Contacts of the strand formed by residues 250 - 256 (chain C) in PDB entry 3ER8
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 HIS 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C VAL* 3.1 26.1 + - + +
162C SER 4.9 0.2 - - - -
165C VAL* 3.1 13.0 - - - +
202C ASP* 6.0 7.8 - - + +
204C ASP* 5.7 1.3 - - - -
240C TYR* 5.0 2.0 + - - -
242C VAL* 4.0 11.1 - - + +
244C LYS* 4.0 16.0 - - + +
248C ASP 3.9 2.4 + - - -
249C ASN* 1.3 68.4 - - - +
251C ILE* 1.3 77.2 + - - +
252C ILE* 3.4 8.7 - - - +
253C ASP* 3.1 42.6 + - + -
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Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C SER* 4.0 12.8 - - - +
164C LEU* 4.7 9.9 - - + -
165C VAL* 4.2 21.6 - - - +
168C VAL* 4.1 18.5 - - + +
202C ASP* 6.1 0.9 - - - +
221C ILE* 3.6 30.5 - - + -
229C ILE* 3.4 34.3 - - + -
243C ILE* 3.2 11.5 + - + +
244C LYS* 3.7 12.6 - - - +
245C ASP* 3.9 7.9 - - + +
249C ASN 3.7 13.0 - - - +
250C HIS* 1.3 81.1 + - - +
252C ILE* 1.3 74.0 + - + +
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C VAL* 4.7 8.1 - - + -
169C ASN* 5.7 1.1 - - - +
172C MET* 5.0 14.6 - - + -
202C ASP* 5.8 2.7 - - + -
203C ILE* 3.0 38.4 - - + +
204C ASP* 5.7 0.2 - - - +
205C ILE* 5.7 1.8 - - + -
213C PHE* 5.2 5.2 - - + -
214C LEU* 4.3 6.2 - - + +
217C LEU* 3.5 31.6 - - + -
242C VAL* 3.0 4.3 - - - +
243C ILE* 3.0 38.2 + - + +
250C HIS* 3.4 5.4 - - - +
251C ILE* 1.3 90.7 - - + +
253C ASP* 1.3 81.0 + - - +
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Residues in contact with ASP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C ASP* 3.8 27.3 - - - +
205C ILE* 4.4 8.0 + - - +
207C GLN* 5.1 0.2 + - - -
213C PHE* 5.2 0.2 - - - -
214C LEU* 4.6 4.0 - - - +
240C TYR* 3.1 34.0 + - + +
241C MET 3.8 2.5 - - - -
242C VAL* 3.4 13.9 - - + -
250C HIS* 3.1 23.1 + - - -
252C ILE* 1.3 93.7 - - - +
254C SER* 1.3 68.1 + - - +
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ILE* 4.0 9.5 + - - -
207C GLN* 2.8 33.1 + - - +
210C SER* 3.0 20.9 + - - -
214C LEU* 4.3 9.0 - - - -
239C ASN 4.1 0.2 - - - +
240C TYR* 2.9 24.1 - - - -
241C MET* 3.2 18.0 + - - +
253C ASP* 1.3 84.6 + - - +
255C PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C TYR* 3.6 25.1 - + - -
205C ILE 3.3 5.4 + - - +
206C LEU* 3.4 24.9 - - + -
207C GLN 3.1 23.7 + - - +
210C SER* 4.0 1.3 - - - -
237C LEU* 3.9 23.8 - - + -
238C ARG 4.4 3.8 - - - -
239C ASN 3.5 4.3 - - - -
240C TYR* 3.5 46.2 - + + -
254C SER* 1.3 77.4 + - - +
256C ASN* 1.3 60.2 + - - +
257C ILE* 5.5 0.2 - - + -
383C SER* 3.8 29.8 - - - +
386C ASN* 6.0 4.3 - - - -
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Residues in contact with ASN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU 5.6 2.4 + - - -
86B GLY* 4.6 19.9 - - - +
207C GLN 2.8 17.5 + - - -
208C THR* 3.7 6.5 - - - +
209C ASN* 4.0 4.6 + - - -
210C SER* 3.2 20.8 + - - +
211C ARG* 4.6 5.9 + - - +
239C ASN* 3.1 35.5 + - + +
255C PHE* 1.3 71.7 - - - +
257C ILE* 1.3 103.9 + - - +
382C GLU* 3.5 10.3 - - - +
383C SER* 3.8 5.2 + - - -
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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