Contacts of the helix formed by residues 447 - 458 (chain A) in PDB entry 5OF4
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 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A THR 4.4 4.7 - - - +
446A ILE* 1.4 90.0 - - + +
448A ALA* 1.3 60.5 + - - +
449A LYS* 3.4 6.1 - - + +
450A MET* 3.2 23.5 + - + +
451A PHE* 3.0 27.4 + - - -
473A GLU* 4.4 15.3 - - - +
475A ASP* 5.6 0.2 - - - -
480A LEU* 5.7 0.2 - - - -
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Residues in contact with ALA 448 (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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447A PRO* 1.3 70.5 - - - +
449A LYS* 1.3 63.3 + - + +
451A PHE* 3.2 10.4 + - - +
452A ARG* 2.9 35.1 + - + +
473A GLU* 4.9 3.6 + - - -
475A ASP* 4.6 16.3 + - + +
478A VAL* 6.0 5.8 - - + -
480A LEU* 5.0 10.3 - - + -
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Residues in contact with LYS 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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447A PRO* 3.4 5.1 - - + +
448A ALA* 1.3 76.7 - - + +
450A MET* 1.3 58.3 + - - +
452A ARG* 3.1 50.7 + - - +
453A ARG* 3.0 56.9 + - - +
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Residues in contact with MET 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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410A TYR* 3.7 32.1 - - + -
411A SER* 3.5 33.7 - - - +
412A MET* 3.6 11.9 - - + +
446A ILE* 3.8 16.4 - - + -
447A PRO* 3.2 30.7 + - + +
449A LYS* 1.3 79.6 - - - +
451A PHE* 1.3 58.3 + - - +
453A ARG* 3.2 37.4 + - + +
454A VAL* 2.8 33.8 + - + +
457A ILE* 5.6 0.4 - - + -
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Residues in contact with PHE 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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440A LEU* 5.3 6.7 - - + -
443A VAL* 3.6 27.6 - - + -
446A ILE* 3.4 35.9 - - + -
447A PRO 3.0 24.8 + - - -
448A ALA 3.2 7.4 + - - +
450A MET* 1.3 73.5 - - - +
452A ARG* 1.3 63.3 - - - +
454A VAL* 3.6 19.3 - - + +
455A LEU* 3.0 29.7 + - - +
480A LEU* 3.5 41.5 - - + -
483A LEU* 3.6 33.2 - - + +
484A ILE* 5.1 14.6 - - + -
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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 ALA* 2.9 20.0 + - - +
449A LYS* 3.1 55.5 - - - +
451A PHE* 1.3 75.7 - - - +
453A ARG* 1.3 54.8 + - + +
455A LEU* 3.3 18.4 - - + +
456A THR* 2.6 37.7 + - - +
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Residues in contact with ARG 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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411A SER 4.3 2.7 - - - -
412A MET* 3.4 45.8 + - - +
413A LEU 4.8 0.2 - - - +
414A GLY 5.8 1.3 - - - +
449A LYS* 3.0 42.8 + - - +
450A MET* 3.2 43.8 + - + +
452A ARG* 1.3 76.2 - - + +
454A VAL* 1.3 58.2 + - - +
456A THR* 4.0 7.0 - - + +
457A ILE* 2.9 44.6 + - + +
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Residues in contact with VAL 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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364A LEU* 5.9 2.2 - - + -
410A TYR* 4.7 24.9 - - + -
438A MET* 4.0 26.9 - - + -
440A LEU* 5.6 4.9 - - + -
446A ILE* 5.3 2.5 - - + -
450A MET* 2.8 27.3 + - + +
451A PHE* 3.2 26.6 + - + +
453A ARG* 1.3 69.5 - - - +
455A LEU* 1.3 64.9 + - + +
457A ILE* 5.1 0.2 - - - -
458A VAL* 2.7 46.6 + - + +
463A LYS* 5.3 9.6 - - - +
483A LEU* 5.8 1.8 - - + -
484A ILE* 6.6 0.2 - - + -
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Residues in contact with LEU 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 PHE 3.0 18.8 + - - +
452A ARG* 3.3 26.7 - - + +
454A VAL* 1.3 81.1 - - + +
456A THR* 1.3 66.9 + - - +
458A VAL 3.7 11.4 - - - +
459A GLN* 4.6 6.2 + - - +
463A LYS* 6.0 2.5 - - - +
482A PHE* 6.3 0.2 - - + -
483A LEU* 3.7 34.3 - - + -
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Residues in contact with THR 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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431A LYS* 5.1 0.3 + - - -
452A ARG* 2.6 25.2 + - - +
453A ARG* 3.7 10.8 - - + +
454A VAL 3.2 0.2 - - - -
455A LEU* 1.3 85.8 - - - +
457A ILE* 1.3 68.4 + - + +
459A GLN* 3.8 16.1 + - - -
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Residues in contact with ILE 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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411A SER* 3.4 38.8 - - - +
426A VAL* 5.8 3.8 - - + -
427A MET* 3.8 25.4 - - + -
430A LEU* 3.4 16.5 - - + +
431A LYS* 2.5 34.5 + - - +
450A MET* 5.6 0.4 - - + -
453A ARG* 2.9 31.1 + - + +
454A VAL* 5.1 0.2 - - - -
456A THR* 1.3 87.9 - - + +
458A VAL* 1.3 68.9 + - + +
459A GLN* 3.5 0.3 + - - +
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Residues in contact with VAL 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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362A LEU* 4.8 5.2 - - + -
364A LEU* 5.7 9.4 - - + -
430A LEU* 3.7 23.8 - - + -
434A GLU* 3.6 20.4 - - - +
438A MET* 3.6 40.7 - - + +
454A VAL* 2.7 37.8 + - + +
455A LEU* 3.7 12.0 - - - +
457A ILE* 1.3 76.5 - - + +
459A GLN* 1.3 62.0 + - - +
460A ALA* 4.0 4.1 + - + -
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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