Contacts of the strand formed by residues 245 - 255 (chain E) in PDB entry 4BEI
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 GLY 245 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209E PRO* 3.9 6.1 - - - -
243E PRO 3.6 1.2 + - - -
244E ALA* 1.3 76.0 - - - +
246E GLU* 1.3 61.7 + - - -
247E TYR* 3.6 6.5 - - - -
269E VAL* 3.3 7.1 - - - +
270E LYS 2.7 43.2 + - - +
210F ASP* 4.7 11.7 - - - -
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Residues in contact with GLU 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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144E LYS* 2.8 31.5 + - - -
207E VAL 3.8 1.0 - - - +
208E GLY* 3.4 20.4 - - - -
209E PRO* 3.6 6.5 - - - +
245E GLY* 1.3 70.9 - - - -
247E TYR* 1.3 66.5 + - - +
248E THR* 5.0 6.5 + - - +
267E THR* 4.1 24.9 + - - +
268E VAL 4.0 2.2 - - - +
269E VAL* 4.4 12.5 - - + +
1272E O4B 4.4 13.6 - - - +
210F ASP* 3.8 15.1 + - - +
211F GLY* 3.6 23.4 - - - +
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Residues in contact with TYR 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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206E ALA* 4.5 8.3 - - + -
207E VAL 3.5 1.3 - - - +
208E GLY* 3.8 14.1 - - - -
209E PRO* 3.5 17.7 - - + -
212E LEU* 4.9 3.1 - - + -
214E ILE* 3.7 28.7 - - + -
238E PHE* 3.6 32.5 - + + -
242E TYR* 3.5 9.0 - - + +
243E PRO* 2.7 53.0 + - - +
245E GLY 3.6 11.4 - - - -
246E GLU* 1.3 74.6 - - - +
248E THR* 1.3 61.6 + - - +
249E ILE* 3.6 7.6 + - + -
267E THR* 3.4 4.3 - - - -
268E VAL* 2.7 46.4 + - - +
270E LYS* 3.8 16.4 - - + -
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Residues in contact with THR 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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81E LYS* 4.5 1.1 - - - +
205E THR 3.7 0.2 - - - +
207E VAL* 2.7 40.4 + - - +
246E GLU* 4.1 8.5 + - - +
247E TYR* 1.3 70.0 - - - +
249E ILE* 1.3 63.8 + - - +
250E ASN* 3.3 5.7 + - + +
265E SER* 4.3 7.9 - - - +
266E MET 3.7 7.6 - - - +
267E THR* 4.6 4.9 - - - +
1272E O4B 3.6 76.7 + - - +
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Residues in contact with ILE 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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186E PHE* 3.7 36.1 - - + -
204E MET* 4.0 24.7 - - + -
205E THR 3.6 5.8 - - - +
206E ALA* 3.5 26.0 - - + -
216E VAL* 4.9 6.3 - - + -
236E ILE* 4.4 8.5 - - + -
238E PHE* 4.0 22.2 - - + -
247E TYR* 3.6 4.9 + - + -
248E THR* 1.3 69.1 - - - +
250E ASN* 1.3 61.4 + - - +
265E SER* 3.2 4.9 - - - -
266E MET* 2.6 52.5 + - + +
268E VAL* 4.0 12.3 - - + -
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Residues in contact with ASN 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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203E TRP* 5.5 0.5 - - - -
204E MET* 3.2 3.9 - - - +
205E THR* 2.8 54.7 + - - +
207E VAL* 4.9 4.0 - - + -
248E THR* 4.0 7.6 - - + +
249E ILE* 1.3 75.3 - - - +
251E ALA* 1.3 62.9 + - - +
252E GLN* 2.9 37.8 + - - +
263E GLU* 3.0 17.7 + - - +
264E GLN 3.6 3.0 - - - +
265E SER* 2.8 23.1 + - - +
1272E O4B 3.8 12.5 - - - +
87F TYR* 4.5 11.8 + - - +
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Residues in contact with ALA 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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166E ILE* 6.1 0.4 - - - +
168E ILE* 3.5 35.6 - - + +
202E PHE* 4.5 1.8 - - + -
203E TRP 3.4 4.5 - - - +
204E MET* 3.7 24.9 - - + -
250E ASN* 1.3 73.7 - - - +
252E GLN* 1.3 64.1 + - - +
253E VAL* 5.6 0.7 - - - -
263E GLU* 3.3 4.9 - - - +
264E GLN 2.8 39.7 + - - +
266E MET* 5.1 0.4 - - - +
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Residues in contact with GLN 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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202E PHE* 3.4 2.1 - - - -
203E TRP* 2.8 68.4 + - + +
250E ASN* 2.9 26.3 + - - +
251E ALA* 1.3 80.1 - - - +
253E VAL* 1.3 69.2 - - - +
261E ARG* 3.2 36.7 - - + +
262E VAL 3.4 7.2 - - - +
263E GLU* 3.5 11.2 - - + -
85F GLY 3.1 19.9 - - - +
86F ILE* 4.1 1.4 - - - +
87F TYR 3.8 14.1 + - - +
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Residues in contact with VAL 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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161E LEU* 3.6 22.2 - - + +
164E LEU* 4.7 1.8 - - + -
166E ILE* 3.6 37.5 - - + -
168E ILE* 5.4 0.7 - - + -
190E LEU* 4.4 8.7 - - + -
200E VAL* 3.9 23.1 - - + -
201E GLU 3.4 9.6 - - - +
202E PHE* 3.8 20.0 - - + -
251E ALA 5.6 0.2 - - - -
252E GLN* 1.3 81.1 - - - +
254E VAL* 1.3 64.4 + - - +
261E ARG* 3.4 1.8 - - - -
262E VAL* 2.9 36.9 + - + +
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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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161E LEU* 4.0 2.9 - - - -
200E VAL* 3.1 6.7 - - - -
201E GLU* 2.8 39.5 + - + +
203E TRP* 3.3 35.7 - - + -
253E VAL* 1.3 75.1 - - - +
255E ASP* 1.3 73.3 + - - +
256E ILE 3.4 0.3 + - - -
259E GLY* 4.1 12.1 - - - +
260E GLU 3.5 11.2 - - - +
261E ARG* 3.9 18.4 - - + -
123F TYR* 3.8 29.4 - - + +
124F MET* 4.2 7.9 - - + -
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Residues in contact with ASP 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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161E LEU* 3.6 18.6 - - + +
194E ARG* 2.7 37.5 + - - +
199E ASN 3.5 10.7 + - - +
200E VAL* 4.3 3.1 - - + -
254E VAL* 1.3 72.2 - - - +
256E ILE* 1.3 56.7 + - - +
257E VAL* 2.9 22.1 + - - +
258E SER* 3.1 30.6 + - - +
259E GLY* 2.8 34.3 + - - -
260E GLU 2.9 12.1 + - - +
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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