Contacts of the strand formed by residues 245 - 255 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210G ASP* 4.7 11.4 - - - -
209H PRO* 3.9 5.8 - - - -
243H PRO 3.6 1.2 + - - -
244H ALA* 1.3 74.7 - - - +
246H GLU* 1.3 61.1 + - - -
247H TYR* 3.7 6.4 - - - -
269H VAL* 3.3 8.0 - - - -
270H LYS 2.7 43.6 + - - +
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Residues in contact with GLU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ASP* 3.8 14.4 + - - +
211G GLY* 3.6 25.0 - - - +
144H LYS* 2.8 32.6 + - - -
207H VAL 3.8 1.2 - - - +
208H GLY* 3.4 19.6 - - - -
209H PRO* 3.6 5.4 - - - +
245H GLY* 1.3 70.5 - - - -
247H TYR* 1.3 65.8 + - - +
248H THR* 4.1 5.5 + - - +
267H THR* 4.1 25.3 + - - +
268H VAL 4.0 2.7 - - - +
269H VAL* 4.4 11.7 - - + +
1272H O4B 4.1 14.4 - - - +
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Residues in contact with TYR 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H ALA* 4.5 7.2 - - + -
207H VAL 3.5 1.3 - - - -
208H GLY* 3.8 13.2 - - - -
209H PRO* 3.5 18.2 - - + -
212H LEU* 4.9 2.5 - - + -
214H ILE* 3.7 28.5 - - + -
238H PHE* 3.6 33.7 - + + -
242H TYR* 3.6 8.7 - - + +
243H PRO* 2.7 52.9 + - - +
245H GLY 3.7 11.4 - - - -
246H GLU* 1.3 75.3 - - - +
248H THR* 1.3 61.0 + - - +
249H ILE* 3.6 7.7 + - + -
267H THR* 3.4 4.0 - - - -
268H VAL 2.7 47.8 + - - +
270H LYS* 3.8 16.6 - - + -
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Residues in contact with THR 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LYS* 4.5 2.9 - - - +
207H VAL* 2.7 40.4 + - - +
246H GLU* 4.1 8.2 + - - +
247H TYR* 1.3 70.6 - - - +
249H ILE* 1.3 64.6 + - - +
250H ASN* 3.3 5.4 + - - +
265H SER* 4.3 10.8 - - - -
266H MET 3.7 8.7 - - - +
267H THR* 4.6 3.4 - - - +
1272H O4B 3.6 73.6 + - - +
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Residues in contact with ILE 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H PHE* 3.7 35.7 - - + -
204H MET* 4.0 24.5 - - + -
205H THR 3.6 5.4 - - - +
206H ALA* 3.5 26.0 - - + -
216H VAL* 4.9 6.5 - - + -
236H ILE* 4.4 8.3 - - + -
238H PHE* 4.0 22.0 - - + -
247H TYR* 4.5 4.7 - - + +
248H THR* 1.3 69.6 - - - +
250H ASN* 1.3 61.3 - - - +
265H SER* 3.2 5.2 - - - -
266H MET* 2.6 52.0 + - + +
268H VAL* 4.0 12.8 - - + -
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Residues in contact with ASN 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G TYR* 4.5 10.9 + - - +
203H TRP* 5.5 0.4 - - - -
204H MET* 3.2 4.5 - - - +
205H THR* 2.8 54.0 + - - +
207H VAL* 4.9 3.1 - - + -
248H THR 3.3 7.8 + - - +
249H ILE* 1.3 76.2 - - - +
251H ALA* 1.3 63.3 + - - +
252H GLN* 2.9 36.8 + - - +
263H GLU* 3.0 16.3 + - - +
264H GLN 3.6 2.7 - - - +
265H SER* 2.8 23.1 + - - +
1272H O4B 3.6 16.1 - - - +
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Residues in contact with ALA 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ILE* 6.1 0.6 - - - +
168H ILE* 3.5 35.4 - - + -
202H PHE* 4.5 2.2 - - + -
203H TRP 3.4 4.7 - - - +
204H MET* 3.7 24.7 - - + -
249H ILE 4.3 0.4 + - - -
250H ASN* 1.3 73.0 - - - +
252H GLN* 1.3 65.4 + - - +
263H GLU* 3.3 4.0 - - - +
264H GLN 2.8 40.0 + - - +
266H MET* 5.3 0.2 - - + -
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Residues in contact with GLN 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G GLY 3.1 19.9 - - - +
86G ILE* 4.1 1.8 - - - +
87G TYR 3.8 12.7 + - - +
201H GLU 4.1 0.2 - - - +
202H PHE* 3.4 1.4 - - - -
203H TRP* 2.8 69.4 + - + +
250H ASN* 2.9 28.1 + - - +
251H ALA* 1.3 80.5 - - - +
253H VAL* 1.3 71.1 + - - +
261H ARG* 3.2 36.5 - - + +
262H VAL 3.4 7.4 - - - +
263H GLU* 3.5 10.9 - - + -
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Residues in contact with VAL 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LEU* 3.6 22.8 - - + +
164H LEU* 4.7 0.7 - - + -
166H ILE* 3.6 38.6 - - + -
168H ILE* 5.4 1.1 - - + -
190H LEU* 4.4 10.1 - - + -
200H VAL* 3.9 22.7 - - + -
201H GLU 3.4 9.9 - - - +
202H PHE* 3.8 19.3 - - + -
251H ALA 5.6 0.2 - - - -
252H GLN* 1.3 81.0 - - - +
254H VAL* 1.3 64.4 + - - +
261H ARG* 3.4 2.6 - - - -
262H VAL* 2.9 37.4 + - + +
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Residues in contact with VAL 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G TYR* 3.8 29.2 - - + +
124G MET* 4.2 7.0 - - + -
161H LEU* 4.0 3.1 - - - -
200H VAL* 3.1 6.6 - - - +
201H GLU* 2.8 38.6 + - + +
203H TRP* 3.3 35.2 - - + -
253H VAL* 1.3 76.3 - - - +
255H ASP* 1.3 73.8 + - - +
256H ILE 3.4 0.3 + - - -
259H GLY* 4.1 11.7 - - - +
260H GLU 3.5 11.4 - - - +
261H ARG* 3.9 19.3 - - + +
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Residues in contact with ASP 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LEU* 3.6 18.9 - - + +
194H ARG* 2.7 37.1 + - - +
199H ASN 3.5 12.3 + - - +
200H VAL* 4.3 3.4 - - + -
254H VAL* 1.3 72.3 - - - +
256H ILE* 1.3 57.1 + - - +
257H VAL* 2.9 21.1 + - - +
258H SER* 3.1 30.3 + - - +
259H GLY* 2.8 34.1 + - - -
260H GLU* 2.9 12.5 + - + +
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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