Contacts of the strand formed by residues 226 - 230 (chain C) in PDB entry 6C9G
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 ALA 226 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C PHE* 4.0 2.2 - - - -
224C VAL* 3.4 3.3 - - - +
225C SER* 1.3 83.8 + - - +
227C LEU* 1.3 66.6 + - - +
228C PRO* 3.8 1.9 - - - +
239C ILE* 4.0 9.2 - - + -
240C TYR 3.4 5.8 - - - +
241C SER* 3.5 15.5 - - - -
298C ARG* 3.3 37.9 - - - +
311C ILE* 5.8 0.2 - - - +
1103C AMP 3.1 26.4 + - - -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ALA* 3.5 24.2 - - + +
205C MET* 4.5 0.4 - - - +
206C VAL* 3.7 32.1 - - + -
215C ALA* 3.6 29.8 - - + +
218C ILE* 3.6 24.2 - - + -
219C PHE* 3.5 23.3 - - + -
224C VAL* 3.8 17.3 - - + -
226C ALA* 1.3 71.2 - - - +
228C PRO* 1.3 68.6 - - - +
229C VAL* 3.5 0.7 + - - +
239C ILE* 3.9 2.7 - - - -
240C TYR* 2.7 42.0 + - + +
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Residues in contact with PRO 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE* 4.6 2.2 - - + -
204C ALA 3.3 17.7 - - - +
205C MET* 3.5 15.6 - - + +
206C VAL* 3.1 23.7 + - - +
226C ALA 3.8 2.5 - - - +
227C LEU* 1.3 83.4 - - - +
229C VAL* 1.3 60.4 + - - +
230C VAL* 3.9 1.3 - - + -
236C VAL* 4.4 9.2 - - + -
238C ASP 3.8 5.2 - - - +
239C ILE* 4.0 8.0 - - + -
300C VAL* 4.6 9.2 - - + -
308C VAL* 4.3 22.0 - - + -
311C ILE* 3.8 25.8 - - + -
1103C AMP 3.7 10.1 - - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL* 3.4 17.7 - - + -
207C ARG 3.9 4.3 - - - +
208C THR* 3.7 38.8 - - + +
228C PRO* 1.3 74.1 - - - +
230C VAL* 1.3 59.6 + - - +
236C VAL* 3.5 2.4 - - - -
237C VAL* 2.8 31.0 + - + +
238C ASP* 2.7 37.3 + - + +
239C ILE 4.0 1.3 - - - +
240C TYR* 3.9 21.5 - - + +
261C VAL* 4.2 9.6 - - + -
262C THR* 5.0 2.2 - - - +
265C LEU* 4.3 4.0 - - + -
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C MET* 3.7 42.0 - - + -
206C VAL 2.9 20.3 + - - +
207C ARG* 3.5 16.7 - - - +
208C THR 3.5 20.1 + - - -
228C PRO 4.3 5.6 - - - +
229C VAL* 1.3 77.7 - - - +
231C ASP* 1.3 68.2 + - - +
234C GLY* 3.8 22.0 - - - +
235C ARG 3.3 7.6 - - - +
236C VAL* 4.4 1.8 - - - -
237C VAL* 4.4 3.6 - - - -
308C VAL* 4.0 13.7 - - + -
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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