Contacts of the helix formed by residues 333 - 346 (chain B) in PDB entry 6PUO
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 GLY 333 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B GLY* 1.3 74.1 - - - -
334B PRO* 1.3 74.1 - - - +
335B GLY 3.6 0.9 - - - -
336B THR* 2.8 24.1 + - - +
337B LEU 3.9 0.3 + - - -
358B ARG* 4.4 9.6 - - - -
359B VAL* 3.4 24.0 - - - +
387B PHE* 5.1 4.0 - - - -
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Residues in contact with PRO 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY* 1.3 83.9 - - - +
335B GLY* 1.3 64.2 + - - +
337B LEU* 3.4 19.7 + - + +
338B HIS* 3.7 4.9 + - - +
358B ARG* 5.3 3.8 - - - +
359B VAL* 5.4 0.2 - - + -
387B PHE* 5.3 3.1 - - + -
394B PHE* 4.9 13.9 - - + -
398B ARG* 4.4 8.5 - - - +
402B TRP* 3.6 40.5 + - + -
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY 3.6 0.2 - - - -
334B PRO* 1.3 80.8 - - - +
336B THR* 1.3 59.3 + - - +
337B LEU 3.2 0.2 - - - -
338B HIS* 3.2 13.8 + - - +
339B THR* 2.8 32.2 + - - -
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Residues in contact with THR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 4.8 6.8 - - - +
175B GLY* 3.5 27.6 - - - +
176B GLY* 4.7 1.3 - - - -
329B VAL* 4.8 11.2 - - - -
332B GLY* 3.8 6.7 - - - -
333B GLY* 2.8 42.0 + - - +
335B GLY* 1.3 77.5 - - - +
337B LEU* 1.3 57.1 + - - +
339B THR* 3.3 9.0 + - - -
340B ILE* 2.9 33.6 + - - +
359B VAL* 3.4 10.6 - - - +
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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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334B PRO* 3.4 11.4 + - + +
335B GLY 3.2 0.4 - - - -
336B THR* 1.3 78.6 + - - +
338B HIS* 1.3 61.8 + - + +
340B ILE* 3.3 11.8 + - + +
341B ASP* 3.0 27.9 + - - +
359B VAL* 3.8 29.2 - - + -
362B VAL* 6.3 0.2 - - + -
363B ILE* 4.1 10.8 - - + -
402B TRP* 5.0 24.0 - - + +
405B LYS* 3.7 34.1 - - + +
406B ILE* 3.9 30.5 - - + -
409B ILE* 4.1 9.6 - - + +
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Residues in contact with HIS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO 3.7 3.6 + - - +
335B GLY* 3.2 17.4 + - - +
337B LEU* 1.3 80.3 - - + +
339B THR* 1.3 64.2 + - - +
341B ASP* 3.4 3.4 + - - +
342B ASN* 2.9 41.4 + - + +
405B LYS* 3.3 31.9 + - - +
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Residues in contact with THR 339 (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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174B THR* 5.1 17.3 - - + +
299B ILE* 6.0 6.7 - - + +
335B GLY 2.8 16.6 + - - -
336B THR* 3.5 11.4 - - - -
337B LEU 3.2 0.4 - - - -
338B HIS* 1.3 82.1 - - - +
340B ILE* 1.3 59.3 - - - +
342B ASN* 3.4 8.1 + - + +
343B ALA* 2.9 30.9 + - + +
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Residues in contact with ILE 340 (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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174B THR* 5.5 4.3 - - + -
327B CYS* 5.5 4.9 - - - -
329B VAL* 3.8 40.2 - - + -
336B THR* 2.9 21.0 + - - +
337B LEU* 3.5 11.0 - - + +
339B THR* 1.3 75.7 - - - +
341B ASP* 1.3 57.7 + - - +
343B ALA* 3.3 6.9 + - - +
344B THR* 2.9 30.7 + - + +
350B CYS* 4.2 26.0 - - + +
352B VAL* 4.8 4.7 - - + -
359B VAL* 5.9 4.3 - - + -
363B ILE* 5.8 7.2 - - + -
409B ILE* 3.7 25.4 - - + -
416B LEU* 5.9 2.5 - - + -
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Residues in contact with ASP 341 (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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337B LEU 3.0 16.0 + - - +
338B HIS* 3.7 5.7 + - - +
340B ILE* 1.3 77.6 - - - +
342B ASN* 1.3 60.2 + - - +
344B THR* 3.3 8.2 + - - +
345B THR* 3.0 35.9 + - - +
405B LYS* 3.9 31.8 - - + +
408B ASP* 4.3 9.5 - - - +
409B ILE* 3.9 22.4 - - + +
412B ARG* 4.0 18.4 + - - -
1245B LEU* 6.1 0.2 - - - +
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Residues in contact with ASN 342 (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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303B THR* 5.3 11.7 - - - +
338B HIS* 2.9 33.8 + - + +
339B THR* 3.8 9.4 + - - +
340B ILE 3.3 0.2 - - - -
341B ASP* 1.3 80.8 + - - +
343B ALA* 1.3 59.9 + - - +
345B THR* 2.6 21.2 + - - -
346B ASN* 3.5 17.8 + - - +
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Residues in contact with ALA 343 (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 CYS* 4.4 20.0 - - + -
339B THR* 2.9 19.0 + - + +
340B ILE 3.6 4.5 - - - +
342B ASN* 1.3 79.3 - - - +
344B THR* 1.3 58.1 + - - +
346B ASN* 3.1 24.9 + - - +
348B THR* 3.0 27.2 + - + +
350B CYS* 6.2 0.2 - - + -
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Residues in contact with THR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ILE* 2.9 24.7 + - + +
341B ASP* 3.4 12.6 - - - +
343B ALA* 1.3 73.4 - - - +
345B THR* 1.3 64.0 + - - +
346B ASN 3.2 0.6 + - - -
347B GLY* 3.5 2.1 + - - -
348B THR 3.7 12.8 - - - -
350B CYS* 5.2 10.5 - - - -
409B ILE* 4.6 14.6 - - + +
412B ARG* 3.3 28.7 + - - +
415B LEU* 3.4 38.8 - - - +
416B LEU* 5.0 5.1 + - + +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASP* 3.0 27.2 + - - +
342B ASN* 2.6 32.0 + - - -
344B THR* 1.3 77.1 - - - +
346B ASN* 1.3 64.7 + - - +
347B GLY 3.4 0.3 + - - -
412B ARG* 3.4 28.9 - - - +
1244B HIS* 4.9 15.0 - - + -
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Residues in contact with ASN 346 (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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307B LYS* 5.2 12.7 - - + +
342B ASN* 3.5 20.7 + - - +
343B ALA* 3.1 9.9 + - - +
345B THR* 1.3 88.4 + - - +
347B GLY* 1.3 59.2 + - - +
348B THR* 3.5 9.5 + - + +
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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