Contacts of the helix formed by residues 447 - 458 (chain B) in PDB entry 5ZCS
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 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B THR* 6.0 6.1 - - - +
413B LEU* 3.3 40.1 - - - +
444B VAL* 3.3 26.8 - - + +
446B SER* 1.3 81.4 + - - +
448B PHE* 1.3 62.3 + - - +
449B LYS* 3.2 4.6 + - - -
450B VAL* 3.5 23.5 + - + +
451B TYR* 4.6 1.0 + - - +
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B SER* 5.6 5.6 - - - -
444B VAL* 4.6 14.5 - - + +
445B ARG* 3.4 24.0 - - + +
446B SER 3.2 3.4 + - - -
447B GLU* 1.3 79.0 - - - +
449B LYS* 1.3 61.4 + - + +
450B VAL 3.2 0.2 - - - -
451B TYR* 2.9 58.4 + + + +
452B LEU* 3.6 31.5 + - + +
455B VAL* 5.7 1.1 - - + -
489B LEU* 4.3 15.3 - - + -
497B ILE* 3.6 33.7 - - + -
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ARG 6.1 0.2 - - - +
446B SER 5.0 7.4 - - - +
447B GLU 3.2 1.9 - - - -
448B PHE* 1.3 81.1 - - + +
450B VAL* 1.3 64.2 + - + +
451B TYR 3.3 0.2 - - - -
452B LEU* 3.5 42.4 + - + +
453B PRO* 4.1 4.2 - - - +
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Residues in contact with VAL 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 5.4 9.2 - - + -
447B GLU* 3.9 23.8 - - + +
448B PHE 3.2 0.6 - - - -
449B LYS* 1.3 78.3 - - + +
451B TYR* 1.3 61.5 + - - +
452B LEU 3.3 1.2 + - - -
453B PRO* 3.3 16.2 - - - +
454B ARG* 4.6 3.1 + - - +
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Residues in contact with TYR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B MET* 6.0 6.7 - - - -
437B LEU* 3.9 38.6 - - + +
441B SER* 4.8 4.6 + - - -
447B GLU 4.6 0.8 + - - +
448B PHE* 2.9 39.5 + + + +
450B VAL* 1.3 78.3 - - - +
452B LEU* 1.3 62.2 + - - +
453B PRO 3.6 0.2 - - - -
454B ARG* 3.1 36.3 + - + +
455B VAL* 3.3 27.7 - - + +
458B ILE* 4.2 8.5 - - + +
489B LEU* 3.7 29.5 - - + +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 3.6 36.6 - - + +
449B LYS* 3.5 46.7 - - + +
450B VAL 3.2 0.4 - - - -
451B TYR* 1.3 77.2 - - - +
453B PRO* 1.3 67.4 - - + +
454B ARG 3.4 0.5 + - - -
455B VAL* 3.6 19.6 + - + +
456B LEU* 4.6 1.7 + - - +
499B GLN* 6.1 2.7 - - - +
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Residues in contact with PRO 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LYS 4.1 4.5 - - - +
450B VAL 3.3 17.0 - - - +
452B LEU* 1.3 90.8 - - + +
454B ARG* 1.3 60.8 + - - +
455B VAL 3.3 0.6 + - - -
456B LEU* 3.7 18.5 + - + +
457B ASP* 4.9 1.0 + - - +
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B MET* 6.4 2.0 - - - -
421B LEU* 4.1 37.7 - - + +
450B VAL 4.9 2.5 - - - +
451B TYR* 3.1 33.6 + - + +
453B PRO* 1.3 78.3 - - - +
455B VAL* 1.3 62.6 + - - +
456B LEU 3.2 1.8 + - - -
457B ASP* 3.5 41.6 + - - +
458B ILE* 3.3 31.6 - - + +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 5.7 0.9 - - + -
451B TYR* 3.3 42.0 - - + +
452B LEU* 3.7 17.9 - - + +
453B PRO 3.3 0.6 - - - -
454B ARG* 1.3 77.0 - - - +
456B LEU* 1.3 62.1 + - - +
457B ASP 3.2 1.2 + - - -
458B ILE* 3.7 14.8 + - - +
459B ILE* 4.3 20.1 + - + +
460B ARG* 5.2 3.1 + - - +
489B LEU* 4.9 5.8 - - + -
500B ASP* 3.4 33.7 - - - +
503B GLU* 5.8 2.2 - - - +
504B LEU* 5.5 2.7 - - + +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LEU 4.6 1.7 + - - +
453B PRO* 3.7 15.2 + - + +
454B ARG 3.2 2.0 - - - -
455B VAL* 1.3 78.0 - - - +
457B ASP* 1.3 87.2 + - - +
458B ILE 3.7 0.8 + - - -
460B ARG* 3.4 55.2 - - - +
503B GLU* 5.3 4.3 - - - +
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Residues in contact with ASP 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B PRO 4.9 0.4 + - - -
454B ARG* 3.5 25.8 + - - +
455B VAL 3.2 0.2 - - - -
456B LEU* 1.3 105.6 - - - +
458B ILE* 1.3 65.4 + - - +
461B ALA* 4.8 16.1 - - + +
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Residues in contact with ILE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B LEU* 5.3 7.4 - - + -
434B PHE* 4.0 25.0 - - + -
437B LEU* 4.3 18.8 - - + -
451B TYR* 4.2 18.4 - - + +
454B ARG* 3.3 47.1 - - + +
455B VAL* 3.7 7.3 + - - +
456B LEU 3.7 0.6 + - - -
457B ASP* 1.3 81.2 - - - +
459B ILE* 1.3 77.0 + - + +
460B ARG 3.5 1.0 - - - +
461B ALA* 3.7 4.5 + - - +
462B ALA* 3.4 20.8 + - - +
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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