Contacts of the helix formed by residues 448 - 458 (chain A) in PDB entry 4PKO
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 GLU 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ILE* 3.9 24.7 - - + -
423A ALA* 5.7 2.2 - - + -
444A LEU 4.2 8.7 - - - +
445A ARG* 3.6 22.6 - - - +
446A ALA 3.1 0.2 - - - -
447A MET* 1.3 80.0 - - - +
449A ALA* 1.3 64.4 + - - +
450A PRO 3.3 0.4 - - - -
451A LEU* 3.1 15.4 + - - +
452A ARG* 3.1 49.7 + - + +
466A ALA* 6.0 0.7 - - + -
470A LYS* 3.7 27.0 + - - +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.9 18.1 - - + +
98A ALA* 3.6 24.0 - - + -
445A ARG 4.3 1.6 + - - +
446A ALA* 3.0 19.3 + - - +
448A GLU* 1.3 77.3 - - - +
450A PRO* 1.3 66.6 - - + +
452A ARG* 3.2 9.2 + - - +
453A GLN* 3.0 26.2 + - - +
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Residues in contact with PRO 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.4 8.0 - - + +
91A THR* 3.6 28.7 - - + +
94A VAL* 4.3 9.0 - - + -
95A LEU* 3.2 33.7 - - + +
416A GLY* 4.6 12.8 - - - -
419A LEU* 4.8 7.0 - - + -
447A MET 3.3 16.8 - - - +
448A GLU 3.4 0.4 - - - -
449A ALA* 1.3 96.9 - - + +
451A LEU* 1.3 61.1 + - - +
454A ILE* 3.0 28.4 + - + +
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Residues in contact with LEU 451 (chain A).
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* 3.3 23.7 + - - +
417A VAL* 4.6 5.6 - - + +
420A ILE* 3.1 36.2 - - + +
448A GLU 3.1 3.8 + - - +
450A PRO* 1.3 78.8 - - - +
452A ARG* 1.3 69.4 + - + +
454A ILE* 3.0 8.9 + - + +
455A VAL* 3.0 41.0 + - + +
462A PRO 5.4 0.2 - - - +
465A VAL* 4.9 2.0 - - + -
466A ALA* 4.3 25.8 - - + +
469A VAL* 4.4 23.8 - - + -
478A TYR* 5.4 9.2 - - + +
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Residues in contact with ARG 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A GLU* 3.1 49.2 + - + +
449A ALA* 3.8 7.6 - - - +
451A LEU* 1.3 88.6 - - + +
453A GLN* 1.3 57.0 + - - +
455A VAL* 3.6 1.7 + - - -
456A LEU* 2.8 29.9 + - - +
462A PRO* 3.7 23.8 - - + +
463A SER* 3.1 39.4 + - - +
466A ALA* 3.3 24.6 - - + +
470A LYS* 4.3 6.3 - - - +
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Residues in contact with GLN 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.3 57.4 - - + +
31A LEU* 3.4 19.7 - - + -
94A VAL* 3.9 13.9 - - + -
449A ALA 3.0 12.5 + - - +
451A LEU 3.1 0.2 - - - -
452A ARG* 1.3 76.7 - - - +
454A ILE* 1.3 55.7 + - - +
456A LEU* 3.6 29.0 - - - +
457A ASN* 2.8 61.2 + - - +
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Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 19.9 - - + +
32A GLY* 4.3 7.4 - - - -
33A PRO* 4.0 15.9 - - + -
34A LYS* 5.3 0.3 - - - +
91A THR* 6.4 1.3 - - + -
415A GLY* 3.9 35.4 - - - +
416A GLY* 4.5 1.3 - - - +
450A PRO* 3.0 19.1 - - + +
451A LEU* 3.0 7.1 + - + +
453A GLN* 1.3 78.6 - - - +
455A VAL* 1.3 63.1 + - + +
457A ASN* 3.4 10.6 + - - +
458A CYS* 3.3 20.5 + - - -
478A TYR* 6.1 0.7 - - + -
480A ALA* 3.7 26.2 - - + -
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.0 28.2 + - + +
452A ARG 3.8 7.0 - - - +
454A ILE* 1.3 76.4 - - + +
456A LEU* 1.3 59.6 + - - +
458A CYS* 2.9 28.6 + - - +
460A GLU* 3.3 32.7 + - + +
461A GLU 3.7 3.6 - - - +
462A PRO* 3.7 24.9 - - + -
465A VAL* 3.6 31.2 - - + -
478A TYR* 4.2 14.6 - - + -
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 5.5 1.3 - - - +
452A ARG 2.8 19.5 + - - +
453A GLN* 3.1 30.5 + - + +
455A VAL* 1.3 76.8 - - - +
457A ASN* 1.3 64.2 + - - +
459A GLY* 3.0 18.4 + - - -
460A GLU 4.0 10.1 - - - +
462A PRO* 4.0 15.7 - - + -
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Residues in contact with ASN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS 3.2 22.0 + - - +
29A VAL* 4.0 16.3 - - - +
31A LEU* 2.7 33.6 + - - +
34A LYS* 3.9 22.2 - - - +
35A GLY* 4.4 1.8 - - - +
36A ARG* 4.9 12.7 + - + +
453A GLN* 2.8 31.8 + - - +
454A ILE 3.7 5.8 - - - +
456A LEU* 1.3 81.1 - - - +
458A CYS* 1.3 59.9 + - - +
459A GLY 3.2 1.0 + - - -
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Residues in contact with CYS 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 3.4 41.6 + - + +
454A ILE 3.3 17.0 - - - -
455A VAL* 2.9 12.4 + - - +
457A ASN* 1.3 77.7 - - - +
459A GLY* 1.3 61.9 + - - +
460A GLU* 3.5 19.3 - - + +
478A TYR* 5.1 3.8 - - + -
480A ALA* 3.8 23.6 - - - -
483A GLU* 4.4 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