Contacts of the strand formed by residues 267 - 270 (chain H) 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 267 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E HIS* 4.4 16.4 - - - +
220H PHE* 3.2 41.7 - - + -
244H ILE 4.1 1.4 + - - -
245H VAL* 3.4 17.9 - - + +
246H ALA 3.2 22.7 + - - -
265H ALA* 3.4 7.2 + - - +
266H ASP* 1.3 79.3 - - + +
268H ILE* 1.3 72.7 + - - +
293H LEU* 4.9 2.9 - - - -
294H LYS* 3.2 35.0 - - + +
296H CYS* 3.6 21.1 - - + +
321H ASP* 3.8 32.8 - - - +
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Residues in contact with ILE 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H VAL* 4.5 0.2 - - - -
246H ALA* 3.9 5.4 - - + +
250H ALA* 3.9 25.4 - - + -
256H VAL* 4.0 20.0 - - + +
259H ILE* 3.9 26.7 - - + -
260H CYS* 3.8 29.6 - - - -
265H ALA* 4.9 0.4 - - + -
267H MSE 1.3 83.7 - - - +
269H CYS* 1.3 61.4 + - - +
270H ILE* 3.7 17.7 + - + -
288H ALA* 4.7 6.3 - - + -
293H LEU* 4.2 11.0 - - + -
294H LYS 3.1 8.8 + - - +
295H ILE* 3.4 13.5 - - + +
296H CYS 2.9 23.9 + - - +
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Residues in contact with CYS 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H GLU* 3.7 23.6 - - - +
245H VAL* 4.0 13.6 - - + +
246H ALA 2.7 18.3 + - - +
247H ASP* 3.5 28.3 - - - +
250H ALA 4.5 0.2 - - - +
268H ILE* 1.3 73.3 - - - +
270H ILE* 1.3 60.4 + - - +
274H GLU* 4.5 0.2 - - - +
296H CYS* 3.2 28.7 - - + +
298H HIS* 3.5 28.0 - - - -
325H GLN* 3.8 9.4 - - - -
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Residues in contact with ILE 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H ALA 3.4 16.8 - - - +
251H PHE 3.4 24.7 - - - +
256H VAL* 3.8 24.0 - - + -
268H ILE* 4.2 8.3 - - + -
269H CYS* 1.3 75.5 - - - +
271H GLY* 1.3 69.4 + - - +
274H GLU* 3.4 11.0 - - + +
275H ILE* 3.9 13.2 - - + -
281H MSE 3.3 29.6 - - + +
284H ALA* 4.7 5.4 - - + -
295H ILE* 4.1 23.3 - - + -
296H CYS 3.0 8.3 + - - +
297H ILE* 3.5 1.2 - - - -
298H HIS* 3.2 15.5 + - - +
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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