Contacts of the helix formed by residues 409 - 416 (chain B) in PDB entry 1DKF
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 LEU 409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B THR* 4.3 23.8 - - + +
236B ILE* 4.2 19.1 - - + -
237B ILE* 4.2 11.0 - - + -
407B PRO* 3.6 14.3 + - + +
408B PRO* 1.3 78.2 - - - +
410B ILE* 1.3 64.8 + - + +
411B GLN* 3.2 3.6 - - - +
412B GLU* 3.8 20.3 - - - +
413B MET* 2.6 77.7 + - + +
600B BMS 5.4 6.5 - - + -
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Residues in contact with ILE 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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236B ILE* 3.6 29.8 - - + -
240B VAL* 4.3 7.8 - - + +
258B ILE* 4.2 10.5 - - - +
261B LEU* 3.7 36.3 - - + +
262B LYS* 4.2 14.8 - - + +
265B CYS* 3.9 25.1 - - + -
409B LEU* 1.3 81.2 - - + +
411B GLN* 1.3 68.1 + - - +
413B MET* 3.7 6.6 - - - +
414B LEU* 2.7 32.9 + - + +
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Residues in contact with GLN 411 (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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258B ILE* 3.4 37.7 - - + +
262B LYS* 3.9 22.7 + - - +
408B PRO* 6.1 3.4 - - + -
409B LEU* 4.7 2.9 - - - +
410B ILE* 1.3 84.8 - - - +
412B GLU* 1.3 56.8 + - + +
414B LEU* 3.5 2.9 - - - +
415B GLU* 2.7 55.5 + - - +
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Residues in contact with GLU 412 (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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408B PRO 4.3 3.7 - - - +
409B LEU* 3.4 27.1 + - - +
410B ILE 3.3 0.2 - - - -
411B GLN* 1.3 80.2 - - + +
413B MET* 1.3 85.2 + - - +
415B GLU* 3.1 22.6 + - - +
416B ASN* 3.2 17.2 + - + +
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Residues in contact with MET 413 (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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236B ILE* 4.0 7.0 - - + -
237B ILE* 3.6 45.8 - - - +
240B VAL* 3.7 36.1 - - + -
241B GLU* 5.9 0.9 - - - -
244B LYS* 4.3 6.1 + - - +
409B LEU* 2.6 53.6 + - + +
410B ILE* 3.7 3.1 - - - +
412B GLU* 1.3 85.5 + - - +
414B LEU* 1.3 62.8 + - - +
416B ASN* 3.5 17.3 + - - +
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Residues in contact with LEU 414 (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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240B VAL* 3.9 15.7 - - + -
244B LYS* 3.5 35.4 + - + +
249B PHE* 5.1 1.3 - - + -
254B ILE* 5.2 10.4 - - + +
257B GLN* 3.7 24.2 - - + +
258B ILE* 3.6 39.5 - - + +
261B LEU* 3.3 26.7 - - + -
410B ILE* 2.7 21.5 + - + +
411B GLN 3.5 3.8 - - - +
413B MET* 1.3 72.5 - - - +
415B GLU* 1.3 67.6 + - - +
416B ASN* 2.9 9.4 - - - +
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Residues in contact with GLU 415 (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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254B ILE* 4.8 18.1 - - - +
258B ILE* 4.0 7.6 - - - +
411B GLN* 2.7 60.7 + - - +
412B GLU* 3.2 13.4 + - - +
414B LEU* 1.3 74.9 - - - +
416B ASN* 1.3 64.6 + - - +
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Residues in contact with ASN 416 (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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244B LYS* 4.1 9.4 + - - -
412B GLU* 3.2 14.4 + - + +
413B MET* 3.5 13.2 - - - +
414B LEU 2.9 12.0 - - - +
415B GLU* 1.3 84.1 - - - +
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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