Contacts of the helix formed by residues 326 - 339 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318H ALA 4.5 1.1 - - - -
319H GLY* 4.5 2.2 - - - +
325H GLY* 1.3 73.4 - - - +
327H ARG* 1.3 66.6 + - - +
328H ASP* 4.7 3.1 - - + +
329H ILE* 4.1 26.3 - - + +
330H THR* 3.0 25.5 + - - -
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Residues in contact with ARG 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318H ALA* 3.6 26.9 + - + +
325H GLY 3.7 0.6 + - - -
326H GLU* 1.3 76.4 - - - +
328H ASP* 1.3 69.3 + - - +
330H THR* 3.1 9.5 + - - -
331H LEU* 3.2 27.0 + - + +
377H PRO 5.3 0.4 + - - -
380H GLU* 5.0 3.8 + - - +
381H ALA* 3.5 38.3 + - + +
382H LEU* 5.1 1.0 - - - +
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Residues in contact with ASP 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H GLU* 3.6 2.7 - - + +
327H ARG* 1.3 82.3 - - - +
329H ILE* 1.3 68.2 + - + +
331H LEU* 3.0 21.8 + - - +
332H GLY* 3.3 7.4 + - - -
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Residues in contact with ILE 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ARG* 5.8 7.6 - - - +
299H PHE* 5.8 0.2 - - - -
325H GLY* 6.4 0.4 - - - -
326H GLU* 3.7 26.4 + - + +
327H ARG 3.3 0.4 - - - -
328H ASP* 1.3 77.3 - - + +
330H THR* 1.3 55.2 + - - +
332H GLY* 2.7 24.1 + - - -
333H PHE* 3.2 42.9 + - + -
351H HIS* 6.3 6.1 - - + -
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Residues in contact with THR 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315H VAL* 4.0 19.0 + - + +
316H GLY 4.3 7.5 - - - +
318H ALA* 3.4 21.4 + - + -
325H GLY* 3.8 7.8 + - - -
326H GLU 3.0 20.5 + - - -
327H ARG 3.1 4.0 + - - -
329H ILE* 1.3 77.8 - - - +
331H LEU* 1.3 63.2 + - - +
333H PHE* 3.1 25.8 + - - +
334H VAL* 3.1 14.5 + - + +
382H LEU* 3.5 33.4 - - + -
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Residues in contact with LEU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327H ARG* 3.2 22.2 + - - +
328H ASP* 3.0 15.5 + - - +
330H THR* 1.3 79.0 - - - +
332H GLY* 1.3 59.3 + - - +
334H VAL* 3.6 4.7 - - + +
335H ASP* 3.2 42.1 + - - +
338H ARG* 4.8 3.6 - - - +
381H ALA* 3.4 26.0 - - + +
382H LEU* 3.9 18.4 - - + +
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Residues in contact with GLY 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H PHE* 4.0 17.2 - - - -
328H ASP 3.3 6.5 + - - -
329H ILE* 2.7 12.5 + - - -
331H LEU* 1.3 75.4 - - - +
333H PHE* 1.3 64.0 + - - -
335H ASP* 3.5 5.6 + - - +
336H LEU* 3.0 25.3 + - - +
342H TYR* 4.7 6.5 - - - -
351H HIS* 6.0 2.2 - - - -
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Residues in contact with PHE 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ARG* 6.3 0.7 - - - -
282H ARG* 5.9 0.9 - - - -
297H SER* 4.7 2.5 - - - -
298H MET* 3.6 30.5 - - + -
299H PHE* 3.3 47.3 - + + -
302H ALA* 4.7 3.1 - - + -
315H VAL* 3.5 41.3 - - + -
325H GLY* 6.5 1.1 - - - -
329H ILE* 3.2 34.3 + - + -
330H THR* 3.1 19.7 + - - +
332H GLY* 1.3 75.2 - - - +
334H VAL* 1.3 61.2 + - - +
336H LEU* 3.2 6.4 + - - +
337H LEU* 2.7 37.3 + - + +
351H HIS* 6.3 0.2 - + - -
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Residues in contact with VAL 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H VAL* 4.3 19.1 - - + -
330H THR 3.1 14.7 + - - +
331H LEU* 3.6 9.2 - - + +
332H GLY 3.2 0.2 - - - -
333H PHE* 1.3 75.6 - - - +
335H ASP* 1.3 65.1 + - - +
337H LEU* 2.9 13.9 + - - +
338H ARG* 2.3 67.4 + - - +
364H PRO* 4.0 17.3 - - + -
382H LEU* 3.7 30.5 - - + +
386H ILE* 5.2 0.4 - - + -
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Residues in contact with ASP 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331H LEU* 3.2 32.9 + - - +
332H GLY* 3.9 5.0 - - - +
334H VAL* 1.3 78.3 - - - +
336H LEU* 1.3 59.7 + - - +
338H ARG* 3.0 15.5 + - - +
339H GLU* 2.7 66.7 + - - +
342H TYR* 4.3 10.2 - - + -
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Residues in contact with LEU 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H PHE* 3.2 59.9 - - + +
302H ALA* 4.2 4.3 - - + -
303H LYS* 3.9 27.1 - - + +
306H ARG* 2.6 28.9 + - - -
332H GLY 3.0 17.3 + - - +
333H PHE 3.3 7.2 - - - +
335H ASP* 1.3 75.8 - - - +
337H LEU* 1.3 55.5 + - + +
342H TYR* 4.3 19.4 - - + -
356H PHE* 3.1 32.0 - - + -
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Residues in contact with LEU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302H ALA* 3.2 40.6 - - + +
306H ARG* 3.2 18.2 + - + +
313H LEU* 4.1 23.3 - - + -
315H VAL* 3.6 25.8 - - + -
333H PHE* 2.7 26.9 + - + +
334H VAL 2.9 8.9 + - - +
336H LEU* 1.3 82.2 - - + +
338H ARG* 1.3 57.9 + - - +
362H ALA* 2.8 47.2 + - + +
364H PRO* 4.3 15.5 - - + -
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Residues in contact with ARG 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H ILE* 3.5 24.7 - - + -
306H ARG* 4.2 1.0 + - - -
331H LEU* 4.8 3.2 - - - +
334H VAL* 2.3 46.0 + - - +
335H ASP* 4.2 13.9 + - - +
337H LEU* 1.3 78.8 - - - +
339H GLU* 1.3 65.5 + - + +
340H SER 3.7 1.6 + - - -
361H ALA* 3.3 19.1 - - - +
362H ALA 3.7 8.1 - - - +
364H PRO* 3.8 6.5 - - + -
382H LEU* 2.7 26.7 + - - +
383H GLY* 4.3 2.8 - - - -
385H ASP* 3.4 47.1 + - - +
386H ILE* 4.3 0.4 - - - +
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Residues in contact with GLU 339 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 2.9 25.4 + - - -
335H ASP* 2.7 50.2 + - - +
338H ARG* 1.3 74.4 - - + +
340H SER* 1.3 62.6 + - - +
341H HIS 4.1 18.6 - - - +
342H TYR* 3.7 21.7 - - - +
343H LYS 4.3 3.4 + - - +
356H PHE* 3.3 7.8 - - - -
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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