Contacts of the strand formed by residues 241 - 249 (chain E) in PDB entry 3BZE
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 PHE 241 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E ASP* 4.0 21.5 - - + -
207E GLY 3.0 7.6 + - - -
208E PHE* 2.8 61.3 + - + +
209E TYR* 3.9 14.4 - + - -
210E PRO 4.2 0.7 - - - -
211E ALA* 3.8 36.6 - - + -
233E THR* 4.0 8.7 - - + -
234E ARG 3.4 17.9 - - - +
235E PRO* 3.9 21.3 - - + -
236E ALA* 4.2 1.6 - - - +
239E GLY 3.8 17.0 - - - -
240E THR* 1.3 76.5 - - - +
242E GLN* 1.3 62.2 + - - +
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Residues in contact with GLN 242 (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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205E ALA 3.2 5.2 - - - +
206E LEU* 3.4 32.2 - - + +
207E GLY 4.5 1.4 - - - +
208E PHE* 3.4 2.5 - - - -
234E ARG* 2.9 62.2 + - + +
236E ALA* 3.6 18.2 - - - +
241E PHE* 1.3 75.6 - - - +
243E LYS* 1.3 61.0 + - - +
10F TYR* 2.7 34.6 - - + -
11F SER 3.6 6.9 + - - +
12F ARG 3.5 22.8 + - - -
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Residues in contact with LYS 243 (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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204E TRP* 4.6 2.9 - - - -
205E ALA* 3.0 32.4 + - + +
206E LEU* 5.1 0.2 - - - +
208E PHE* 3.7 12.9 - - + -
213E ILE* 3.5 26.0 - - + -
214E THR* 5.8 0.2 - - - +
215E LEU* 3.9 19.7 - - + +
230E LEU* 3.4 28.9 - - - +
231E VAL* 2.9 36.0 + - - +
232E GLU* 4.3 1.4 - - - +
233E THR* 3.4 31.3 + - - +
234E ARG* 5.4 0.4 - - - +
242E GLN* 1.3 76.7 - - - +
244E TRP* 1.3 79.1 + - - +
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Residues in contact with TRP 244 (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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202E ARG* 3.0 44.0 - - + -
203E CYS 3.1 20.2 - - - +
204E TRP* 3.4 29.8 - + + -
215E LEU* 3.5 6.3 - - - -
229E GLU* 3.5 35.4 - - + -
230E LEU* 3.4 14.0 - - - +
231E VAL* 3.3 45.0 + - + +
234E ARG* 4.0 6.8 - - - +
243E LYS* 1.3 78.0 - - - +
245E ALA* 1.3 63.4 + - - +
246E ALA* 3.6 8.3 - - + -
99F MET* 2.8 51.4 + - + +
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Residues in contact with ALA 245 (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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203E CYS* 2.8 30.5 + - + +
215E LEU* 3.7 24.8 - - + +
216E THR* 5.5 0.7 - - - -
217E TRP* 3.3 19.9 + - + +
228E THR* 6.1 2.0 - - + -
229E GLU 3.6 6.5 - - - +
230E LEU* 3.7 19.7 - - + -
244E TRP* 1.3 78.2 - - - +
246E ALA* 1.3 60.0 + - - +
259E CYS* 5.7 0.4 - - - -
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Residues in contact with ALA 246 (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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200E THR* 3.7 15.9 - - + -
201E LEU 3.2 7.4 - - - +
202E ARG* 3.1 30.7 - - - +
217E TRP* 3.8 3.4 - - - -
228E THR* 3.0 30.0 - - - +
229E GLU* 2.8 15.2 + - + +
244E TRP* 3.6 7.6 - - + -
245E ALA* 1.3 73.0 - - - +
247E VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 247 (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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200E THR* 3.5 2.7 - - - -
201E LEU* 2.8 48.9 + - + +
217E TRP* 3.6 33.0 - - + -
228E THR* 4.4 17.5 - - + +
246E ALA* 1.3 76.5 - - - +
248E VAL* 1.3 71.3 + - - +
249E VAL* 3.6 17.7 + - + -
257E TYR* 4.3 21.5 - - + -
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Residues in contact with VAL 248 (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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194E ILE* 4.6 10.8 - - + -
198E GLU* 3.6 37.9 - - + +
199E ALA 3.3 8.1 - - - +
200E THR* 4.2 17.5 - - + +
228E THR 4.8 9.9 - - - +
247E VAL* 1.3 80.0 - - - +
249E VAL* 1.3 65.2 + - - +
250E PRO* 4.4 3.3 - - - +
257E TYR* 5.0 2.4 + - - -
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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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198E GLU* 3.2 5.3 - - - -
199E ALA* 2.7 43.5 + - + +
201E LEU* 4.2 11.7 - - + -
247E VAL* 3.6 23.8 - - + +
248E VAL* 1.3 79.2 - - - +
250E PRO* 1.3 87.4 - - + +
251E SER 3.3 0.2 + - - -
253E GLU* 3.9 11.7 - - + -
254E GLU* 4.1 8.5 - - + +
257E TYR* 3.4 44.0 - - + -
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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