Contacts of the helix formed by residues 333 - 345 (chain D) in PDB entry 1KOH
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 ASP 333 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A THR* 5.3 6.7 - - + -
158A ARG* 5.6 4.5 - - - +
190A ILE* 4.5 11.7 - - + -
206A PRO* 3.4 28.4 - - + +
331D PHE* 3.3 5.1 - - - +
332D ARG* 1.3 82.5 - - + +
334D GLN* 1.3 60.2 + - - +
335D SER* 3.0 18.1 + - - -
336D THR* 2.7 35.1 + - - -
337D TYR* 3.3 10.9 + - - +
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Residues in contact with GLN 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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123A THR* 5.8 0.4 - - - +
125A PRO* 3.5 44.2 - - + +
126A TYR* 3.8 36.7 + - + +
188A SER* 4.9 5.2 + - - -
190A ILE* 4.1 8.9 - - - +
333D ASP* 1.3 73.2 - - - +
335D SER* 1.3 57.5 + - - +
337D TYR* 3.6 34.9 - - - +
338D ILE* 3.3 23.9 + - - +
351D LEU* 4.9 4.8 - - - +
352D ASP* 4.6 5.3 + - - -
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Residues in contact with SER 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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206A PRO* 3.8 22.6 + - - +
210A GLU* 3.9 20.9 + - - +
333D ASP* 3.0 16.3 + - - -
334D GLN* 1.3 75.2 - - - +
336D THR* 1.3 60.9 + - - +
337D TYR 3.0 5.2 - - - -
338D ILE* 2.6 31.4 + - - +
339D SER* 3.5 10.2 + - - -
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Residues in contact with THR 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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258A ARG* 5.6 9.0 + - - +
262A GLU* 6.2 0.2 - - - +
307B ARG* 5.3 13.0 - - - +
331D PHE* 3.3 28.5 - - + -
332D ARG* 5.1 5.8 - - + +
333D ASP* 2.7 28.6 + - - -
335D SER* 1.3 77.4 - - - +
337D TYR* 1.3 60.0 + - - +
339D SER* 3.9 8.0 - - - -
340D ALA* 3.6 11.6 + - - +
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Residues in contact with TYR 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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322D LEU* 3.0 37.3 - - + +
323D ASP* 4.3 1.4 + - - -
327D LEU* 4.1 13.9 - - + -
328D SER* 4.3 14.3 + - - -
331D PHE* 3.6 26.7 - + + -
333D ASP 3.3 10.2 + - - +
334D GLN* 3.6 37.7 - - - +
335D SER 3.0 0.2 - - - -
336D THR* 1.3 78.0 - - - +
338D ILE* 1.3 68.8 + - - +
340D ALA* 3.5 2.9 + - - +
341D ILE* 3.1 36.3 + - + +
351D LEU* 3.7 13.4 - - + +
352D ASP* 3.4 23.2 + - - -
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Residues in contact with ILE 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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126A TYR* 5.2 1.1 - - - +
210A GLU* 3.7 25.1 - - - +
334D GLN* 3.3 13.5 - - - +
335D SER* 2.6 37.5 - - - +
337D TYR* 1.3 70.5 - - + +
339D SER* 1.3 55.6 + - - +
341D ILE* 2.6 7.6 + - - +
342D ARG* 2.4 54.8 + - - +
348D LEU* 5.2 1.5 - - + +
351D LEU* 4.0 16.6 - - + -
356D LEU* 3.1 49.6 - - + -
357D PRO* 5.1 4.9 - - + -
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Residues in contact with SER 339 (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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210A GLU* 5.4 2.1 + - - -
213A LYS* 5.1 8.1 + - - -
262A GLU* 5.2 9.2 + - - +
307B ARG* 6.1 2.2 - - - -
335D SER 3.8 8.8 + - - -
336D THR* 3.9 11.8 - - - -
338D ILE* 1.3 79.8 - - - +
