Contacts of the helix formed by residues 405 - 410 (chain B) in PDB entry 3D5E
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 TRP 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B HIS* 4.3 17.5 - + - -
386B LYS* 3.7 70.7 - - + +
389B LEU* 4.0 15.5 - - + -
390B ALA* 3.6 10.0 - - - +
401B ASP* 5.6 0.2 - - - -
402B PHE* 2.9 48.5 + + + +
404B GLN* 1.4 115.3 + - + +
406B ASP* 1.3 56.2 + - - +
407B CYS* 3.1 6.5 - - - -
408B LEU* 2.9 40.3 + - + +
409B ILE 3.8 0.7 + - - -
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Residues in contact with ASP 406 (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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15B FMT 4.4 8.9 - - - +
390B ALA* 3.9 13.6 - - - +
394B LYS* 4.1 20.4 + - - +
403B ASP* 3.3 37.9 + - - +
404B GLN 3.5 1.0 - - - -
405B TRP* 1.3 76.1 - - - +
407B CYS* 1.3 60.7 + - - +
409B ILE* 3.3 32.5 + - - +
410B GLU* 3.7 10.3 + - - +
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Residues in contact with CYS 407 (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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404B GLN 4.3 15.9 + - - -
405B TRP* 3.1 2.8 - - - -
406B ASP* 1.3 79.4 - - - +
408B LEU* 1.3 78.5 + - - +
410B GLU* 3.2 11.8 + - - +
412B ASP* 3.0 50.6 + - + +
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Residues in contact with LEU 408 (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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344B ILE* 3.5 8.8 - - - +
383B LEU* 4.2 15.9 - - + +
386B LYS* 3.5 34.1 - - + -
387B ALA* 3.9 18.8 - - + +
405B TRP* 2.9 28.1 + - + +
407B CYS* 1.3 86.1 - - - +
409B ILE* 1.3 59.8 + - - +
410B GLU 3.1 1.3 - - - -
411B GLY 2.9 16.1 + - - -
412B ASP 4.4 0.4 - - - +
413B ASP* 3.6 36.6 - - + +
416B LEU* 3.4 20.8 - - + +
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Residues in contact with ILE 409 (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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315B PHE* 3.9 16.8 - - + -
342B LYS* 3.7 41.4 - - + +
343B MET 4.6 1.6 - - - +
344B ILE* 3.4 14.6 - - - +
387B ALA* 4.1 10.7 - - - +
390B ALA* 3.7 23.3 - - + +
391B PHE* 3.7 37.5 - - + +
394B LYS* 4.5 14.8 - - + +
405B TRP 3.8 0.4 + - - -
406B ASP* 3.3 21.9 + - - +
408B LEU* 1.3 77.0 - - - +
410B GLU* 1.3 64.3 + - - +
411B GLY 3.3 0.4 - - - -
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Residues in contact with GLU 410 (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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342B LYS* 2.5 42.0 + - - +
344B ILE* 4.3 1.6 - - - -
394B LYS* 5.7 2.4 + - - -
406B ASP 4.1 10.0 - - - +
407B CYS* 3.2 11.2 + - - +
408B LEU 3.1 1.0 - - - -
409B ILE* 1.3 84.5 - - - +
411B GLY* 1.3 62.1 + - - +
412B ASP* 3.2 7.8 + - + +
418B PRO* 3.4 19.7 - - - +
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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