Contacts of the strand formed by residues 249 - 255 (chain C) in PDB entry 2PWZ
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 VAL 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C ARG* 5.1 2.6 + - - -
247C GLY* 3.3 13.6 + - - +
248C VAL* 1.3 79.4 - - - +
250C GLU* 1.3 75.6 + - - +
251C CYS* 5.2 0.7 - - - +
267C PRO* 4.5 8.3 - - + -
268C LEU 3.1 21.1 - - - +
269C LEU* 4.1 16.2 - - + -
279C LYS* 4.3 22.4 - - + +
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C THR* 4.5 7.0 + - - +
151C ILE* 6.0 0.7 - - - +
233C ARG* 3.0 45.9 + - - +
234C PHE* 4.0 31.6 - - + -
237C SER* 2.6 39.3 + - - +
248C VAL* 4.3 1.1 + - + -
249C VAL* 1.3 80.5 - - - +
251C CYS* 1.3 67.1 + - - +
267C PRO* 4.5 0.9 - - - -
268C LEU* 2.9 35.5 + - - +
270C LEU* 4.1 11.7 - - + +
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Residues in contact with CYS 251 (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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147C THR* 3.5 8.6 + - - -
148C THR* 4.5 10.2 + - - -
151C ILE* 4.0 21.7 - - + +
170C GLU* 6.0 1.3 - - - -
172C PRO* 4.4 8.5 - - - -
173C VAL 3.5 39.7 - - - +
174C ILE* 5.3 0.4 - - - -
233C ARG* 5.8 0.8 - - - +
234C PHE* 4.7 0.3 - - - -
249C VAL* 6.2 0.7 - - - -
250C GLU* 1.3 82.1 + - - +
252C ALA* 1.3 62.9 + - - +
265C SER* 4.2 1.8 - - - +
266C GLN 3.3 7.4 - - - +
267C PRO* 4.0 28.3 - - - -
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Residues in contact with ALA 252 (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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144C PHE* 4.0 11.4 - - + -
145C GLY 3.6 11.4 - - - +
147C THR* 3.7 6.7 - - - +
234C PHE* 4.0 22.4 - - + -
250C GLU 3.7 1.2 + - - -
251C CYS* 1.3 76.7 - - - +
253C TYR* 1.3 62.4 + - - +
254C VAL* 3.5 4.7 + - - +
264C PHE 3.6 0.7 - - - +
265C SER* 3.1 22.5 + - - -
266C GLN 3.3 12.0 + - - +
268C LEU* 3.7 21.8 - - + +
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Residues in contact with TYR 253 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C VAL* 3.5 15.7 - - + -
122C ASN* 2.7 35.6 + - - -
125C VAL* 3.0 44.0 - - + +
143C LEU 4.2 0.2 - - - +
144C PHE* 3.5 1.9 - - - -
145C GLY* 2.7 43.2 + - - +
147C THR* 3.9 12.9 - - + +
175C GLY 3.5 19.1 - - - -
176C GLY* 4.2 5.2 - - - -
252C ALA* 1.3 68.5 - - - +
254C VAL* 1.3 62.0 + - - +
263C PHE* 3.3 26.1 - - + +
264C PHE 3.9 2.2 - - - -
265C SER* 3.5 9.9 + - - +
299C LEU* 3.6 19.1 - - + +
303C ILE* 3.3 20.6 - - - +
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Residues in contact with VAL 254 (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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140C LYS 5.0 0.2 - - - +
143C LEU 3.5 22.7 - - - +
144C PHE* 3.6 24.2 - - + -
252C ALA 4.0 3.4 - - - +
253C TYR* 1.3 78.2 - - - +
255C GLU* 1.3 64.0 + - - +
256C GLY* 3.4 1.7 + - - -
263C PHE* 3.2 9.2 - - - -
264C PHE* 2.9 36.1 + - - +
266C GLN* 4.7 6.3 - - + +
268C LEU* 3.6 34.3 - - + -
275C VAL* 4.3 4.7 - - + -
278C ARG* 4.2 23.6 - - + +
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Residues in contact with GLU 255 (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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133C LYS* 5.9 0.2 - - - -
138C TYR* 2.7 41.6 + - - +
140C LYS* 3.5 23.6 + - + +
143C LEU 5.0 0.8 + - - -
254C VAL* 1.3 72.5 - - - +
256C GLY* 1.3 60.8 + - - +
262C ARG* 2.8 62.4 + - + +
263C PHE* 3.6 12.4 - - + -
278C ARG* 2.6 33.2 + - - +
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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