Contacts of the helix formed by residues 327 - 331 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TYR* 4.5 0.2 - - - +
32D PHE* 4.5 5.4 - - + -
140D PHE* 4.6 4.9 - - - -
142D PHE* 4.1 33.2 - - + -
299D SER* 3.4 27.2 + - - +
300D SER* 3.4 21.8 - - - +
301D PHE* 3.4 42.0 - - + -
302D THR 4.6 6.1 - - - +
307D THR* 4.7 2.2 + - - -
325D GLN* 5.5 2.7 - - - +
326D ILE* 1.3 87.7 - - - +
328D TRP* 1.3 67.5 + - - +
329D GLN* 3.1 8.3 - - - +
330D LEU* 3.1 42.2 + - + +
331D VAL 4.4 0.9 + - - -
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Residues in contact with TRP 328 (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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19D LYS* 6.2 2.2 - - - -
302D THR 4.6 10.3 + - - -
303D THR 4.7 0.6 + - - -
304D GLY* 3.9 18.2 - - - +
307D THR* 3.4 20.3 + - - +
326D ILE* 3.4 28.0 - - + +
327D MSE 1.3 77.2 - - - +
329D GLN* 1.3 78.1 + - + +
330D LEU 3.0 5.8 + - - -
331D VAL* 3.1 23.8 + - - +
334D ASP* 3.8 26.1 - - + +
336D VAL 6.1 0.4 - - - -
340D ASP* 5.0 0.9 - - - -
341D LEU* 2.8 53.9 + - + -
342D THR* 3.5 21.3 - - + -
343D PRO* 4.6 2.4 - - + +
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Residues in contact with GLN 329 (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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19D LYS* 3.2 36.3 + - - +
142D PHE* 4.2 17.8 - - - +
326D ILE* 2.9 35.8 + - - +
327D MSE 3.4 15.7 + - - +
328D TRP* 1.3 109.7 + - + +
330D LEU* 1.3 72.5 + - + +
331D VAL 3.3 0.7 - - - -
343D PRO* 6.1 1.1 - - + +
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Residues in contact with LEU 330 (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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18D LEU* 3.4 10.2 - - + +
19D LYS* 2.9 27.7 + - - +
20D GLN* 4.8 3.1 + - + -
22D TYR* 4.3 9.0 - - + -
32D PHE* 4.0 23.6 - - + -
142D PHE* 3.9 21.3 - - + +
144D GLN* 4.0 23.8 - - + +
327D MSE 3.4 44.2 - - + +
328D TRP 3.0 1.2 + - - -
329D GLN* 1.3 90.3 - - + +
331D VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 331 (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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16D LEU* 4.1 20.0 - - + -
17D PRO* 3.6 13.0 - - + +
18D LEU* 4.3 3.4 - - + +
19D LYS* 3.6 13.4 - - - -
32D PHE* 4.1 17.9 - - + -
302D THR 3.8 22.7 - - - +
303D THR* 4.9 4.0 - - + -
327D MSE 4.7 0.2 - - - +
328D TRP* 3.1 20.2 + - - +
329D GLN* 5.0 0.3 - - - -
330D LEU* 1.3 79.2 - - - +
332D GLN* 1.3 67.5 + - - +
333D GLU 3.4 15.9 + - - +
334D ASP* 3.8 27.0 + - - +
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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