Contacts of the strand formed by residues 245 - 255 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASP* 4.5 15.0 - - - -
209B PRO* 3.9 7.2 - - - -
243B PRO 3.6 0.8 + - - -
244B ALA* 1.3 77.0 - - - +
246B GLU* 1.3 61.4 + - - -
247B TYR* 3.7 3.6 - - - -
269B VAL* 3.3 7.1 - - - -
270B LYS* 2.7 43.2 + - - -
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP* 3.8 8.7 - - - +
211A GLY* 3.5 31.1 + - - +
144B LYS* 2.7 29.3 + - - -
207B VAL 3.8 1.2 - - - +
208B GLY* 3.4 19.9 - - - -
209B PRO* 3.6 6.0 - - - +
245B GLY* 1.3 71.1 - - - -
247B TYR* 1.3 66.7 + - - +
248B THR* 4.1 5.7 + - - +
267B THR* 4.1 22.7 + - - +
268B VAL 4.0 3.1 - - - +
269B VAL* 4.4 12.5 - - + +
1272B O4B 3.9 18.1 - - - +
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA* 4.5 8.1 - - + -
207B VAL 3.5 1.3 - - - -
208B GLY* 3.8 13.7 - - - -
209B PRO* 3.5 18.2 - - + -
212B LEU* 4.9 3.1 - - + -
214B ILE* 3.8 28.5 - - + -
238B PHE* 3.7 31.4 - + + -
242B TYR* 3.5 8.9 - - + +
243B PRO* 2.7 53.0 + - - +
245B GLY 3.7 10.5 - - - -
246B GLU* 1.3 74.4 - - - +
248B THR* 1.3 61.3 + - - +
249B ILE* 3.6 7.2 + - + -
267B THR* 3.4 3.8 - - - -
268B VAL* 2.7 47.5 + - - +
270B LYS* 3.8 18.4 - - + -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 4.2 1.6 - - - +
205B THR 3.7 0.2 - - - +
207B VAL* 2.7 38.3 + - - +
246B GLU* 5.0 5.0 + - - +
247B TYR* 1.3 70.7 - - - +
249B ILE* 1.3 65.9 + - - +
250B ASN* 3.3 5.4 + - + +
265B SER* 4.3 5.6 - - - -
266B MET 3.7 7.9 - - - +
267B THR* 4.6 4.8 - - - +
1272B O4B 3.2 84.8 + - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B PHE* 3.7 37.5 - - + -
204B MET* 4.0 24.0 - - + -
205B THR 3.6 5.2 - - - +
206B ALA* 3.5 25.6 - - + -
216B VAL* 4.9 6.7 - - + -
236B ILE* 4.4 8.5 - - + -
238B PHE* 4.0 22.0 - - + -
247B TYR* 4.5 5.2 - - + -
248B THR* 1.3 70.5 - - - +
250B ASN* 1.3 61.4 + - - +
265B SER* 3.2 4.7 - - - -
266B MET* 2.6 53.2 + - + +
268B VAL* 4.0 12.1 - - + -
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.5 10.7 + - - +
203B TRP* 4.1 0.4 - - - +
204B MET* 3.2 4.6 - - - +
205B THR* 2.7 55.7 + - - +
207B VAL* 4.9 2.0 - - + -
248B THR* 4.0 6.3 - - + +
249B ILE* 1.3 75.1 - - - +
251B ALA* 1.3 62.6 + - - +
252B GLN* 2.9 37.6 + - - +
263B GLU* 3.0 18.0 - - - +
264B GLN 3.6 3.1 - - - +
265B SER* 2.8 22.6 + - - +
1272B O4B 4.0 15.1 - - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 6.1 0.4 - - - +
168B ILE* 3.5 34.9 - - + +
202B PHE* 4.5 2.2 - - + -
203B TRP 3.4 4.3 - - - +
204B MET* 3.7 25.5 - - + +
250B ASN* 1.3 72.7 - - - +
252B GLN* 1.3 64.9 + - - +
253B VAL* 5.6 0.4 - - - -
263B GLU* 3.3 4.0 - - - +
264B GLN 2.8 40.5 + - - +
266B MET* 5.1 0.4 - - - +
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Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLY 3.1 19.8 - - - +
86A ILE* 4.1 9.3 - - - +
87A TYR 3.7 4.8 + - - +
202B PHE* 3.4 2.1 - - - -
203B TRP* 2.8 68.8 + - + +
250B ASN* 2.9 25.4 + - - +
251B ALA* 1.3 80.3 - - - +
253B VAL* 1.3 67.7 - - - +
261B ARG* 3.2 36.1 - - + +
262B VAL 3.4 7.6 - - - +
263B GLU* 3.5 11.1 - - + -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 3.6 21.9 - - + +
164B LEU* 4.7 0.7 - - + -
166B ILE* 3.6 38.1 - - + -
168B ILE* 5.3 1.6 - - + -
190B LEU* 4.4 9.0 - - + -
200B VAL* 3.8 22.9 - - + -
201B GLU 3.4 10.8 - - - +
202B PHE* 3.8 20.2 - - + -
251B ALA 5.6 0.2 - - - -
252B GLN* 1.3 80.1 - - - +
254B VAL* 1.3 63.3 + - - +
261B ARG* 3.4 1.8 - - - -
262B VAL* 2.9 36.6 + - + +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TYR* 3.8 29.2 - - + +
124A MET* 4.4 7.2 - - + -
161B LEU* 4.0 3.6 - - - -
200B VAL* 3.1 6.6 - - - +
201B GLU* 2.8 39.8 + - + +
203B TRP* 3.3 35.2 - - + -
253B VAL* 1.3 76.1 - - - +
255B ASP* 1.3 75.1 + - - +
256B ILE* 3.4 0.7 + - - +
259B GLY* 4.1 11.4 - - - +
260B GLU 3.5 10.8 - - - +
261B ARG* 3.9 18.8 - - + +
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Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 3.5 18.1 - - + +
194B ARG* 2.7 37.3 + - - +
199B ASN 3.5 11.8 + - - +
200B VAL* 4.3 3.4 - - + -
254B VAL* 1.3 71.6 - - - +
256B ILE* 1.3 58.6 + - - +
257B VAL* 2.9 21.5 + - - +
258B SER* 3.1 30.8 + - - +
259B GLY* 2.8 34.3 + - - -
260B GLU 2.9 13.1 + - - +
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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