Contacts of the helix formed by residues 447 - 452 (chain F) in PDB entry 3CB4
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 MET 447 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294F GLN* 3.7 33.0 - - + +
370F VAL* 3.8 17.3 - - + -
402F PRO* 2.8 32.5 + - + +
404F ALA* 3.7 21.1 - - + +
445F ILE 3.3 3.1 + - - -
446F PRO* 1.3 67.2 - - - +
448F ALA* 1.3 61.9 + - - +
449F GLU 3.0 6.1 + - - -
450F VAL* 3.0 17.3 + - - -
451F VAL* 3.0 27.6 + - + +
470F TYR* 3.7 29.4 - - + -
471F ASN* 5.1 0.2 - - - -
472F PHE* 4.1 28.3 - - + +
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Residues in contact with ALA 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F VAL* 3.8 20.2 - - + +
372F TYR* 3.2 28.5 - - + +
401F GLU* 4.3 16.2 - - + +
402F PRO* 4.5 1.2 + - - +
426F ARG* 4.9 4.9 - - - +
446F PRO* 4.6 0.2 - - - +
447F MET* 1.3 77.9 - - - +
449F GLU* 1.3 60.9 - - - +
451F VAL* 4.5 0.6 - - - +
452F LEU* 3.1 33.6 + - + +
480F MET* 6.1 0.7 - - - -
498F ILE 4.9 4.7 - - - +
499F THR* 6.1 1.1 - - - -
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Residues in contact with GLU 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424F GLU 5.3 0.7 - - - +
425F LYS* 3.2 54.9 - - + +
426F ARG* 3.6 27.2 + - - +
445F ILE* 4.4 2.2 - - + -
446F PRO* 3.0 16.0 + - + +
447F MET 3.0 0.6 - - - -
448F ALA* 1.3 83.7 - - - +
450F VAL* 1.3 59.3 + - - +
451F VAL 3.2 1.8 - - - -
452F LEU* 2.8 32.8 - - - +
454F PHE* 3.5 9.9 - - - +
499F THR* 4.9 3.5 + - - -
507F ARG* 3.2 36.1 + - - -
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Residues in contact with VAL 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F LEU* 3.8 12.0 - - - +
404F ALA* 4.1 8.7 - - + -
406F CYS* 4.2 5.6 - - - -
445F ILE* 3.8 28.5 - - + +
446F PRO 3.1 14.8 + - - +
447F MET* 3.0 14.7 + - - +
449F GLU* 1.3 76.2 - - - +
451F VAL* 1.3 60.0 + - - +
452F LEU 4.1 2.8 - - - +
454F PHE* 4.1 33.1 + - + +
455F PHE* 4.6 1.8 + - + +
468F LEU* 4.8 2.2 - - + -
470F TYR* 3.9 40.6 - - + -
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Residues in contact with VAL 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLN* 5.3 0.2 - - - +
295F VAL* 3.8 33.0 - - + -
345F LEU* 3.6 34.1 - - + +
368F PRO* 3.3 38.6 - - + +
370F VAL* 3.9 12.3 - - + -
447F MET* 3.0 29.9 + - + +
448F ALA 4.5 1.8 - - - +
450F VAL* 1.3 78.2 - - - +
452F LEU* 1.3 63.4 + - + +
453F ASP* 3.1 5.0 + - - -
470F TYR* 5.0 5.8 - - - +
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Residues in contact with LEU 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F ALA* 4.3 20.2 - - + -
368F PRO* 3.4 32.1 - - + +
370F VAL* 6.4 0.4 - - + -
425F LYS* 4.4 5.7 - - - -
448F ALA* 3.1 26.6 + - + +
449F GLU* 2.8 33.1 + - + +
451F VAL* 1.3 75.0 - - + +
453F ASP* 1.3 71.8 + - - +
454F PHE* 2.9 1.8 + - - +
497F LEU* 6.0 4.9 - - + -
507F ARG* 5.9 7.6 - - + +
514F LYS* 5.8 2.2 - - - +
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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