Contacts of the helix formed by residues 419 - 431 (chain C) in PDB entry 4P5O
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 PRO 419 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418C SER* 1.4 84.1 - - - +
420C GLU* 1.3 66.7 + - - +
421C GLU 3.2 0.4 - - - -
422C LEU* 3.8 4.0 - - + -
423C ALA* 3.1 22.0 + - - +
456C ILE* 3.4 31.1 - - + -
458C ASP* 3.8 19.1 - - + +
461C VAL* 3.8 23.3 - - + -
462C PHE* 3.5 16.9 - - + -
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Residues in contact with GLU 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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418C SER 2.8 4.4 + - - +
419C PRO* 1.3 79.6 - - - +
421C GLU* 1.3 59.5 - - + +
423C ALA* 3.3 5.2 + - - +
424C ARG* 2.6 63.8 + - - +
461C VAL* 4.1 9.0 - - + +
465C PHE* 3.6 32.9 - - + -
696C GLN* 3.0 25.2 + - - +
700C HIS* 3.1 19.7 + - + -
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Residues in contact with GLU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LYS* 2.6 39.3 - - + +
418C SER 2.6 19.8 + - - +
420C GLU* 1.3 75.2 - - + +
422C LEU* 1.3 58.8 + - - +
424C ARG* 3.3 13.9 + - + +
425C TYR* 2.9 28.6 + - - +
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Residues in contact with LEU 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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417C LYS* 3.9 31.2 - - + +
418C SER* 3.6 4.6 + - - -
419C PRO* 4.0 12.8 - - + +
420C GLU 3.3 0.4 - - - -
421C GLU* 1.3 77.7 - - - +
423C ALA* 1.3 57.8 + - - +
425C TYR* 3.1 9.7 - - + +
426C CYS* 3.0 26.3 + - - +
449C VAL* 3.9 52.5 - - + +
452C LYS* 4.0 17.9 - - + -
453C PHE* 4.0 8.7 - - + +
456C ILE* 3.9 22.0 - - + -
462C PHE* 4.0 9.4 - - + -
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Residues in contact with ALA 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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419C PRO 3.1 15.2 + - - +
420C GLU 3.4 8.3 - - - +
422C LEU* 1.3 74.7 - - - +
424C ARG* 1.3 67.0 + - - +
426C CYS* 3.1 6.5 + - - +
427C ASP* 2.9 20.3 + - - +
462C PHE* 3.5 25.5 - - + +
465C PHE* 3.9 26.5 - - + -
466C TYR* 4.2 9.2 - - - +
469C MET* 3.9 5.7 - - - +
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Residues in contact with ARG 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C GLU* 2.6 52.9 + - - +
421C GLU* 3.6 15.7 - - + +
423C ALA* 1.3 75.6 - - - +
425C TYR* 1.3 55.7 + - - +
427C ASP* 3.2 4.7 - - - +
428C SER* 2.9 27.5 + - - -
431C LYS* 4.3 1.2 + - - -
465C PHE* 4.1 13.1 - - + -
469C MET* 3.3 34.8 - - + +
692C GLN* 5.7 4.0 + - - +
696C GLN* 3.2 19.6 + - - +
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Residues in contact with TYR 425 (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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417C LYS* 4.1 24.2 - - + -
421C GLU 2.9 12.7 + - - +
422C LEU* 3.1 23.1 - - + +
424C ARG* 1.3 76.4 - - - +
426C CYS* 1.3 55.8 + - - +
428C SER* 2.9 27.3 + - - -
429C LEU* 2.9 16.5 + - + +
445C THR* 3.7 24.0 - - + +
448C GLN* 5.0 6.9 + - + -
449C VAL* 3.7 32.3 - - + -
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Residues in contact with CYS 426 (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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422C LEU 3.0 12.5 + - - +
423C ALA* 3.1 8.3 + - - +
425C TYR* 1.3 72.2 - - - +
427C ASP* 1.3 66.1 + - - +
429C LEU* 3.3 6.8 + - - +
430C LEU* 3.0 30.7 + - + +
446C LEU* 4.1 11.2 - - + -
449C VAL* 3.4 43.1 - - - -
462C PHE* 4.7 3.4 - - - -
466C TYR* 3.8 20.4 - - + -
473C ARG* 4.7 1.3 - - - -
488C MET* 3.9 17.0 - - - -
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Residues in contact with ASP 427 (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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423C ALA 2.9 12.2 + - - +
424C ARG 3.2 10.3 - - - +
426C CYS* 1.3 75.0 - - - +
428C SER* 1.3 52.7 + - - +
430C LEU* 3.1 2.6 + - - +
431C LYS* 2.6 71.6 + - - +
466C TYR* 5.2 0.4 - - - -
469C MET* 3.7 35.9 - - + +
473C ARG* 3.1 40.0 + - - +
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Residues in contact with SER 428 (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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424C ARG 2.9 14.2 + - - -
425C TYR* 2.9 17.4 + - - -
427C ASP* 1.3 72.0 - - - +
429C LEU* 1.3 63.1 + - - +
430C LEU 3.4 0.2 + - - -
431C LYS* 2.8 30.9 + - - +
433C SER* 5.7 2.8 - - - -
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Residues in contact with LEU 429 (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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425C TYR* 2.9 14.0 + - + +
426C CYS* 3.7 8.3 - - - +
428C SER* 1.3 77.8 - - - +
430C LEU* 1.3 69.8 + - + +
431C LYS 3.6 4.7 + - - +
437C PRO* 4.2 14.2 - - + +
441C GLU* 4.8 1.3 - - + +
442C LEU* 3.6 38.3 - - + +
445C THR* 3.2 51.1 - - + +
446C LEU* 3.6 26.9 - - + -
480C ALA* 5.0 0.7 - - - +
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Residues in contact with LEU 430 (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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426C CYS* 3.0 19.8 + - + +
427C ASP 3.9 0.7 - - - +
429C LEU* 1.3 98.3 - - + +
431C LYS* 1.3 60.4 + - - +
442C LEU* 4.2 5.8 - - + -
446C LEU* 4.4 10.5 - - + -
466C TYR* 3.9 10.8 - - + +
473C ARG* 3.5 22.9 - - - +
479C SER* 3.8 5.7 - - - -
480C ALA* 3.0 27.6 + - - +
481C SER 4.5 2.4 + - - +
484C ALA* 4.2 20.2 - - + -
485C GLU* 3.0 45.0 - - + +
488C MET* 4.8 4.7 - - + -
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Residues in contact with LYS 431 (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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424C ARG 4.3 1.0 + - - -
427C ASP* 2.6 48.8 + - - +
428C SER* 2.8 44.7 + - - +
429C LEU 3.4 5.1 - - - +
430C LEU* 1.3 81.1 - - - +
432C LYS* 1.3 70.0 + - - +
433C SER* 3.3 8.4 + - - -
437C PRO* 5.4 1.6 - - - +
473C ARG* 4.0 9.0 - - + +
478C ASN* 3.5 19.7 - - - +
480C ALA* 3.5 9.6 - - - +
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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