Contacts of the helix formed by residues 398 - 405 (chain B) in PDB entry 5KX8
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 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B PRO* 3.6 23.3 - - + +
394B GLN 5.1 0.3 + - - -
395B LEU* 3.4 32.9 + - - +
396B LEU 3.1 0.4 + - - -
397B LEU* 1.4 80.3 - - - +
399B ILE* 1.4 57.8 + - - +
401B GLU* 3.0 32.7 + - + +
402B GLU* 3.4 12.4 + - - +
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Residues in contact with ILE 399 (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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378B LEU* 4.1 22.2 - - + -
382B THR* 4.2 19.7 - - + -
384B LEU* 5.7 0.4 - - + -
393B PRO* 4.0 11.4 - - + -
396B LEU* 3.1 29.3 + - + +
398B ASP* 1.4 74.6 - - - +
400B LYS* 1.3 64.1 + - - +
402B GLU* 3.2 13.9 + - - +
403B ILE* 3.0 39.3 + - + +
410B ILE* 4.5 2.2 - - + -
413B TYR* 3.4 56.5 - - + +
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Residues in contact with LYS 400 (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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378B LEU* 5.2 1.8 - - + -
397B LEU 3.3 15.0 + - - +
398B ASP 3.2 0.6 - - - -
399B ILE* 1.3 80.2 - - - +
401B GLU* 1.3 69.4 + - - +
403B ILE 3.6 0.5 + - - -
404B GLU* 3.0 56.3 + - - +
430B TYR* 3.4 25.2 + - + +
434B SER* 2.9 37.0 + - - +
437B LEU* 3.3 45.7 + - + +
438B HIS* 3.7 10.1 - - - +
439B GLU* 5.1 2.4 - - - +
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Residues in contact with GLU 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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397B LEU 4.7 2.8 - - - +
398B ASP* 3.0 21.5 + - + +
400B LYS* 1.3 94.3 - - - +
402B GLU* 1.4 59.5 + - + +
404B GLU* 2.9 20.5 + - - +
405B ASP* 2.7 49.6 + - - +
407B GLU* 5.1 0.2 - - - -
439B GLU* 4.9 10.0 - - - +
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Residues in contact with GLU 402 (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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392B GLU 5.2 0.2 - - - +
393B PRO* 3.4 33.9 - - - +
398B ASP* 3.4 5.0 + - - +
399B ILE* 3.2 18.4 + - - +
401B GLU* 1.4 76.0 - - - +
403B ILE* 1.3 59.9 + - - +
405B ASP 3.6 2.3 - - - -
407B GLU* 3.0 51.0 + - + +
408B LYS* 2.7 47.6 + - + +
413B TYR* 3.2 14.1 + - + -
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Residues in contact with ILE 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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399B ILE* 3.0 28.7 + - + +
402B GLU* 1.3 75.3 - - - +
404B GLU* 1.4 65.0 + - + +
406B GLU* 3.3 21.1 + - - +
408B LYS* 3.6 8.4 - - + +
409B THR* 3.8 23.3 - - - +
410B ILE* 3.9 32.5 - - + +
413B TYR* 4.4 7.6 - - + -
430B TYR* 3.6 48.5 - - + +
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Residues in contact with GLU 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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400B LYS* 3.0 47.0 + - + +
401B GLU* 2.9 27.9 + - - +
403B ILE* 1.4 69.1 - - + +
405B ASP* 1.4 65.7 + - - +
406B GLU* 3.1 18.2 + - - +
430B TYR* 5.2 2.7 - - + +
434B SER* 4.1 8.8 + - - +
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Residues in contact with ASP 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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401B GLU* 2.7 30.9 + - - +
402B GLU 3.6 2.5 - - - -
404B GLU* 1.4 76.5 - - - +
406B GLU* 1.4 49.3 + - - +
407B GLU* 2.6 47.6 + - - +
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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