Contacts of the helix formed by residues 447 - 452 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E GLN* 3.6 42.2 - - + +
370E VAL* 3.7 19.5 - - + -
402E PRO* 2.7 33.0 + - + +
403E ILE 4.6 0.2 - - - +
404E ALA* 3.9 20.4 - - + -
445E ILE 3.2 4.1 + - - -
446E PRO* 1.3 69.9 - - - +
448E ALA* 1.3 61.7 + - - +
450E VAL* 3.0 19.0 + - - +
451E VAL* 3.2 22.8 + - + +
470E TYR* 3.9 15.0 - - + -
472E PHE* 4.0 33.9 - - + +
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Residues in contact with ALA 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E PRO 5.3 0.2 - - - +
370E VAL* 3.7 21.0 - - + +
372E TYR* 3.3 27.6 - - + +
401E GLU* 4.2 16.2 - - + +
402E PRO 4.4 1.0 + - - -
426E ARG* 5.0 1.1 - - - +
446E PRO 3.2 0.2 - - - -
447E MET* 1.3 78.3 - - - +
449E GLU* 1.3 63.8 + - - +
451E VAL* 4.0 1.2 + - - +
452E LEU* 3.6 30.0 + - + +
480E MET* 5.7 1.3 - - - -
498E ILE 5.0 2.9 - - - +
499E THR* 6.3 0.9 - - - -
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Residues in contact with GLU 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424E GLU 5.7 0.2 - - - +
425E LYS* 3.4 58.8 - - + +
426E ARG* 2.8 34.4 + - - -
445E ILE* 4.3 4.7 - - + -
446E PRO* 3.0 16.1 + - + +
448E ALA* 1.3 82.8 - - - +
450E VAL* 1.3 58.5 + - - +
452E LEU* 2.9 26.2 + - - +
454E PHE* 3.6 7.3 - - - +
499E THR* 5.5 1.2 + - - -
500E HIS* 5.3 1.6 + - - +
507E ARG* 3.1 34.3 + - - -
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Residues in contact with VAL 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E LEU* 4.0 10.2 - - + +
404E ALA* 4.3 9.0 - - + -
406E CYS* 4.4 6.7 - - - -
445E ILE* 4.0 23.6 - - + +
446E PRO 3.4 15.5 - - - +
447E MET* 3.0 15.8 + - - +
449E GLU* 1.3 78.7 - - - +
451E VAL* 1.3 62.3 + - + +
452E LEU 3.5 0.5 - - - +
454E PHE* 3.4 42.4 + - + +
455E PHE* 4.3 0.6 + - + -
468E LEU* 4.5 3.4 - - + -
470E TYR* 4.2 36.3 - - + +
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Residues in contact with VAL 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E GLN* 5.0 2.0 - - - +
295E VAL* 3.7 29.8 - - + -
345E LEU* 3.8 28.3 - - + +
368E PRO* 3.5 41.8 - - + +
370E VAL* 3.7 21.1 - - + -
447E MET* 3.2 26.6 + - + +
448E ALA 4.6 1.8 - - - +
450E VAL* 1.3 74.2 - - + +
452E LEU* 1.3 64.0 + - - +
453E ASP* 3.3 5.2 + - - -
470E TYR* 5.1 4.0 - - - +
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Residues in contact with LEU 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E ALA* 4.9 16.4 - - + -
368E PRO* 3.5 31.6 - - + +
425E LYS* 4.4 6.0 - - - -
448E ALA* 3.6 20.0 + - + +
449E GLU* 2.9 24.6 - - - +
451E VAL* 1.3 75.5 - - - +
453E ASP* 1.3 68.8 + - - +
454E PHE* 2.8 5.8 + - - +
497E LEU* 5.6 6.5 - - + -
507E ARG* 4.6 32.3 - - + +
510E GLU* 5.8 0.7 - - - +
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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