Contacts of the helix formed by residues 333 - 346 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D GLY* 4.7 0.6 - - - -
332D GLY* 1.3 75.8 - - - -
334D PRO* 1.3 74.7 - - - +
335D GLY 3.6 0.9 - - - -
336D THR* 2.8 24.3 + - - +
337D LEU 3.9 0.5 + - - -
358D ARG* 4.4 9.0 - - - -
359D VAL* 3.4 22.5 - - - +
387D PHE* 5.1 4.0 - - - -
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Residues in contact with PRO 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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333D GLY* 1.3 84.4 - - - +
335D GLY* 1.3 64.2 + - - +
337D LEU* 3.4 19.9 + - + +
338D HIS* 3.7 5.0 + - - +
358D ARG* 5.3 4.5 - - - +
359D VAL* 5.4 0.2 - - + -
387D PHE* 5.3 3.4 - - + -
394D PHE* 4.9 13.2 - - + -
398D ARG* 4.4 8.5 - - - +
402D TRP* 3.6 40.5 + - + -
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Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D PRO* 1.3 81.1 - - - +
336D THR* 1.3 58.4 + - - +
338D HIS* 3.2 13.5 + - - +
339D THR* 2.8 31.5 + - - -
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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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174D THR* 4.8 6.6 - - - +
175D GLY* 3.5 28.9 - - - +
176D GLY* 4.7 1.6 - - - -
329D VAL* 4.8 11.7 - - - -
332D GLY* 3.8 6.1 - - - -
333D GLY* 2.8 43.3 + - - +
335D GLY* 1.3 76.4 - - - +
337D LEU* 1.3 56.6 + - - +
339D THR* 3.3 8.6 + - - -
340D ILE* 2.9 34.1 + - - +
359D VAL* 3.4 10.4 - - - +
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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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334D PRO 3.4 12.4 + - - +
335D GLY 3.2 0.4 - - - -
336D THR* 1.3 79.7 + - - +
338D HIS* 1.3 61.4 + - + +
340D ILE* 3.3 12.3 + - + +
341D ASP* 3.0 27.5 + - - +
359D VAL* 3.8 28.9 - - + -
362D VAL* 6.2 0.2 - - + -
363D ILE* 4.1 10.3 - - + -
402D TRP* 5.0 22.9 - - + +
405D LYS* 3.7 34.1 - - + +
406D ILE* 3.9 31.6 - - + -
409D ILE* 4.1 9.5 - - + +
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Residues in contact with HIS 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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334D PRO 3.7 3.8 + - - +
335D GLY* 3.2 17.6 + - - +
337D LEU* 1.3 79.5 - - + +
339D THR* 1.3 64.1 + - - +
341D ASP* 3.4 4.2 + - - +
342D ASN* 2.9 42.5 + - + +
405D LYS* 3.3 32.8 + - - +
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Residues in contact with THR 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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174D THR* 5.1 18.6 - - + +
299D ILE* 6.0 6.4 - - + +
335D GLY 2.8 17.2 + - - -
336D THR* 3.5 10.5 - - - -
337D LEU 3.2 0.2 - - - -
338D HIS* 1.3 81.6 - - - +
340D ILE* 1.3 60.1 - - - +
342D ASN* 3.8 7.3 + - + +
343D ALA* 2.9 30.9 + - + +
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Residues in contact with ILE 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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174D THR* 5.5 4.5 - - + -
327D CYS* 5.5 4.9 - - - -
329D VAL* 3.8 40.4 - - + -
336D THR* 2.9 21.0 + - - +
337D LEU* 3.3 12.3 + - - +
339D THR* 1.3 77.2 - - - +
341D ASP* 1.3 57.8 + - - +
343D ALA* 3.3 5.7 + - - +
344D THR* 2.9 31.4 + - + +
350D CYS* 4.2 26.2 - - + +
352D VAL* 4.8 4.7 - - + -
359D VAL* 5.9 4.0 - - + -
363D ILE* 5.8 8.5 - - + -
409D ILE* 3.7 24.5 - - + -
416D LEU* 5.9 2.5 - - + -
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Residues in contact with ASP 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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337D LEU 3.0 16.0 + - - +
338D HIS* 3.7 5.6 + - - +
340D ILE* 1.3 77.9 - - - +
342D ASN* 1.3 60.1 + - - +
344D THR* 3.3 7.9 + - - +
345D THR* 3.0 36.2 + - - +
405D LYS* 3.9 31.6 + - + +
408D ASP* 4.3 10.1 - - - +
409D ILE* 3.9 21.1 - - + +
412D ARG* 4.0 18.9 + - - -
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Residues in contact with ASN 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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303D THR* 5.3 11.9 - - - +
338D HIS* 2.9 35.1 + - + +
339D THR* 3.8 8.1 + - - +
341D ASP* 1.3 80.6 + - - +
343D ALA* 1.3 60.1 + - - +
345D THR* 2.6 22.1 + - - -
346D ASN* 3.5 17.3 + - - +
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Residues in contact with ALA 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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327D CYS* 4.4 20.2 - - + -
339D THR* 2.9 19.4 + - + +
340D ILE 3.6 4.7 - - - +
342D ASN* 1.3 78.6 - - - +
344D THR* 1.3 58.2 + - - +
346D ASN* 3.1 25.3 + - - +
348D THR* 3.0 26.7 + - + +
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Residues in contact with THR 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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340D ILE* 2.9 23.2 + - + +
341D ASP* 3.4 12.6 - - - +
343D ALA* 1.3 74.3 - - - +
345D THR* 1.3 64.2 + - - +
346D ASN 3.2 0.2 - - - -
347D GLY 3.5 1.9 + - - -
348D THR 3.7 13.2 - - - -
350D CYS* 5.2 10.1 - - - -
409D ILE* 4.6 15.7 - - + +
412D ARG* 3.3 28.3 + - - +
415D LEU* 3.4 39.8 - - - +
416D LEU* 5.0 5.5 + - + +
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Residues in contact with THR 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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341D ASP* 3.0 27.2 + - - +
342D ASN* 2.6 32.3 + - - -
344D THR* 1.3 77.9 - - - +
346D ASN* 1.3 65.0 + - - +
347D GLY 3.4 0.9 + - - -
412D ARG* 3.4 29.8 - - - +
1244D HIS* 4.9 13.9 - - + -
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Residues in contact with ASN 346 (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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307D LYS* 5.2 12.7 - - + +
342D ASN* 3.5 20.7 + - - +
343D ALA* 3.1 10.2 + - - +
345D THR* 1.3 88.3 + - - +
347D GLY* 1.3 58.5 + - - +
348D THR* 3.5 9.1 - - + +
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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