Contacts of the strand formed by residues 223 - 231 (chain C) in PDB entry 5O67
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 ASP 223 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 3.9 19.1 - - + -
100C SER* 5.7 3.8 - - - -
213C LYS* 3.0 32.5 + - - -
215C LEU 3.6 1.5 - - - +
216C ASP* 3.8 8.1 - - - +
217C GLU* 3.1 32.6 + - + +
222C PRO* 1.3 73.7 - - - +
224C ALA* 1.3 57.8 + - - +
225C VAL* 4.1 1.9 + - - +
272C SER* 3.5 2.4 + - - +
273C MET* 3.4 6.6 - - - -
274C VAL* 3.0 42.3 + - + +
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Residues in contact with ALA 224 (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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213C LYS* 3.5 9.2 - - - +
214C PHE* 3.1 48.9 + - + -
215C LEU* 2.9 35.2 + - + +
222C PRO* 3.8 1.3 + - + +
223C ASP* 1.3 73.1 - - - +
225C VAL* 1.3 61.2 + - - +
271C LEU* 5.2 0.7 - - + -
272C SER 3.5 6.3 - - - +
273C MET* 4.6 10.3 - - + -
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C SER* 4.8 11.0 - - - +
102C PHE* 4.1 34.1 - - + -
211C ALA* 4.1 8.7 - - + -
212C TYR 3.6 7.4 - - - +
213C LYS* 4.0 26.5 - - + -
214C PHE* 4.0 4.2 - - - -
223C ASP 5.4 1.6 - - - +
224C ALA* 1.3 78.4 - - - +
226C VAL* 1.3 75.1 + - - +
227C SER* 4.6 5.3 + - - +
270C GLY 3.9 0.3 - - - +
271C LEU* 3.4 6.1 - - - +
272C SER* 3.1 44.4 + - - +
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Residues in contact with VAL 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ALA* 3.4 0.3 - - - -
212C TYR* 2.9 57.4 + - + +
214C PHE* 3.8 24.5 - - + -
225C VAL* 1.3 74.4 - - - +
227C SER* 1.3 69.4 + - - +
228C VAL* 6.2 1.3 - - + -
269C PRO* 6.3 1.6 - - + -
270C GLY 3.4 10.1 - - - +
271C LEU* 4.7 3.8 - - + -
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Residues in contact with SER 227 (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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210C ILE 3.4 13.5 - - - -
211C ALA* 4.1 10.1 - - - +
225C VAL* 4.6 6.3 + - - +
226C VAL* 1.3 80.2 - - - +
228C VAL* 1.3 68.9 + - - +
268C THR 4.4 0.4 - - - -
269C PRO* 3.2 5.5 - - - +
270C GLY* 2.8 45.8 + - - +
271C LEU 5.6 0.3 - - - -
501C LDA 5.4 6.1 - - - +
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Residues in contact with VAL 228 (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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208C PHE 4.1 0.2 - - - +
209C GLY* 3.0 23.0 - - - -
210C ILE* 3.0 24.9 + - + +
226C VAL* 6.2 1.1 - - + -
227C SER* 1.3 81.6 - - - +
229C ARG* 1.3 64.7 + - - +
230C VAL* 4.3 6.5 - - + +
267C ILE* 3.5 36.1 - - + -
268C THR 3.4 9.9 - - - +
269C PRO* 4.6 7.9 - - + -
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Residues in contact with ARG 229 (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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157C ARG* 6.0 1.0 - - - +
167C ASP* 4.2 21.0 - - - +
169C ASN* 4.8 6.1 - - - +
207C ASN* 2.8 42.7 + - + +
208C PHE* 3.5 7.3 - - - +
209C GLY* 3.9 23.1 - - - +
228C VAL* 1.3 75.6 - - - +
230C VAL* 1.3 63.8 - - - +
231C LYS* 4.2 2.4 + - + +
266C SER 3.8 0.9 - - - +
267C ILE* 3.4 3.5 - - - -
268C THR* 2.9 48.3 + - + +
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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
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207C ASN* 3.1 5.0 - - - +
208C PHE* 2.8 73.0 + - + +
210C ILE* 6.0 1.8 - - + -
228C VAL* 4.6 8.5 - - + +
229C ARG* 1.3 78.6 - - - +
231C LYS* 1.3 62.2 + - - +
232C ALA 4.2 0.6 + - - -
265C TRP* 4.3 23.1 - - + -
266C SER 3.4 9.9 - - - +
267C ILE* 4.4 19.1 - - + -
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Residues in contact with LYS 231 (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 ASP* 2.9 46.4 + - + +
206C VAL 3.8 2.5 - - - -
207C ASN* 3.8 8.5 - - + +
229C ARG* 4.2 3.6 - - + +
230C VAL* 1.3 73.6 - - - +
232C ALA* 1.3 63.2 + - - +
233C PRO* 4.6 0.2 - - - +
262C ASN* 2.8 30.1 + - - +
264C VAL 2.8 27.7 + - - +
265C TRP* 3.4 12.8 - - - -
266C SER* 2.8 53.3 + - - +
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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