Contacts of the helix formed by residues 326 - 334 (chain B) in PDB entry 2PKG
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 ILE 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B VAL* 5.2 7.0 - - + -
287B PHE* 4.5 5.2 - - + -
288B GLN* 5.8 1.1 - - + -
291B MET* 4.2 25.1 - - + -
306B VAL* 4.4 3.1 - - + -
309B PHE* 4.1 18.8 - - + -
310B CYS* 3.8 30.7 - - - -
313B LEU* 4.3 7.4 - - + -
321B VAL* 3.1 18.7 + - + +
322B ILE* 3.6 12.3 - - + +
325B GLN* 1.3 80.5 - - + +
327B LEU* 1.3 57.7 + - - +
328B PRO* 2.6 3.0 - - - -
329B CYS* 2.4 42.1 + - - +
330B ILE* 3.3 28.6 + - + -
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Residues in contact with LEU 327 (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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322B ILE* 2.6 25.4 + - + +
323B MET* 3.8 34.1 - - + +
326B ILE* 1.3 75.0 - - - +
328B PRO* 1.3 67.5 - - + +
329B CYS 3.2 0.2 - - - -
330B ILE* 3.6 16.1 - - + +
331B LYS* 3.2 23.5 + - + +
352B LEU* 5.7 1.1 - - + -
356B LEU* 4.9 5.2 - - + -
364B HIS* 3.8 30.3 - - + +
365B LEU* 4.2 24.7 - - + -
368B LEU* 4.5 11.2 - - + -
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Residues in contact with PRO 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LYS* 5.8 0.4 - - - -
323B MET 3.3 17.7 - - - +
324B SER* 3.7 14.4 - - - +
325B GLN 4.0 3.6 - - - +
326B ILE 2.6 11.4 - - - +
327B LEU* 1.3 100.2 - - + +
329B CYS* 1.3 62.3 + - - +
331B LYS* 3.7 7.1 + - + +
332B GLU* 3.5 15.1 + - - +
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Residues in contact with CYS 329 (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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288B GLN* 4.2 27.6 - - - -
291B MET* 3.8 25.1 - - + -
292B LYS* 3.5 28.5 - - + +
325B GLN 3.8 15.7 - - - -
326B ILE 2.4 26.7 + - - +
328B PRO* 1.3 67.3 - - - +
330B ILE* 1.3 56.7 + - - +
332B GLU* 2.5 30.6 + - - +
333B LEU* 2.9 14.7 + - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B MET* 5.1 2.9 - - - -
306B VAL* 3.6 16.6 - - + -
322B ILE* 5.9 0.9 - - + -
326B ILE* 3.5 31.0 - - + +
327B LEU* 3.6 18.8 - - + +
329B CYS* 1.3 77.7 - - - +
331B LYS* 1.3 58.7 + - - +
333B LEU* 2.7 32.5 + - - +
334B VAL* 2.9 16.6 + - + +
345B LEU* 3.8 25.4 - - + -
349B ILE* 4.2 14.6 - - + -
352B LEU* 3.6 29.4 - - + -
368B LEU* 4.8 9.0 - - + -
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Residues in contact with LYS 331 (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 LEU* 3.2 15.6 + - + +
328B PRO* 3.8 8.5 - - + +
329B CYS 3.1 0.8 - - - -
330B ILE* 1.3 81.5 - - - +
332B GLU* 1.3 59.2 + - - +
334B VAL* 3.8 19.7 - - - +
335B SER* 4.1 9.0 + - - -
368B LEU* 4.1 21.3 - - + -
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Residues in contact with GLU 332 (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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292B LYS* 5.8 4.9 - - - +
328B PRO 3.5 8.8 + - - +
329B CYS* 2.5 20.4 + - - +
331B LYS* 1.3 73.1 - - - +
333B LEU* 1.3 61.2 - - - -
335B SER* 3.5 17.0 + - - -
336B ASP* 3.6 10.2 + - - +
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Residues in contact with LEU 333 (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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291B MET* 3.5 55.4 - - + +
299B ARG* 4.3 3.8 - - + -
303B SER* 4.0 17.7 - - - +
306B VAL* 5.3 0.7 - - + -
329B CYS* 2.9 13.3 + - + +
330B ILE* 2.7 15.1 + - - +
332B GLU* 1.3 76.4 - - + +
334B VAL* 1.3 56.7 + - - +
335B SER 3.1 2.0 - - - -
336B ASP* 2.7 49.9 + - - +
341B VAL* 3.8 19.2 - - + +
342B LYS* 4.1 5.4 - - - +
345B LEU* 4.2 19.7 - - + -
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 2.9 18.0 + - + +
331B LYS* 3.8 15.7 - - - +
333B LEU* 1.3 76.5 - - - +
335B SER* 1.3 57.6 + - - +
336B ASP 3.3 0.4 - - - -
342B LYS* 3.4 24.4 - - - +
345B LEU* 3.6 19.9 - - + +
349B ILE* 4.7 1.8 - - + -
368B LEU* 4.2 18.6 - - + +
371B ALA* 4.8 14.6 - - + -
372B GLN* 3.8 34.5 + - + +
375B ASP* 5.0 0.9 - - - +
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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