Contacts of the helix formed by residues 326 - 339 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318D ALA* 4.1 0.2 - - - -
319D GLY* 4.4 3.1 - - - +
324D GLU* 4.6 13.7 + - + +
325D GLY* 1.3 76.5 - - - +
327D ARG* 1.3 67.0 + - - +
328D ASP* 3.5 2.9 - - + +
329D ILE* 3.3 31.5 + - + +
330D THR* 2.9 25.1 + - - -
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Residues in contact with ARG 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ALA* 3.6 29.2 - - + +
319D GLY* 4.2 1.4 - - - +
326D GLU* 1.3 74.1 - - - +
328D ASP* 1.3 86.5 + - - +
330D THR* 3.2 2.8 + - - -
331D LEU* 3.1 35.4 + - - +
377D PRO 5.4 0.8 + - - -
380D GLU* 4.7 11.7 + - - +
381D ALA* 3.8 39.8 + - + +
382D LEU* 4.9 0.2 - - - +
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Residues in contact with ASP 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D GLU* 3.5 2.1 - - + +
327D ARG* 1.3 107.9 + - - +
329D ILE* 1.3 64.8 + - + +
331D LEU* 3.6 10.6 + - - +
332D GLY* 3.3 14.9 + - - -
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Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D GLY* 6.2 1.1 - - - -
326D GLU* 3.3 34.8 + - + +
327D ARG 3.2 0.2 - - - -
328D ASP* 1.3 78.8 - - + +
330D THR* 1.3 66.2 + - - +
332D GLY* 3.0 12.0 + - - -
333D PHE* 3.2 43.2 + - + -
351D HIS* 6.2 6.7 - - + -
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Residues in contact with THR 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D VAL* 3.8 25.5 + - + +
316D GLY 4.0 5.1 - - - +
317D THR 4.5 1.0 + - - -
318D ALA* 3.3 24.5 + - - +
325D GLY* 4.1 8.3 - - - -
326D GLU 2.9 18.5 + - - -
327D ARG 3.2 4.7 + - - -
329D ILE* 1.3 74.8 - - - +
331D LEU* 1.3 64.0 + - - +
333D PHE* 2.9 23.1 + - - +
334D VAL* 3.0 11.1 + - - +
382D LEU* 3.6 28.9 - - + -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ARG* 3.1 26.0 + - - +
328D ASP* 3.6 14.4 - - - +
330D THR* 1.3 75.3 - - - +
332D GLY* 1.3 61.5 + - - +
334D VAL* 3.2 7.9 + - + +
335D ASP* 2.9 46.0 + - - +
338D ARG* 5.4 1.6 - - - +
381D ALA* 3.6 25.6 - - + +
382D LEU* 3.7 16.9 - - + +
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Residues in contact with GLY 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D PHE* 4.0 15.2 - - - -
328D ASP 3.3 7.8 + - - -
329D ILE* 3.0 10.9 + - - -
331D LEU* 1.3 80.1 - - - +
333D PHE* 1.3 63.8 + - - +
335D ASP* 3.4 5.8 + - - +
336D LEU* 3.0 23.9 + - - +
342D TYR* 4.3 6.1 - - - -
351D HIS* 6.0 2.5 - - - -
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Residues in contact with PHE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ARG* 5.0 1.6 - - - -
297D SER* 4.7 2.2 - - - -
298D MET* 3.6 34.3 - - + -
299D PHE* 3.5 44.2 - + + -
302D ALA* 4.7 7.8 - - + +
315D VAL* 3.4 39.7 - - + -
325D GLY* 6.5 1.3 - - - -
329D ILE* 3.2 38.5 + - + -
330D THR* 2.9 10.2 + - - +
332D GLY* 1.3 75.0 - - - +
334D VAL* 1.3 64.1 + - - +
336D LEU* 3.2 7.6 + - - +
337D LEU* 2.9 29.6 + - - +
351D HIS* 5.6 1.3 - + - -
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Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D VAL* 4.1 11.0 - - + -
330D THR 3.0 9.1 + - - +
331D LEU* 3.5 12.6 - - + +
333D PHE* 1.3 75.4 - - - +
335D ASP* 1.3 66.9 + - - +
337D LEU* 3.1 3.0 + - - -
338D ARG* 2.9 70.0 + - - +
364D PRO* 4.0 25.4 - - + -
382D LEU* 3.6 35.7 - - + +
386D ILE* 4.9 0.4 - - + -
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Residues in contact with ASP 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D LEU* 2.9 40.5 + - - +
332D GLY* 3.7 5.5 - - - +
334D VAL* 1.3 80.0 - - - +
336D LEU* 1.3 58.4 + - - +
338D ARG* 4.5 7.6 + - - +
339D GLU* 2.8 60.7 + - - +
342D TYR* 4.1 11.2 - - + -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D PHE* 3.2 59.0 - - + +
302D ALA* 4.3 4.7 - - + -
303D LYS* 3.9 27.8 - - + +
306D ARG* 2.8 22.5 + - - -
332D GLY 3.0 17.0 + - - +
333D PHE* 3.6 6.1 - - - +
335D ASP* 1.3 77.7 - - - +
337D LEU* 1.3 58.7 + - - +
342D TYR* 3.9 23.3 - - + -
354D GLN* 5.0 0.7 - - + -
356D PHE* 3.5 37.4 - - + -
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Residues in contact with LEU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ALA* 3.4 37.0 - - + +
306D ARG* 3.2 28.9 + - + +
313D LEU* 4.1 20.2 - - + +
315D VAL* 3.4 33.0 - - + -
333D PHE 2.9 16.0 + - - +
334D VAL 3.1 4.7 + - - +
336D LEU* 1.3 79.2 - - - +
338D ARG* 1.3 57.2 + - - +
361D ALA* 3.4 0.2 - - - -
362D ALA* 3.0 42.1 + - + +
364D PRO* 4.1 21.3 - - + -
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Residues in contact with ARG 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 3.6 24.5 - - + -
306D ARG* 4.3 0.3 + - - -
331D LEU* 5.4 2.0 - - - +
334D VAL* 2.9 37.5 + - - +
335D ASP* 4.4 8.1 + - - +
337D LEU* 1.3 80.5 - - - +
339D GLU* 1.3 65.9 + - + +
340D SER* 3.7 1.4 + - - -
361D ALA* 3.4 19.5 - - - +
364D PRO* 3.7 13.2 - - + +
382D LEU 2.9 31.3 + - - -
383D GLY* 4.5 4.4 - - - -
385D ASP* 2.9 47.3 + - - +
386D ILE* 3.6 3.6 - - - +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ARG* 2.7 29.3 + - - -
335D ASP* 2.8 39.9 + - + +
337D LEU 3.8 0.2 - - - -
338D ARG* 1.3 74.5 - - + +
340D SER* 1.3 61.4 + - - +
341D HIS* 3.8 19.2 - - - +
342D TYR* 3.3 35.3 - - + +
343D LYS* 3.7 6.5 + - - +
356D PHE* 3.6 4.3 - - - -
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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