Contacts of the helix formed by residues 338 - 347 (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 ASN 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B ALA* 3.9 15.9 - - + +
299B ARG* 4.0 8.9 - - - +
300B ALA* 5.2 0.8 - - - +
336B ASP* 3.3 13.9 + - - +
337B ALA* 1.3 79.1 - - - +
339B GLN* 1.3 66.3 + - - +
340B HIS* 2.9 29.1 + - - +
341B VAL* 2.7 40.7 - - + +
342B LYS* 3.1 24.6 + - - +
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Residues in contact with GLN 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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337B ALA 3.6 6.0 + - - +
338B ASN* 1.3 75.4 + - - +
340B HIS* 1.3 68.6 + - + +
342B LYS* 3.3 26.4 + - - +
343B SER* 2.8 30.3 + - - -
376B GLU* 5.8 1.8 - - - +
377B CYS* 3.9 35.4 - - - +
380B VAL* 4.5 2.4 - - - +
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Residues in contact with HIS 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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467A LYS* 6.0 0.6 + - - -
468A LYS* 6.5 1.1 - - - -
471A GLU* 3.5 37.7 + - + +
300B ALA* 4.7 8.7 - - + -
338B ASN* 2.9 21.3 + - - +
339B GLN* 1.3 80.5 - - + +
341B VAL* 1.3 58.9 + - - +
343B SER* 3.5 7.0 - - - -
344B ALA* 2.7 32.6 + - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA* 3.8 11.9 - - + +
299B ARG* 3.8 8.7 - - + +
300B ALA* 3.7 25.4 - - + +
303B SER* 3.5 19.2 + - - +
333B LEU* 3.8 15.9 - - + +
336B ASP* 3.6 39.0 - - + +
338B ASN* 2.7 28.8 - - + +
340B HIS* 1.3 73.9 - - - +
342B LYS* 1.3 69.2 + - - +
344B ALA* 3.1 8.0 + - - +
345B LEU* 3.1 12.0 + - - +
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Residues in contact with LYS 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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333B LEU 4.1 8.3 - - - +
334B VAL* 3.4 26.9 - - - +
335B SER 4.9 0.9 - - - -
336B ASP* 3.1 25.9 + - + +
337B ALA 4.7 3.0 + - - -
338B ASN 3.1 14.9 + - - +
339B GLN* 3.4 28.5 - - - +
341B VAL* 1.3 82.1 - - - +
343B SER* 1.3 63.2 + - - +
345B LEU* 3.3 5.2 + - - +
346B ALA* 3.1 20.8 + - - +
372B GLN* 4.1 7.2 + - - +
375B ASP* 3.3 33.5 + - - +
376B GLU* 6.4 0.2 - - - +
377B CYS* 5.9 0.2 - - - -
380B VAL* 4.2 11.9 - - + -
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Residues in contact with SER 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN 2.8 20.7 + - - -
340B HIS* 3.5 10.1 - - - -
342B LYS* 1.3 74.7 - - - +
344B ALA* 1.3 64.5 + - - +
346B ALA* 3.3 13.0 + - - +
347B SER 3.4 7.1 + - - -
377B CYS* 5.5 0.2 - - - -
379B GLU* 3.7 29.0 + - - +
380B VAL* 3.7 18.1 - - - +
383B ASN* 3.7 15.8 + - - -
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Residues in contact with ALA 344 (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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300B ALA* 3.9 17.9 - - + +
303B SER* 3.9 5.2 - - - -
304B HIS* 3.7 35.8 - - + +
340B HIS 2.7 20.8 + - - +
341B VAL* 3.4 6.7 - - - +
343B SER* 1.3 73.3 - - - +
345B LEU* 1.3 61.6 + - - +
347B SER* 2.8 25.3 + - - -
348B VAL* 3.9 6.2 + - - +
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Residues in contact with LEU 345 (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 SER* 3.9 11.8 - - - +
306B VAL* 3.9 30.3 - - + -
330B ILE* 3.8 31.2 - - + +
333B LEU* 4.2 11.4 - - + -
334B VAL* 3.6 37.9 - - + +
341B VAL 3.1 8.0 + - - +
342B LYS* 3.7 7.0 - - - +
344B ALA* 1.3 78.5 - - - +
346B ALA* 1.3 59.5 + - - +
347B SER 3.0 0.3 + - - -
348B VAL* 3.1 6.4 + - + -
349B ILE* 2.8 49.1 + - + +
372B GLN* 4.2 6.3 - - - +
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Residues in contact with ALA 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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342B LYS 3.1 12.8 + - - +
343B SER* 3.5 11.0 - - - +
345B LEU* 1.3 76.5 - - - +
347B SER* 1.3 58.1 + - - +
348B VAL 3.4 0.4 + - - -
349B ILE* 3.7 10.9 - - - +
372B GLN* 3.8 20.6 - - - +
380B VAL* 3.7 28.7 - - + +
383B ASN* 3.9 21.2 - - + +
384B ILE* 3.8 11.1 - - + +
387B ASN* 4.5 4.0 + - - -
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Residues in contact with SER 347 (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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304B HIS* 4.2 9.7 + - - -
343B SER 3.4 1.2 + - - -
344B ALA* 2.8 18.3 + - - -
345B LEU 3.1 0.2 - - - -
346B ALA* 1.3 78.3 - - - +
348B VAL* 1.3 68.7 + - - +
383B ASN* 2.8 30.3 - - - +
387B ASN* 3.7 20.4 + - - +
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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