* 4.4 10.1 - - + -
527C VAL* 5.2 1.3 - - + -
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Residues in contact with SER 420 (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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416C ALA 3.0 15.5 + - - -
417C VAL* 2.5 24.8 + - - -
419C ALA* 1.3 77.4 - - - +
421C PHE* 1.3 58.6 + - - +
424C CYS* 3.1 23.6 + - - -
425C SER* 3.2 25.6 + - - -
428C ILE* 3.7 22.4 - - - +
446C PRO* 4.0 9.7 - - - +
447C ARG 5.2 0.7 + - - -
448C ALA* 4.6 8.3 - - - +
510C ILE* 3.4 5.8 - - - +
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Residues in contact with PHE 421 (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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404A ILE* 4.3 6.6 - - - +
391C HIS* 4.2 16.8 - - + -
392C LEU* 5.3 2.9 - - + -
395C PHE* 3.5 52.3 - + + -
417C VAL* 3.2 28.9 + - + -
418C GLU* 3.2 7.7 + - - +
420C SER* 1.3 80.7 + - - +
422C ARG* 1.3 62.8 + - - +
423C CYS 3.4 0.5 + - - -
424C CYS* 3.7 15.3 + - - +
445C ARG 3.8 9.6 - - - -
446C PRO* 3.9 4.7 - - + -
447C ARG* 3.5 56.8 + - + +
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Residues in contact with ARG 422 (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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399A ARG* 3.4 45.2 + - - +
402A ALA* 3.3 25.7 + - - +
403A PRO 3.5 20.9 - - - -
404A ILE* 3.2 12.8 - - - +
405A THR* 3.2 30.6 + - + +
411A ALA* 5.2 3.8 - - + -
414A VAL* 3.3 44.9 - - + +
444A TYR* 3.9 10.7 + - - -
418C GLU* 3.2 22.7 + - - +
419C ALA* 3.1 13.4 + - - +
421C PHE* 1.3 79.5 - - - +
423C CYS* 1.3 57.8 + - + +
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Residues in contact with CYS 423 (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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404A ILE* 3.9 10.5 - - - +
405A THR* 3.9 15.3 - - - +
406A SER* 4.4 13.5 - - - +
411A ALA* 4.3 15.5 - - + -
419C ALA 3.1 21.2 + - - +
422C ARG* 1.3 77.5 - - - +
424C CYS* 1.3 74.8 + - - +
425C SER* 2.9 30.4 - - - -
508C VAL* 3.8 27.5 - - + +
510C ILE* 4.8 3.6 - - - -
527C VAL* 5.2 0.4 - - - -
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Residues in contact with CYS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ILE* 3.7 31.2 - - + -
420C SER 3.1 9.8 + - - -
421C PHE 3.7 6.4 + - - -
422C ARG 3.6 0.4 - - - -
423C CYS* 1.3 81.7 - - - +
425C SER* 1.3 64.9 + - - +
426C GLY* 3.7 1.2 + - - -
447C ARG* 4.8 15.9 - - - +
508C VAL* 4.5 2.1 + - - +
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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