Contacts of the helix formed by residues 326 - 339 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B ALA 4.0 0.4 - - - -
319B GLY* 4.5 3.4 - - - +
324B GLU* 4.7 12.4 + - + +
325B GLY* 1.3 74.6 - - - +
327B ARG* 1.3 59.0 + - - +
328B ASP* 3.6 2.7 - - + +
329B ILE* 3.2 37.9 + - + +
330B THR* 2.5 37.7 + - - -
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Residues in contact with ARG 327 (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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318B ALA* 3.5 24.9 + - - +
319B GLY* 4.8 0.8 - - - -
326B GLU* 1.3 74.7 - - - +
328B ASP* 1.3 69.6 + - - +
330B THR* 3.7 2.1 - - - -
331B LEU* 3.1 41.2 + - - +
380B GLU 4.9 2.8 + - - -
381B ALA* 3.7 39.2 + - + +
382B LEU* 5.1 0.5 - - - +
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Residues in contact with ASP 328 (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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326B GLU* 4.7 1.4 - - + +
327B ARG* 1.3 87.4 - - - +
329B ILE* 1.3 65.8 + - + +
331B LEU* 3.3 11.1 + - - +
332B GLY* 3.1 17.0 + - - -
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Residues in contact with ILE 329 (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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324B GLU* 5.9 1.8 - - - +
325B GLY* 6.4 0.2 - - - -
326B GLU* 3.2 40.3 + - + +
327B ARG 3.3 0.4 - - - -
328B ASP* 1.3 77.1 - - + +
330B THR* 1.3 65.0 + - - +
332B GLY* 3.0 11.9 + - - -
333B PHE* 3.2 41.8 + - + -
351B HIS* 6.2 5.8 - - + -
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Residues in contact with THR 330 (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 VAL* 3.5 26.3 + - + +
316B GLY* 3.9 10.5 - - - +
317B THR 4.8 0.5 + - - -
318B ALA* 3.3 31.5 + - + +
325B GLY* 3.8 9.4 - - - -
326B GLU 2.5 24.6 + - - -
327B ARG 3.7 2.0 - - - -
329B ILE* 1.3 75.8 - - - +
331B LEU* 1.3 62.2 + - - +
333B PHE* 3.1 21.1 + - - +
334B VAL* 3.2 13.2 + - - +
382B LEU* 3.9 14.6 - - + -
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Residues in contact with LEU 331 (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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327B ARG* 3.1 31.4 + - - +
328B ASP* 3.5 11.4 - - - +
329B ILE 3.2 0.2 - - - -
330B THR* 1.3 75.7 - - - +
332B GLY* 1.3 62.3 + - - +
334B VAL* 3.3 5.5 + - + -
335B ASP* 3.1 43.9 + - - +
338B ARG* 5.3 1.3 - - - +
381B ALA* 3.2 28.5 - - + +
382B LEU* 3.9 16.7 - - + +
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Residues in contact with GLY 332 (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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299B PHE* 3.7 14.4 - - - -
328B ASP 3.1 9.4 + - - -
329B ILE* 3.0 10.4 + - - -
331B LEU* 1.3 78.2 - - - +
333B PHE* 1.3 62.4 + - - +
335B ASP* 3.6 6.5 + - - +
336B LEU* 3.1 23.2 + - - +
342B TYR* 4.1 7.5 - - - -
351B HIS* 6.0 2.9 - - - -
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Residues in contact with PHE 333 (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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282B ARG* 5.2 1.3 - - - -
297B SER* 4.7 2.5 - - - -
298B MET* 3.8 32.8 - - + -
299B PHE* 3.6 46.0 - + + -
302B ALA* 4.6 8.5 - - + -
315B VAL* 3.6 38.6 - - + -
325B GLY* 6.5 0.7 - - - -
329B ILE* 3.2 43.7 - - + -
330B THR* 3.1 9.6 + - - +
332B GLY* 1.3 74.4 - - - +
334B VAL* 1.3 66.3 + - - +
336B LEU* 3.1 8.0 + - - +
337B LEU* 2.9 28.4 + - - +
351B HIS* 5.7 1.3 - + - -
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Residues in contact with VAL 334 (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 VAL* 4.1 17.5 - - + -
330B THR 3.2 14.1 + - - +
331B LEU* 3.3 9.8 + - + +
333B PHE* 1.3 76.7 - - - +
335B ASP* 1.3 59.3 + - - +
337B LEU* 3.1 2.3 + - - +
338B ARG* 2.9 78.4 + - - +
364B PRO* 4.0 16.2 - - + -
382B LEU* 3.5 31.4 - - + +
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Residues in contact with ASP 335 (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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331B LEU* 3.1 37.8 + - - +
332B GLY* 3.9 5.4 - - - +
334B VAL* 1.3 75.7 - - - +
336B LEU* 1.3 58.4 + - - +
338B ARG* 4.5 10.8 + - - -
339B GLU* 2.8 65.9 + - - +
342B TYR* 4.1 9.7 - - + -
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Residues in contact with LEU 336 (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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299B PHE* 3.0 63.3 - - + +
302B ALA* 4.0 6.3 - - + -
303B LYS* 3.7 32.1 - - + +
306B ARG* 2.9 20.1 + - - -
332B GLY 3.1 14.8 + - - +
333B PHE* 3.1 9.6 + - - +
335B ASP* 1.3 77.2 - - - +
337B LEU* 1.3 57.5 + - - +
342B TYR* 4.0 13.2 - - + -
354B GLN* 6.0 0.2 - - + -
356B PHE* 3.1 27.6 - - + -
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Residues in contact with LEU 337 (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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302B ALA* 3.2 39.5 - - + +
306B ARG* 3.3 26.9 + - + +
313B LEU* 4.1 22.7 - - + -
315B VAL* 3.5 32.8 - - + -
333B PHE 2.9 15.5 + - - +
334B VAL 3.7 3.6 - - - +
336B LEU* 1.3 80.1 - - - +
338B ARG* 1.3 57.9 + - - +
361B ALA* 3.3 1.2 - - - -
362B ALA* 2.8 43.9 + - + +
364B PRO* 4.2 15.0 - - + -
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Residues in contact with ARG 338 (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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143B ILE* 3.7 17.5 - - + -
306B ARG* 4.4 0.3 + - - -
331B LEU* 5.3 1.6 - - - +
334B VAL* 2.9 42.0 + - - +
335B ASP* 4.4 11.3 + - - +
337B LEU* 1.3 78.4 - - - +
339B GLU* 1.3 65.4 + - + +
340B SER 3.7 1.2 + - - -
361B ALA* 3.3 19.8 - - + +
362B ALA 3.8 7.6 - - - +
364B PRO* 3.8 5.5 - - + +
382B LEU 2.6 27.9 + - - -
383B GLY* 4.5 3.2 - - - -
385B ASP* 2.8 59.3 + - - +
386B ILE* 3.4 7.3 - - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ARG* 2.8 28.6 + - - -
335B ASP* 2.8 43.1 + - + +
338B ARG* 1.3 74.9 - - + +
340B SER* 1.3 62.6 + - - +
341B HIS 4.0 12.0 - - - +
342B TYR* 3.3 41.5 - - + +
343B LYS 4.0 5.2 + - - +
356B PHE* 3.5 5.0 - - - -
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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