Contacts of the strand formed by residues 238 - 245 (chain A) in PDB entry 3PE7
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 GLU 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A HIS 4.8 2.3 - - - +
212A ASP* 5.7 1.4 - - - -
232A LYS* 2.8 31.4 + - - -
234A HIS* 2.9 28.6 + - + +
235A ALA* 2.8 48.1 + - - +
236A GLU 3.2 0.8 - - - -
237A GLY* 1.3 77.6 - - - +
239A SER* 1.3 67.7 + - - +
240A CYS* 3.5 15.3 - - - -
256A SER* 2.7 28.9 + - - +
257A TYR 3.4 5.6 - - - +
258A LEU* 3.7 14.6 - - + -
267A TYR* 5.1 0.9 - - - -
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Residues in contact with SER 239 (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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211A HIS* 2.7 44.7 + - - -
212A ASP* 4.2 4.2 + - - +
234A HIS* 4.3 0.2 - - - -
237A GLY 3.8 3.4 + - - -
238A GLU* 1.3 75.2 + - - +
240A CYS* 1.3 64.5 + - - +
241A THR* 6.0 0.2 - - - -
256A SER* 3.4 5.2 - - - -
257A TYR* 2.9 63.4 + - - +
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Residues in contact with CYS 240 (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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211A HIS* 5.2 5.3 + - - +
217A ARG* 2.9 32.4 - - + +
218A MET* 4.5 7.9 - - + -
232A LYS* 3.9 17.9 - - - -
234A HIS* 3.8 30.2 - - + +
238A GLU* 3.5 29.6 - - - -
239A SER* 1.3 78.2 - - - +
241A THR* 1.3 63.8 + - - +
254A TYR* 4.0 17.3 - - + -
255A VAL 3.3 4.5 - - - -
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Residues in contact with THR 241 (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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211A HIS* 5.8 6.1 - - - -
217A ARG* 4.6 8.9 + - - +
218A MET* 5.5 0.2 - - - -
240A CYS* 1.3 78.1 - - - +
242A HIS* 1.3 97.4 + - + +
243A GLU* 3.2 11.6 + - - -
254A TYR* 3.5 3.8 - - - +
255A VAL* 2.8 44.3 + - + +
257A TYR* 4.2 22.9 - - + +
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Residues in contact with HIS 242 (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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38A PHE* 5.8 5.1 - - + -
217A ARG* 4.9 1.8 - - - +
241A THR* 1.3 105.7 + - + +
243A GLU* 1.3 69.1 + - - +
244A PHE* 3.5 17.3 - - - -
253A VAL 3.9 1.6 - - - +
254A TYR* 4.2 2.5 - - - -
255A VAL* 3.9 27.4 - - + +
282A MET* 6.0 0.6 - - - +
285A CYS* 3.0 28.8 + - - +
286A SER* 3.2 27.2 + - - -
287A HIS* 4.1 10.1 + + - -
288A LEU* 4.6 12.6 - - + +
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Residues in contact with GLU 243 (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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38A PHE* 5.7 2.6 - - - -
192A HIS* 2.9 43.6 + - + +
194A ILE* 4.8 7.6 - - + -
204A ALA* 6.0 2.0 - - + -
205A PHE 5.3 3.0 - - - +
206A CYS* 3.8 11.8 + - - +
217A ARG* 2.8 47.0 + - - -
218A MET* 3.3 41.1 - - + +
241A THR 3.2 2.6 - - - -
242A HIS* 1.3 84.0 + - - +
244A PHE* 1.3 62.3 + - - +
252A LEU* 4.6 4.3 - - + -
253A VAL 3.2 7.2 - - - -
254A TYR* 3.9 2.0 - - + -
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Residues in contact with PHE 244 (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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38A PHE* 4.7 12.6 - - + -
39A TYR* 5.3 7.2 - - + -
192A HIS* 4.9 2.0 - - + -
194A ILE* 4.4 6.3 - - - -
242A HIS 3.5 13.5 - - - -
243A GLU* 1.3 76.5 - - - +
245A TRP* 1.3 82.3 + - - +
246A VAL* 4.4 1.8 - - - -
252A LEU* 3.4 10.1 - - - +
253A VAL* 2.8 68.6 + - + +
288A LEU* 3.5 33.2 - - + -
289A MET* 3.8 16.4 - - - -
290A SER* 3.4 45.8 - - - -
297A MET* 4.3 2.7 - - - -
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Residues in contact with TRP 245 (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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194A ILE* 3.0 48.3 + - + +
195A TYR 3.3 18.8 + - - -
196A ARG* 3.5 39.2 - - + +
197A PRO* 3.5 20.2 - - + -
202A THR* 4.1 6.3 - - + -
204A ALA* 3.7 18.4 - - + -
220A LEU* 3.9 18.8 - - + -
244A PHE* 1.3 85.1 - - - +
246A VAL* 1.3 65.4 + - - +
247A PRO* 3.3 6.9 - - - +
249A GLY* 4.8 2.9 - - - -
251A ALA* 3.4 18.6 - - - -
252A LEU* 3.7 22.7 - - + -
271A PRO* 3.6 29.4 - - + -
289A MET* 5.2 1.6 - - - +
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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