Contacts of the helix formed by residues 327 - 331 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C TYR* 4.6 0.4 - - - +
32C PHE* 4.8 2.8 - - + -
140C PHE* 4.8 7.2 - - - -
142C PHE* 4.1 25.6 - - + -
299C SER* 3.4 29.9 + - - +
300C SER* 3.4 22.2 - - - +
301C PHE* 3.6 37.7 - - + -
302C THR* 4.7 8.4 - - - +
307C THR* 4.7 2.0 + - - -
325C GLN* 5.6 2.0 - - - +
326C ILE* 1.3 83.9 - - - +
328C TRP* 1.3 67.7 + - - +
329C GLN* 3.0 8.6 + - - +
330C LEU* 3.0 42.4 + - + +
331C VAL* 4.4 1.4 + - - +
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Residues in contact with TRP 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 6.0 3.8 - - - -
302C THR 4.7 5.3 + - - -
303C THR 4.7 0.8 + - - -
304C GLY* 3.9 17.5 - - - +
307C THR* 3.3 21.8 + - + +
326C ILE* 3.5 26.9 - - + +
327C MSE 1.3 76.6 - - - +
329C GLN* 1.3 81.4 + - + +
330C LEU 3.1 2.0 + - - -
331C VAL* 3.3 27.1 + - - +
334C ASP* 3.8 26.3 - - + +
340C ASP* 4.9 1.3 - - - -
341C LEU* 2.8 47.4 + - + +
342C THR* 3.3 29.8 - - + -
343C PRO* 4.6 2.0 - - + +
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Residues in contact with GLN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 3.0 38.0 + - - +
142C PHE* 4.3 18.4 - - - +
326C ILE* 2.8 47.7 + - - +
327C MSE 3.4 10.1 - - - +
328C TRP* 1.3 103.4 + - + +
330C LEU* 1.3 72.4 + - + +
331C VAL 3.4 0.4 - - - -
343C PRO* 6.1 0.6 - - + +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.5 10.1 - - + +
19C LYS* 2.8 30.9 + - - +
20C GLN* 4.7 4.2 + - + -
22C TYR* 4.3 10.5 - - + -
32C PHE* 4.1 20.9 - - + -
142C PHE* 4.2 14.8 - - + -
144C GLN* 3.9 28.7 - - + +
327C MSE 3.0 46.0 + - + +
329C GLN* 1.3 94.3 - - + +
331C VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.1 22.0 - - + +
17C PRO* 3.6 13.7 - - + +
18C LEU* 4.3 2.0 - - + -
19C LYS* 3.7 13.4 - - - +
32C PHE* 4.2 17.5 - - + -
302C THR 3.8 21.8 - - - +
303C THR* 4.8 4.3 - - + -
327C MSE 4.7 0.2 - - - +
328C TRP* 3.3 20.6 + - - +
329C GLN 4.4 0.2 - - - -
330C LEU* 1.3 79.6 - - - +
332C GLN* 1.3 69.5 + - - +
333C GLU 3.4 15.2 + - - +
334C ASP* 3.9 26.7 + - - +
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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