Contacts of the helix formed by residues 327 - 331 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F PHE* 4.7 1.8 - - + -
140F PHE* 4.5 5.2 - - - -
142F PHE* 3.8 35.9 - - + -
299F SER* 3.5 22.8 + - - +
300F SER* 3.4 26.9 - - - +
301F PHE* 3.5 40.4 - - + -
302F THR* 4.6 8.0 - - - +
307F THR* 4.8 2.0 + - - -
325F GLN* 5.6 2.5 - - - +
326F ILE* 1.3 88.0 - - - +
328F TRP* 1.3 67.9 + - - +
329F GLN* 3.1 11.8 + - - +
330F LEU* 3.1 39.9 + - + +
331F VAL* 4.5 0.7 + - - +
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Residues in contact with TRP 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LYS* 5.9 4.9 - - - -
302F THR 4.6 10.3 - - - -
303F THR 4.1 1.5 + - - -
304F GLY* 3.9 17.0 - - - +
307F THR* 3.3 23.0 + - + +
326F ILE* 3.6 26.4 - - + +
327F MSE 1.3 76.8 - - - +
329F GLN* 1.3 78.1 + - + +
330F LEU 2.9 6.3 + - - -
331F VAL* 3.1 23.7 + - - +
334F ASP* 3.6 27.3 - - + +
340F ASP* 4.8 1.1 - - - -
341F LEU* 2.9 54.6 + - + -
342F THR* 3.4 22.7 - - + -
343F PRO* 4.6 2.5 - - + +
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Residues in contact with GLN 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F LYS* 3.0 40.2 + - - +
142F PHE* 4.3 14.6 - - - +
326F ILE* 3.1 35.8 + - - +
327F MSE 3.4 17.1 + - - +
328F TRP* 1.3 107.0 + - + +
330F LEU* 1.3 75.7 + - + +
331F VAL 3.4 0.7 - - - -
343F PRO* 6.0 1.0 - - + +
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Residues in contact with LEU 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LEU* 3.5 11.0 - - + +
19F LYS* 2.9 27.6 + - - +
20F GLN* 4.8 6.9 + - + +
22F TYR* 4.5 8.7 - - + -
32F PHE* 4.1 23.1 - - + -
142F PHE* 3.9 21.5 - - + +
144F GLN* 4.5 19.5 - - + +
327F MSE 3.5 44.6 - - + +
328F TRP 2.9 1.2 + - - -
329F GLN* 1.3 93.8 - - + +
331F VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.3 22.2 - - + -
17F PRO 3.6 13.7 - - - +
18F LEU* 4.4 2.2 - - + +
19F LYS* 3.4 16.8 - - - -
32F PHE* 4.3 16.2 - - + -
302F THR 3.9 21.5 - - - +
303F THR* 4.9 1.6 - - - -
327F MSE 4.9 0.2 - - - +
328F TRP* 3.1 18.6 + - - +
329F GLN 4.1 0.3 - - - +
330F LEU* 1.3 79.8 - - - +
332F GLN* 1.3 68.0 + - - +
333F GLU 3.6 25.1 - - - +
334F ASP* 3.7 18.5 + - - +
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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