Contacts of the strand formed by residues 248 - 255 (chain E) 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 248 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237E SER* 3.7 37.2 - - - +
240E ARG* 4.0 15.0 - - + +
241E ALA* 4.2 21.1 - - + +
245E GLU* 3.7 45.3 - - + +
246E GLN 4.2 0.2 - - - +
247E GLY* 1.3 77.4 - - - +
249E VAL* 1.3 64.9 + - - +
268E LEU 3.6 0.3 - - - +
269E LEU* 3.5 5.4 - - - +
270E LEU* 2.8 38.5 + - + +
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Residues in contact with VAL 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ARG* 5.0 2.1 + - - -
247E GLY* 3.4 9.1 + - - +
248E VAL* 1.3 83.0 - - - +
250E GLU* 1.3 78.7 + - - +
251E CYS* 5.1 0.9 - - - +
267E PRO* 4.3 13.5 - - + -
268E LEU 3.2 20.9 - - - +
269E LEU* 4.1 12.8 - - + -
279E LYS* 4.1 24.9 - - + -
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Residues in contact with GLU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E THR* 4.6 6.7 + - - +
151E ILE* 5.7 1.7 - - - +
233E ARG* 2.7 46.3 + - - +
234E PHE* 3.4 35.0 - - + -
237E SER* 2.7 29.1 + - - -
248E VAL 4.3 0.2 - - - -
249E VAL* 1.3 80.8 - - - +
251E CYS* 1.3 68.7 + - - +
267E PRO* 4.4 0.7 - - - -
268E LEU* 2.9 37.5 + - - +
270E LEU* 4.0 20.4 - - + -
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Residues in contact with CYS 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E THR* 3.4 10.5 + - - -
148E THR* 4.3 9.0 + - - -
151E ILE* 4.1 20.4 - - + +
172E PRO* 4.4 7.9 - - - -
173E VAL 3.5 39.3 - - - +
249E VAL* 5.1 0.8 - - - +
250E GLU* 1.3 82.7 + - - +
252E ALA* 1.3 61.0 + - - +
265E SER* 4.2 2.9 - - - +
266E GLN 3.3 9.4 - - - +
267E PRO* 3.9 29.2 - - - -
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Residues in contact with ALA 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PHE* 3.8 11.7 - - + -
145E GLY 3.6 12.8 - - - +
147E THR* 3.8 2.9 - - - +
234E PHE* 3.7 24.7 - - + -
250E GLU 3.5 1.4 + - - -
251E CYS* 1.3 76.5 - - - +
253E TYR* 1.3 63.1 + - - +
254E VAL* 3.4 5.9 + - - +
265E SER* 3.3 17.4 + - - -
266E GLN 3.4 10.4 + - - +
268E LEU* 3.7 23.2 - - + +
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Residues in contact with TYR 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E VAL* 3.7 7.9 - - + -
122E ASN* 2.8 44.2 + - - +
125E VAL* 3.6 38.4 - - + +
143E LEU 4.2 0.3 - - - +
144E PHE* 3.7 1.6 - - - -
145E GLY* 2.8 37.5 + - - +
147E THR* 3.8 19.9 - - + +
175E GLY 3.4 24.5 - - - -
176E GLY* 4.3 4.9 - - - -
252E ALA* 1.3 68.9 - - - +
254E VAL* 1.3 61.5 + - - +
263E PHE* 3.3 39.8 - - + +
264E PHE* 3.9 2.0 - - - -
265E SER* 3.5 12.6 + - - -
299E LEU* 3.8 13.4 - - + +
303E ILE* 3.4 13.5 - - - +
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E VAL* 5.7 0.2 - - - -
143E LEU 3.5 22.9 - - - +
144E PHE* 3.8 12.8 - - + -
252E ALA 3.9 2.7 - - - +
253E TYR* 1.3 77.5 - - - +
255E GLU* 1.3 60.2 + - - +
256E GLY 3.3 5.9 + - - +
263E PHE* 3.2 9.3 - - - -
264E PHE 2.8 38.7 + - - +
266E GLN* 4.7 4.3 - - + +
268E LEU* 3.7 44.4 - - + -
275E VAL* 4.4 5.2 - - + -
278E ARG* 3.8 24.5 - - + +
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Residues in contact with GLU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E TYR* 2.6 44.9 + - - +
140E LYS* 3.1 35.1 + - + +
143E LEU 5.1 1.0 + - - -
254E VAL* 1.3 69.8 - - - +
256E GLY* 1.3 59.7 + - - +
262E ARG* 3.0 58.9 + - + +
263E PHE* 3.6 12.1 - - + -
278E ARG* 2.9 22.2 + - - +
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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