Contacts of the helix formed by residues 450 - 459 (chain A) in PDB entry 5ZF6
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 HIS 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A TYR* 3.6 51.7 - + + -
449A GLY* 1.3 74.3 - - - +
451A GLY* 1.3 60.1 + - - +
453A LEU* 5.0 0.9 - - - -
454A ALA* 3.5 12.6 + - - +
482A SER* 6.4 0.2 - - - -
483A SER* 4.1 7.3 + - - -
484A SER* 3.1 39.8 + - - -
546A LYS* 6.1 2.8 + - + -
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Residues in contact with GLY 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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425A LEU* 3.5 29.2 - - - +
427A TYR* 3.9 18.7 - - - +
449A GLY 3.2 4.0 - - - +
450A HIS* 1.3 75.7 - - - +
452A ALA* 1.3 60.0 + - - +
453A LEU 3.2 1.6 - - - -
454A ALA 3.4 0.5 + - - -
455A GLU* 2.9 29.5 + - - +
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Residues in contact with ALA 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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129A LEU* 4.6 28.3 - - + -
449A GLY 3.7 14.1 + - - +
450A HIS 3.6 0.2 - - - -
451A GLY* 1.3 75.9 - - - +
453A LEU* 1.3 57.8 + - - +
455A GLU* 3.6 10.4 - - - +
456A LYS* 2.9 40.0 + - + +
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Residues in contact with LEU 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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230A GLU* 4.4 5.4 - - - +
449A GLY 3.6 13.5 + - - +
450A HIS* 4.1 0.7 - - - +
451A GLY 3.2 0.6 - - - -
452A ALA* 1.3 77.8 - - - +
454A ALA* 1.3 64.3 + - - +
456A LYS* 3.4 9.3 + - - +
457A ALA* 3.0 21.3 + - - +
484A SER* 3.6 18.6 - - - +
485A MET* 3.6 24.2 - - + -
546A LYS* 4.2 15.0 - - + +
556A ALA* 4.2 19.7 - - + -
557A LEU 4.5 1.6 - - - +
558A GLN* 3.5 51.8 - - + +
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Residues in contact with ALA 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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425A LEU* 3.7 28.0 - - + -
450A HIS 3.5 10.6 + - - +
451A GLY 3.4 1.0 + - - -
453A LEU* 1.3 79.1 - - - +
455A GLU* 1.3 61.7 + - - +
457A ALA* 3.3 9.1 + - - +
458A LEU* 3.2 27.2 + - - +
484A SER* 3.7 22.6 + - - +
485A MET* 5.4 0.7 - - - -
487A SER* 4.0 11.7 - - - -
488A ALA* 4.2 7.1 - - - +
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Residues in contact with GLU 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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423A PHE* 3.9 29.9 - - + +
424A MET* 3.3 11.5 - - - +
425A LEU* 2.9 38.9 + - + +
426A HIS* 5.6 0.9 - - - -
451A GLY 2.9 19.4 + - - +
452A ALA* 3.6 10.6 - - - +
453A LEU 3.2 0.2 - - - -
454A ALA* 1.3 74.3 - - - +
456A LYS* 1.3 59.9 + - + +
458A LEU 3.2 1.7 + - - -
459A TYR* 2.9 34.3 + - + +
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Residues in contact with LYS 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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129A LEU* 6.3 2.5 - - + -
230A GLU* 2.3 42.8 + - - -
231A ALA 3.7 11.1 + - - -
232A SER* 3.6 31.6 - - - -
452A ALA* 2.9 28.8 + - + +
453A LEU* 3.4 10.4 + - - +
455A GLU* 1.3 75.8 - - + +
457A ALA* 1.3 62.1 + - - +
459A TYR* 4.0 7.0 - - - +
460A PRO* 3.4 18.9 - - - +
555A THR 3.7 8.7 - - - +
556A ALA* 3.9 8.3 - - + -
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Residues in contact with ALA 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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453A LEU 3.0 17.0 + - - +
454A ALA* 3.6 6.3 - - - +
455A GLU 3.1 0.4 - - - -
456A LYS* 1.3 77.9 - - - +
458A LEU* 1.3 59.8 + - - +
460A PRO* 3.9 0.2 - - - +
485A MET* 5.3 2.5 - - + -
488A ALA* 4.1 15.5 - - + -
506A VAL* 3.6 11.9 - - + +
548A ALA* 3.8 28.3 - - + -
555A THR* 2.7 31.4 + - - +
556A ALA* 3.7 7.6 - - + +
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Residues in contact with LEU 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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423A PHE* 4.0 20.9 - - + -
425A LEU* 3.8 28.3 - - + -
454A ALA 3.2 10.6 + - - +
455A GLU 3.2 0.4 + - - +
457A ALA* 1.3 76.8 - - - +
459A TYR* 1.3 66.3 + - - +
460A PRO* 3.5 1.1 - - - -
461A VAL* 3.1 19.6 + - + +
462A ILE* 3.3 14.7 + - + +
472A VAL* 5.3 0.4 - - + -
488A ALA* 3.6 24.7 - - - +
491A GLY* 3.9 21.3 - - - +
492A SER* 3.7 15.9 - - - +
495A LEU* 4.6 7.2 - - + -
502A ILE* 6.0 1.1 - - + -
506A VAL* 3.8 24.9 - - + -
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Residues in contact with TYR 459 (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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234A GLU* 3.6 20.6 - - - -
420A ASP* 2.9 36.2 + - + +
421A LYS* 3.0 57.1 + - + +
423A PHE* 4.5 15.3 - + + -
455A GLU* 2.9 20.4 + - + +
456A LYS* 4.0 7.4 - - - +
458A LEU* 1.3 75.0 - - - +
460A PRO* 1.3 74.3 - - + +
461A VAL 3.0 1.0 + - - -
462A ILE* 3.1 15.5 + - - +
464A ARG* 4.1 4.7 + - - -
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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