Contacts of the strand formed by residues 249 - 255 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ARG* 5.1 1.7 + - - -
247A GLY 3.4 11.5 + - - +
248A VAL* 1.3 79.6 - - - +
250A GLU* 1.3 79.5 + - - +
251A CYS* 6.0 0.9 - - - -
267A PRO* 4.3 9.0 - - + -
268A LEU 3.1 20.0 - - - +
269A LEU* 4.3 12.3 - - + -
279A LYS* 4.0 30.1 - - + +
168E GLU* 4.9 4.0 - - - +
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 4.5 6.3 + - - +
151A ILE* 5.8 1.6 - - - +
233A ARG* 2.6 46.8 + - - +
234A PHE* 3.7 32.8 - - + -
237A SER* 2.8 28.8 + - - -
248A VAL 4.3 0.2 - - - -
249A VAL* 1.3 82.4 - - - +
251A CYS* 1.3 66.8 + - - +
252A ALA* 5.5 0.2 - - + -
268A LEU* 2.7 43.7 + - - +
270A LEU* 4.0 19.7 - - + +
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Residues in contact with CYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 3.1 13.5 + - - -
148A THR* 4.4 8.1 + - - -
151A ILE* 3.8 20.5 - - + +
172A PRO* 4.5 9.0 - - - -
173A VAL 3.6 37.9 - - - +
174A ILE* 5.3 0.2 - - - -
234A PHE* 4.9 0.5 - - - -
249A VAL* 6.0 0.9 - - - -
250A GLU* 1.3 81.7 + - - +
252A ALA* 1.3 63.7 + - - +
265A SER* 4.3 2.2 - - - +
266A GLN 3.5 6.3 - - - +
267A PRO* 3.9 28.9 - - - -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 4.1 7.6 - - + -
145A GLY 3.8 9.9 - - - +
147A THR* 3.6 5.8 - - - +
234A PHE* 3.8 27.4 - - + -
250A GLU 3.8 1.8 + - - +
251A CYS* 1.3 75.8 - - - +
253A TYR* 1.3 61.6 + - - +
254A VAL* 3.5 4.7 + - - +
264A PHE 3.6 1.4 - - - +
265A SER* 3.2 21.8 + - - -
266A GLN 3.4 11.1 + - - +
268A LEU* 3.7 24.0 - - + +
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Residues in contact with TYR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL* 3.5 19.7 - - + -
122A ASN* 2.9 42.5 + - - +
125A VAL* 3.5 43.9 - - + +
143A LEU 4.0 0.5 - - - +
144A PHE* 3.5 1.4 - - - -
145A GLY* 2.8 43.2 + - - +
147A THR* 3.9 11.6 - - + +
175A GLY 3.5 21.8 - - - -
176A GLY* 4.1 3.1 - - - -
252A ALA* 1.3 69.0 - - - +
254A VAL* 1.3 62.3 + - - +
263A PHE* 3.4 27.3 - + + +
264A PHE 3.8 4.9 - - - -
265A SER* 3.5 5.5 + - - +
299A LEU* 3.8 6.9 - - + +
303A ILE* 3.2 22.7 - - - +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS 4.8 0.9 - - - +
143A LEU 3.5 20.0 - - - +
144A PHE* 3.7 13.5 - - + -
252A ALA 4.1 1.1 - - - +
253A TYR* 1.3 80.7 - - - +
255A GLU* 1.3 76.0 + - - +
256A GLY* 3.4 1.8 + - - +
263A PHE* 3.4 9.3 - - - -
264A PHE* 3.0 30.4 + - - +
266A GLN* 5.2 2.8 - - - +
268A LEU* 3.6 46.0 - - + -
275A VAL* 4.2 5.4 - - + -
278A ARG* 3.9 16.8 - - + +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.5 30.0 + - - +
140A LYS* 3.4 38.4 + - + +
143A LEU 4.9 1.2 + - - -
254A VAL* 1.3 72.6 - - - +
256A GLY* 1.3 53.2 + - - +
262A ARG* 2.5 65.1 + - + +
263A PHE* 3.4 13.2 - - + -
278A ARG* 2.7 38.3 + - - -
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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