Contacts of the helix formed by residues 400 - 406 (chain B) in PDB entry 3KHU
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 ASP 400 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B TYR* 3.6 9.4 - - - -
398B SER* 3.4 6.5 - - - -
399B LYS* 1.3 83.2 - - - +
401B PRO* 1.3 73.0 - - + +
402B TYR* 2.8 41.5 + - + +
403B GLU* 3.2 29.6 + - - +
404B ALA 3.3 14.2 + - - -
427B ARG* 5.3 0.2 + - - -
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Residues in contact with PRO 401 (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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334B LEU* 4.0 17.5 - - + -
367B TYR* 3.9 30.0 - - + +
400B ASP* 1.3 92.5 - - + +
402B TYR* 1.3 64.3 + - + +
404B ALA* 3.2 10.8 + - + +
405B CYS* 3.0 32.5 + - - -
419B MET* 3.9 16.6 - - + -
420B PHE* 5.2 0.4 - - + -
423B LEU* 4.0 28.3 - - + -
428B ILE* 6.0 0.2 - - - -
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Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ASP* 2.8 20.9 + - - +
401B PRO* 1.3 74.5 - - + +
403B GLU* 1.3 65.0 + - - +
405B CYS* 3.3 4.3 + - - +
406B ASP* 3.0 25.2 + - - +
423B LEU* 3.5 23.6 - - + +
424B ASP* 2.9 45.9 + - + +
427B ARG* 3.6 54.1 - - + +
428B ILE* 3.8 24.5 - - + -
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Residues in contact with GLU 403 (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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330B LYS* 3.0 22.0 + - - -
365B HIS* 4.5 1.1 + - - +
398B SER* 4.0 9.4 + - - +
399B LYS* 3.3 29.3 + - - +
400B ASP* 3.2 29.9 + - - +
402B TYR* 1.3 76.0 - - - +
404B ALA* 1.3 63.1 + - - +
406B ASP* 3.3 11.3 + - - +
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Residues in contact with ALA 404 (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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330B LYS* 3.2 19.9 - - - -
332B ALA* 3.4 20.5 + - + +
334B LEU* 4.4 7.4 - - + -
365B HIS* 3.8 24.4 - - - +
367B TYR* 4.5 2.7 - - + -
398B SER* 3.6 21.3 + - - +
400B ASP 3.3 4.9 + - - +
401B PRO* 3.2 18.1 + - + +
403B GLU* 1.3 79.5 - - - +
405B CYS* 1.3 56.2 + - - +
408B ALA* 3.9 2.6 - - - +
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Residues in contact with CYS 405 (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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332B ALA* 3.8 11.0 - - - -
334B LEU* 4.7 7.4 - - - -
401B PRO* 3.0 21.8 + - - +
402B TYR 3.3 3.6 + - - +
403B GLU 3.2 0.2 - - - -
404B ALA* 1.3 75.9 - - - +
406B ASP* 1.3 64.7 + - - +
407B GLY 3.2 1.2 + - - -
408B ALA* 3.1 21.6 + - - +
411B VAL* 3.6 31.9 - - + -
428B ILE* 3.7 38.0 - - + +
431B LYS* 4.3 1.3 - - - +
432B MET* 3.5 12.4 - - + +
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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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330B LYS* 2.7 30.9 + - - +
402B TYR 3.0 15.7 + - - +
403B GLU* 3.3 13.4 + - - +
405B CYS* 1.3 74.2 - - - +
407B GLY* 1.3 63.3 + - - +
431B LYS* 3.7 40.7 + - + +
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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