340D ALA* 1.3 52.6 + - - -
342D ARG* 2.6 14.4 + - - +
343D GLU* 2.5 44.5 + - - +
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Residues in contact with ALA 340 (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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307B ARG* 3.9 17.6 - - - +
306D GLU* 3.1 25.8 - - - +
309D LEU* 5.2 0.4 - - - +
331D PHE* 3.4 28.9 - - + -
336D THR 3.6 2.3 + - - +
337D TYR 3.5 3.5 + - - +
338D ILE 3.0 1.0 + - - -
339D SER* 1.3 80.0 - - - +
341D ILE* 1.3 62.7 + - + +
343D GLU* 3.5 7.1 + - - -
344D ARG* 3.2 28.6 + - - -
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Residues in contact with ILE 341 (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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306D GLU* 5.3 1.8 - - + -
309D LEU* 3.7 15.9 - - + -
320D LEU* 3.7 21.8 - - + -
322D LEU* 3.4 24.5 - - + -
327D LEU* 4.6 6.1 - - + -
331D PHE* 4.9 1.3 - - + -
337D TYR* 3.1 41.1 - - + +
338D ILE* 2.6 11.7 + - - +
340D ALA* 1.3 78.5 - - + +
342D ARG* 1.3 65.7 + - - +
343D GLU 3.2 0.4 - - - -
344D ARG 3.6 0.9 + - - +
345D PHE* 3.0 24.7 + - + +
348D LEU* 3.2 27.4 - - + -
351D LEU* 4.5 7.0 - - + -
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Residues in contact with ARG 342 (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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210A GLU* 5.9 1.4 + - - -
338D ILE* 2.4 37.2 + - - +
339D SER* 2.6 20.8 + - - +
341D ILE* 1.3 73.1 - - - +
343D GLU* 1.3 60.0 + - - +
345D PHE 2.5 36.0 - - - +
346D PRO* 3.0 25.3 + - + +
348D LEU* 2.4 42.6 + - - +
356D LEU* 4.0 17.2 - - - +
357D PRO* 3.1 28.7 + - - +
358D PRO 4.8 3.2 + - - -
359D PRO* 4.6 18.9 - - - +
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Residues in contact with GLU 343 (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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262A GLU* 6.1 0.9 - - - +
307B ARG* 3.5 27.8 + - - -
313D LYS* 5.1 6.9 - - - +
339D SER* 2.5 25.4 + - - +
340D ALA* 3.6 3.6 - - - +
341D ILE 3.2 0.4 - - - -
342D ARG* 1.3 76.6 - - - +
344D ARG* 1.3 102.8 + - - +
346D PRO* 3.3 12.8 - - - +
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Residues in contact with ARG 344 (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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307B ARG* 4.4 2.2 - - - +
306D GLU* 2.7 55.4 + - - +
307D ARG* 4.4 1.4 - - - +
309D LEU* 3.6 9.1 - - + +
310D ASP* 2.6 53.5 + - - +
313D LYS* 3.6 40.1 - - + +
340D ALA 3.2 17.5 + - - +
341D ILE 3.6 3.2 + - - +
343D GLU* 1.3 106.0 + - - +
345D PHE* 1.3 81.0 + - + +
346D PRO* 3.6 5.5 - - - +
347D LYS* 5.2 1.4 + - - -
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Residues in contact with PHE 345 (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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309D LEU* 4.0 13.9 - - + -
312D ILE* 3.5 42.2 - - + -
313D LYS* 4.6 2.2 - - - -
315D LEU* 4.0 15.3 - - + -
317D LEU* 3.1 51.6 - - + +
320D LEU* 3.8 24.5 - - + -
341D ILE* 3.0 14.2 + - + +
342D ARG* 2.5 25.9 - - - +
344D ARG* 1.3 91.0 - - + +
346D PRO* 1.3 59.8 - - - +
347D LYS* 3.6 3.1 - - - +
348D LEU* 3.5 25.0 - - + +
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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