Contacts of the helix formed by residues 452 - 463 (chain A) in PDB entry 4CCZ
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 ASN 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A ASP* 5.4 1.3 - - - +
425A PRO* 5.7 3.4 - - - +
450A SER* 2.8 18.4 + - - +
451A SER* 1.3 83.0 - - - +
453A PHE* 1.3 64.7 + - - +
454A ALA* 2.9 25.9 + - - +
455A VAL* 3.0 26.3 + - + +
456A ILE* 3.2 8.6 + - - +
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Residues in contact with PHE 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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451A SER 4.1 2.0 + - - -
452A ASN* 1.3 72.8 + - - +
454A ALA* 1.3 53.3 + - - +
456A ILE* 3.2 22.5 + - + +
457A GLU* 2.7 53.4 + - + +
460A LEU* 5.8 0.4 - - + -
471A SER 5.4 0.9 - - - -
472A ILE* 4.3 8.1 - - + -
484A LYS* 3.6 70.0 - - + +
487A LYS* 3.7 32.8 - - + -
488A ILE* 3.9 21.5 - - + -
491A TYR* 5.7 2.2 - + - -
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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 PRO* 4.5 14.0 - - + +
452A ASN* 2.9 16.1 + - - +
453A PHE* 1.3 73.9 - - - +
455A VAL* 1.3 59.0 + - - +
457A GLU* 3.8 12.4 - - - +
458A ALA* 3.0 26.5 + - - +
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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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417A MET* 5.4 1.3 - - + -
418A ASP* 4.4 7.2 - - - +
424A GLY* 3.8 11.0 - - - +
425A PRO* 3.7 27.8 - - + -
428A MET* 3.5 41.3 - - + +
450A SER* 3.3 27.6 - - - +
452A ASN* 3.0 18.3 + - + +
454A ALA* 1.3 74.5 - - - +
456A ILE* 1.3 68.2 + - - +
458A ALA* 3.0 7.7 + - - +
459A GLY* 3.0 17.5 + - - -
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Residues in contact with ILE 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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448A ILE* 3.2 38.7 - - + +
450A SER 3.6 17.5 - - - +
452A ASN 3.2 11.4 + - - +
453A PHE* 3.2 28.2 + - + +
455A VAL* 1.3 79.7 - - - +
457A GLU* 1.3 64.6 + - - +
459A GLY* 3.0 10.0 + - - -
460A LEU* 3.0 20.8 + - + +
469A VAL* 3.5 34.3 - - + -
470A ASN 3.5 19.7 - - - +
471A SER 4.9 4.7 - - - +
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Residues in contact with GLU 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 PHE* 2.7 40.9 + - + +
454A ALA* 3.8 11.0 - - - +
456A ILE* 1.3 72.5 - - - +
458A ALA* 1.3 61.6 + - - +
460A LEU* 3.6 12.0 + - - +
461A LYS* 3.3 39.4 + - - +
487A LYS* 3.7 27.6 + - - +
491A TYR* 3.1 35.8 + - + +
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Residues in contact with ALA 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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425A PRO* 3.8 21.8 - - + +
428A MET* 4.8 1.1 - - + -
429A THR* 3.7 18.4 - - - +
454A ALA 3.0 18.3 + - - +
455A VAL 3.0 5.6 + - - +
457A GLU* 1.3 76.8 - - - +
459A GLY* 1.3 61.7 + - - +
461A LYS* 3.4 13.4 + - - +
462A CYS* 3.3 28.0 + - - -
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Residues in contact with GLY 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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428A MET* 3.8 21.2 - - - +
432A CYS* 4.3 10.8 - - - -
448A ILE* 4.4 14.3 - - - +
455A VAL 3.0 6.3 + - - -
456A ILE 3.0 7.3 + - - -
458A ALA* 1.3 75.4 - - - +
460A LEU* 1.3 63.2 + - - +
462A CYS* 3.1 5.6 + - - +
463A CYS* 3.0 25.5 + - - +
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Residues in contact with LEU 460 (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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169A PHE* 5.3 2.3 - - - -
203A LYS* 4.6 4.9 + - - -
448A ILE* 4.6 3.6 - - + +
453A PHE* 5.8 1.1 - - + -
456A ILE* 3.0 25.5 + - + +
457A GLU* 3.8 9.0 - - - +
458A ALA 3.3 0.2 - - - -
459A GLY* 1.3 73.5 - - - +
461A LYS* 1.3 64.0 + - - +
463A CYS* 3.3 22.9 + - - +
467A CYS* 4.4 16.4 - - + -
469A VAL* 3.7 34.1 - - + -
488A ILE* 4.8 7.9 - - + -
491A TYR* 3.5 49.2 - - + -
493A ALA* 3.7 16.6 - - + -
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Residues in contact with LYS 461 (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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153A LEU* 5.7 3.1 - - - +
169A PHE* 3.7 48.9 - - + +
170A ASP* 3.2 38.0 + - - +
200A ALA* 5.0 7.6 - - - +
457A GLU* 3.3 26.7 + - - +
458A ALA* 3.5 11.6 - - - +
459A GLY 3.3 0.4 - - - -
460A LEU* 1.3 78.2 - - - +
462A CYS* 1.3 63.3 + - - +
463A CYS 3.7 2.1 + - - +
491A TYR* 3.4 26.2 - - + -
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Residues in contact with CYS 462 (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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153A LEU 5.2 6.2 - - - +
154A SER* 5.7 4.2 - - - -
200A ALA* 6.0 1.6 - - - -
429A THR* 3.5 39.5 - - - +
432A CYS* 3.9 24.6 - - + +
433A ASN* 3.7 24.7 - - - +
436A ALA* 5.4 5.4 - - - +
458A ALA 3.3 15.0 + - - +
459A GLY 3.1 9.0 + - - +
461A LYS* 1.3 79.7 - - - +
463A CYS* 1.3 60.1 + - - +
464A GLN* 3.9 1.4 + - - +
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Residues in contact with CYS 463 (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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200A ALA* 5.0 4.0 - - - +
203A LYS* 3.1 20.8 + - - +
432A CYS* 5.7 1.6 - - - -
446A LEU* 4.9 14.4 - - + -
448A ILE* 5.2 1.3 - - + -
459A GLY 3.0 13.2 + - - +
460A LEU 3.3 10.4 + - - +
461A LYS 4.6 2.0 - - - +
462A CYS* 1.3 77.4 - - - +
464A GLN* 1.3 60.4 + - - +
465A GLY 4.2 1.1 - - - +
467A CYS* 3.2 35.2 - - - -
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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