Contacts of the helix formed by residues 327 - 331 (chain B) in PDB entry 2PGW
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 MSE 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 4.5 0.2 - - - +
32B PHE* 4.9 1.7 - - + -
140B PHE* 4.7 4.9 - - - -
142B PHE* 4.1 32.3 - - + -
299B SER* 3.3 29.9 + - - +
300B SER* 3.4 22.2 - - - +
301B PHE* 3.5 39.9 - - + -
302B THR* 4.6 8.8 - - - +
307B THR* 4.7 2.4 + - - -
325B GLN* 5.4 2.9 - - - +
326B ILE* 1.3 83.2 - - - +
328B TRP* 1.3 67.4 + - - +
329B GLN* 3.1 7.4 - - - +
330B LEU* 3.1 42.4 + - + +
331B VAL* 4.4 1.2 + - - +
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Residues in contact with TRP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 6.0 4.0 - - - -
302B THR 4.7 5.1 + - - -
303B THR 4.7 1.1 + - - -
304B GLY* 3.9 18.2 - - - +
307B THR* 3.4 22.2 + - + +
326B ILE* 3.5 26.9 - - + +
327B MSE 1.3 76.4 - - - +
329B GLN* 1.3 77.6 + - + +
330B LEU 2.9 6.5 + - - -
331B VAL* 3.0 29.5 + - - +
334B ASP* 3.9 24.1 - - + +
340B ASP* 5.0 0.7 - - - -
341B LEU* 2.9 55.0 + - + +
342B THR* 3.5 22.4 - - + -
343B PRO* 4.6 2.7 - - + +
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Residues in contact with GLN 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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19B LYS* 3.2 35.7 + - - +
142B PHE* 4.1 18.0 - - - +
326B ILE* 2.8 47.7 + - - +
327B MSE 3.3 13.3 - - - +
328B TRP* 1.3 105.1 + - + +
330B LEU* 1.3 73.8 + - + +
331B VAL 3.3 0.2 - - - -
343B PRO* 6.1 1.3 - - + +
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Residues in contact with LEU 330 (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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18B LEU* 3.2 21.6 - - + +
19B LYS* 3.0 27.6 + - - +
20B GLN* 6.4 2.7 - - + -
22B TYR* 4.3 13.5 - - + -
32B PHE* 4.8 9.2 - - + -
142B PHE* 4.0 19.7 - - + +
144B GLN* 4.2 22.9 - - + +
301B PHE* 5.4 0.7 - - + -
327B MSE 3.1 45.8 + - + +
328B TRP 2.9 1.6 + - - -
329B GLN* 1.3 90.1 - - + +
331B VAL* 1.3 59.5 + - - +
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Residues in contact with VAL 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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16B LEU* 4.1 19.3 - - + -
17B PRO* 3.6 13.2 - - + +
18B LEU* 4.1 1.6 - - + -
19B LYS* 3.5 15.1 - - - -
32B PHE* 3.7 19.5 - - + -
302B THR 3.7 24.0 - - - +
303B THR* 4.8 7.2 - - + -
327B MSE 4.7 0.2 - - - +
328B TRP* 3.0 20.6 + - - +
329B GLN* 4.0 1.0 - - - +
330B LEU* 1.3 80.1 - - - +
332B GLN* 1.3 68.1 + - - +
333B GLU 3.5 23.7 + - - +
334B ASP* 3.8 13.3 + - - +
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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