Contacts of the strand formed by residues 229 - 238 (chain F) 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 THR 229 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189F ASP* 4.2 10.3 - - + +
190F LEU 3.5 19.1 - - - +
191F ASN* 4.0 16.4 + - + -
224F ILE* 4.9 2.2 - - - -
227F GLY 4.3 3.3 + - - -
228F ASP* 1.3 80.9 + - - +
230F TYR* 1.3 73.0 + - - +
231F SER* 3.5 16.2 + - - -
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Residues in contact with TYR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E VAL* 4.1 10.3 - - + +
188F VAL* 3.7 8.0 - - + +
189F ASP* 3.5 2.3 - - - -
190F LEU* 2.9 56.2 + - + -
202F PHE* 4.3 17.3 - + - -
220F GLU* 2.5 27.1 + - - -
222F TRP* 3.6 40.8 - + + -
224F ILE* 4.1 26.2 - - + +
228F ASP 4.4 0.2 - - - -
229F THR* 1.3 70.2 - - - +
231F SER* 1.3 63.4 + - - +
232F LYS* 3.1 43.2 + - + +
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Residues in contact with SER 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F VAL 3.4 3.4 - - - -
189F ASP* 2.6 26.2 + - - -
229F THR* 3.5 14.7 + - - -
230F TYR* 1.3 80.2 - - - +
232F LYS* 1.3 66.1 + - - +
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Residues in contact with LYS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E VAL* 3.7 12.9 - - + +
97E ASP 3.2 16.0 + - - -
187F THR* 3.7 2.9 - - - -
188F VAL* 2.8 48.0 + - + +
189F ASP* 5.3 0.2 - - - +
202F PHE* 4.6 4.9 - - - -
217F ASN* 3.0 27.9 + - - -
220F GLU* 3.2 18.4 + - - -
230F TYR* 3.1 31.3 + - + +
231F SER* 1.3 78.4 + - - +
233F VAL* 1.3 69.7 + - - +
234F ARG* 4.0 16.3 - - - +
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Residues in contact with VAL 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F GLN* 3.9 24.5 - - - +
183F PHE* 6.5 0.2 - - + -
185F PRO* 4.0 14.8 - - + -
186F PHE 3.4 10.8 - - - +
187F THR* 4.4 15.5 - - + -
232F LYS* 1.3 87.2 - - - +
234F ARG* 1.3 68.0 + - - +
235F GLY 4.9 0.9 - - - +
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Residues in contact with ARG 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASP* 2.9 40.2 + - - -
98E THR* 3.3 16.6 + - - +
99E ALA 2.6 31.1 + - - +
100E GLN* 4.5 8.4 - - - +
186F PHE* 2.8 42.3 + - - +
188F VAL* 4.4 10.7 - - + +
204F MET* 4.5 10.1 - - - +
216F VAL* 2.9 28.5 + - + +
217F ASN* 3.6 23.2 + - + +
232F LYS* 4.0 13.9 - - - +
233F VAL* 1.3 78.8 - - - +
235F GLY* 1.3 71.3 + - - +
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Residues in contact with GLY 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E GLN* 3.3 17.8 + - - +
183F PHE* 3.6 19.5 - - - -
184F VAL 3.4 11.2 - - - -
185F PRO* 3.7 4.5 - - - -
216F VAL* 4.6 5.7 - - - +
233F VAL* 4.3 1.8 - - - +
234F ARG* 1.3 93.5 + - - +
236F ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E GLN* 4.1 2.7 - - - +
183F PHE* 3.5 6.0 - - - -
184F VAL 2.9 36.0 + - - +
186F PHE* 3.7 20.4 - - + -
206F ALA* 4.0 11.7 - - + -
214F ILE* 4.7 13.5 - - + -
215F PRO 5.6 0.2 - - - +
216F VAL* 4.0 31.9 - - + -
235F GLY* 1.3 75.0 - - - +
237F ASN* 1.3 74.0 + - - +
238F PHE* 3.6 40.6 + - + -
242F TYR* 4.9 3.6 - - + -
249F ILE* 4.4 6.1 - - + -
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Residues in contact with ASN 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LYS* 5.8 1.6 - - - +
100E GLN* 3.7 24.5 + - + +
182F GLY 3.5 16.5 + - - +
183F PHE* 3.8 16.7 - - + +
236F ILE* 1.3 77.7 - - - +
238F PHE* 1.3 60.4 + - - +
239F ASP* 3.0 33.2 + - - +
242F TYR* 3.4 15.8 + - - -
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Residues in contact with PHE 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F VAL* 3.8 25.6 - - + -
181F GLY* 3.1 4.5 - - - -
182F GLY 2.7 38.9 + - - +
184F VAL* 3.8 16.4 - - + -
236F ILE* 3.7 42.8 - - + -
237F ASN* 1.3 70.9 - - - +
239F ASP* 1.3 67.1 + - - +
242F TYR* 3.8 13.7 - + + -
247F TYR* 3.7 38.8 - + + -
249F ILE* 4.0 11.4 - - + -
268F VAL* 3.7 32.5 - - + -
270F LYS* 4.7 6.7 - - + -
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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