Contacts of the helix formed by residues 326 - 339 (chain J) in PDB entry 3KDO
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 GLU 326 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318J ALA 4.0 1.1 - - - -
319J GLY* 4.9 2.2 - - - -
324J GLU* 4.5 6.0 + - - +
325J GLY* 1.3 73.0 - - - +
327J ARG* 1.3 61.2 + - - +
328J ASP* 3.7 2.2 - - + +
329J ILE* 4.0 29.1 - - + +
330J THR* 2.6 34.5 + - - -
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Residues in contact with ARG 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318J ALA* 3.6 25.3 + - + +
319J GLY* 5.2 0.2 - - - -
326J GLU* 1.3 73.1 - - - +
328J ASP* 1.3 83.5 + - - +
330J THR* 3.3 3.8 + - - -
331J LEU* 3.1 34.3 + - - +
377J PRO* 5.2 2.2 + - - +
380J GLU* 4.5 6.3 + - - +
381J ALA* 3.1 47.3 - - + +
382J LEU* 5.2 0.7 - - - +
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Residues in contact with ASP 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326J GLU* 4.8 2.1 - - + +
327J ARG* 1.3 95.8 + - - +
329J ILE* 1.3 65.4 + - + +
331J LEU* 3.2 13.5 + - - +
332J GLY* 3.1 17.8 + - - -
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Residues in contact with ILE 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324J GLU* 5.9 2.5 - - - +
325J GLY* 6.2 1.1 - - - -
326J GLU* 3.8 27.5 + - + +
327J ARG 3.2 0.4 - - - -
328J ASP* 1.3 79.0 - - + +
330J THR* 1.3 63.5 + - - +
332J GLY* 3.0 13.1 + - - -
333J PHE* 3.1 47.1 + - + -
351J HIS* 6.5 2.0 - - + -
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Residues in contact with THR 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J VAL* 3.9 25.2 + - + +
316J GLY 3.9 9.4 - - - +
318J ALA* 3.2 29.0 + - - +
325J GLY* 4.1 6.6 + - - -
326J GLU 2.6 22.4 + - - -
327J ARG 3.7 4.0 - - - -
329J ILE* 1.3 78.5 - - - +
331J LEU* 1.3 63.1 + - - +
333J PHE* 3.1 15.1 + - - +
334J VAL* 3.1 20.8 + - - +
382J LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327J ARG* 3.1 26.8 + - - +
328J ASP* 3.4 14.8 - - - +
329J ILE 3.2 0.2 - - - -
330J THR* 1.3 76.7 - - - +
332J GLY* 1.3 57.3 + - - +
334J VAL* 3.3 4.7 + - + +
335J ASP* 3.0 47.3 + - - +
338J ARG* 5.3 1.6 - - - +
381J ALA* 2.8 31.4 - - + +
382J LEU* 3.8 15.0 - - + +
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Residues in contact with GLY 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299J PHE* 4.2 13.6 - - - -
328J ASP 3.1 9.0 + - - -
329J ILE* 3.0 10.2 + - - -
331J LEU* 1.3 73.4 - - - +
333J PHE* 1.3 61.1 + - - +
335J ASP* 3.4 8.2 + - - +
336J LEU* 2.9 29.9 + - - +
342J TYR* 4.3 6.3 - - - -
351J HIS* 6.2 1.8 - - - -
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Residues in contact with PHE 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282J ARG* 5.0 0.9 - - - -
297J SER* 4.7 2.2 - - - -
298J MET* 3.6 34.8 - - + -
299J PHE* 3.6 43.1 - + + -
302J ALA* 4.7 7.6 - - + -
315J VAL* 3.6 41.5 - - + -
329J ILE* 3.1 42.0 - - + -
330J THR* 3.1 10.0 + - - +
332J GLY* 1.3 76.6 - - - +
334J VAL* 1.3 64.2 + - - +
336J LEU* 3.1 7.1 + - - +
337J LEU* 2.9 29.3 + - - +
351J HIS* 5.8 0.4 - + - -
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Residues in contact with VAL 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J VAL* 4.2 6.7 - - + -
330J THR 3.1 8.0 + - - +
331J LEU* 3.6 9.2 - - + +
333J PHE* 1.3 75.4 - - - +
335J ASP* 1.3 65.4 + - - +
337J LEU* 3.0 3.0 + - - +
338J ARG* 2.9 70.4 + - - +
364J PRO* 3.9 28.3 - - + -
382J LEU* 3.5 42.4 - - + +
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Residues in contact with ASP 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331J LEU* 3.0 38.6 + - - +
332J GLY* 3.7 5.7 - - - +
334J VAL* 1.3 76.5 - - - +
336J LEU* 1.3 60.8 + - - +
338J ARG* 4.3 12.0 + - - +
339J GLU* 2.9 64.8 + - - +
342J TYR* 4.1 9.1 - - + -
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Residues in contact with LEU 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299J PHE* 3.2 64.4 - - + +
302J ALA* 4.3 6.1 - - + -
303J LYS* 3.9 30.6 - - + +
306J ARG* 2.8 21.5 + - - -
332J GLY 2.9 17.7 + - - +
333J PHE* 3.1 6.3 + - - +
335J ASP* 1.3 76.2 - - - +
337J LEU* 1.3 58.2 + - - +
342J TYR* 4.0 24.1 - - + -
354J GLN* 5.0 0.2 - - + -
356J PHE* 3.6 25.2 - - + -
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Residues in contact with LEU 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302J ALA* 3.4 32.8 - - + +
306J ARG* 3.3 30.0 + - + +
313J LEU* 4.1 24.2 - - + +
315J VAL* 3.5 31.6 - - + -
333J PHE 2.9 15.4 + - - +
334J VAL 3.0 4.7 + - - +
336J LEU* 1.3 81.6 - - - +
338J ARG* 1.3 57.5 + - - +
362J ALA* 2.8 43.4 + - + +
364J PRO* 4.0 20.9 - - + -
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Residues in contact with ARG 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J ILE* 3.7 21.5 - - + -
306J ARG* 4.0 0.9 + - - -
331J LEU* 5.3 2.0 - - - +
334J VAL* 2.9 34.7 + - - +
335J ASP* 4.3 12.2 + - - +
337J LEU* 1.3 77.9 - - - +
339J GLU* 1.3 67.9 + - + +
340J SER* 3.6 1.7 + - - -
361J ALA* 3.3 21.2 - - + +
362J ALA 3.7 8.5 - - - +
364J PRO* 3.8 6.5 - - + -
382J LEU 2.9 29.3 + - - -
383J GLY* 4.6 2.6 - - - -
385J ASP* 3.2 48.4 + - - +
386J ILE* 3.9 1.4 - - - +
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Residues in contact with GLU 339 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306J ARG* 2.8 28.8 + - - -
335J ASP* 2.9 36.3 + - - +
338J ARG* 1.3 78.7 - - + +
340J SER* 1.3 62.3 + - - +
341J HIS 3.3 17.0 - - - +
342J TYR* 3.1 40.2 - - + +
343J LYS 3.9 4.2 + - - +
356J PHE* 3.6 4.9 - - - -
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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