Contacts of the strand formed by residues 226 - 236 (chain C) in PDB entry 1AF6
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 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C SER* 3.7 9.4 + - - -
223C VAL 2.7 28.1 + - - +
224C LEU 3.1 2.3 + - - -
225C LYS* 1.3 75.2 - - - +
227C PHE* 1.3 69.1 + - - +
277C ALA* 3.2 15.5 - - - -
278C ILE* 4.6 0.7 - - - -
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Residues in contact with PHE 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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220C THR* 4.5 11.7 - - + -
221C GLN 3.2 12.1 - - - +
222C SER* 4.9 0.7 - - - -
223C VAL* 3.7 7.4 + - - +
226C GLY* 1.3 80.3 - - - +
228C ASN* 1.3 65.4 + - - +
229C LYS* 3.8 38.1 - - + -
275C HIS* 4.4 9.4 - + - -
276C GLY* 3.1 22.4 - - - -
277C ALA* 2.9 40.9 + - + +
278C ILE* 4.2 1.6 - - - +
288C TYR* 3.8 2.8 + - - -
358C TRP* 3.9 37.5 - + - -
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Residues in contact with ASN 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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219C HIS* 3.6 2.8 + - - +
220C THR* 3.4 4.0 - - - +
221C GLN* 2.9 38.9 + - + +
223C VAL* 4.0 16.4 - - + -
227C PHE* 1.3 76.2 - - - +
229C LYS* 1.3 65.7 + - - +
230C PHE* 4.0 4.3 + - - +
274C ASP* 2.5 41.6 + - - +
275C HIS 3.6 1.8 + - - -
288C TYR* 2.7 24.5 + - - +
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Residues in contact with LYS 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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110C HIS* 5.1 2.0 + - - -
119C TYR* 4.2 6.5 - - - +
218C GLU* 3.0 29.7 + - + -
219C HIS 3.3 3.6 - - - +
220C THR* 3.0 30.1 + - + +
227C PHE* 3.8 23.1 - - + -
228C ASN* 1.3 78.3 - - - +
230C PHE* 1.3 61.5 - - - +
231C VAL* 4.1 2.7 - - + -
273C LEU 4.0 0.3 - - - +
274C ASP* 3.2 6.4 - - - +
275C HIS* 2.6 71.1 + - + +
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Residues in contact with PHE 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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217C ALA 3.8 0.9 - - - +
218C GLU* 3.4 2.4 - - - -
219C HIS* 2.9 49.5 + - + +
228C ASN* 4.0 5.1 + - - +
229C LYS* 1.3 72.5 - - - +
231C VAL* 1.3 60.0 + - - +
232C VAL* 3.5 31.2 - - + -
272C ILE* 4.0 22.2 - - + -
273C LEU 3.5 7.4 - - - -
274C ASP* 3.3 23.6 - - + +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TYR* 3.6 45.8 - - + +
216C THR* 4.7 4.0 - - + -
217C ALA 3.4 9.4 - - - +
218C GLU* 3.7 16.8 - - + +
229C LYS* 4.6 5.2 - - + -
230C PHE* 1.3 84.4 - - - +
232C VAL* 1.3 67.9 + - - +
233C GLN* 4.1 20.6 - - + +
271C ARG* 3.9 1.3 - - - +
272C ILE* 3.5 4.5 - - - +
273C LEU* 2.6 56.8 + - + +
275C HIS* 4.8 1.1 - - + -
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Residues in contact with VAL 232 (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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215C PHE 4.0 0.7 - - - +
216C THR* 3.7 0.5 - - - -
217C ALA* 2.9 42.6 + - + +
230C PHE* 3.5 30.3 - - + -
231C VAL* 1.3 78.5 - - - +
233C GLN* 1.3 66.5 + - - +
234C TYR* 5.9 1.3 - - + -
270C LEU* 4.5 15.3 - - + -
271C ARG 3.4 7.2 - - - +
272C ILE* 4.6 10.3 - - + -
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Residues in contact with GLN 233 (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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119C TYR* 3.0 30.7 + - - +
120C TRP* 3.9 9.5 - - - +
214C LEU* 4.0 17.0 - - + +
215C PHE 3.2 4.7 - - - +
216C THR* 3.0 39.8 + - + +
231C VAL* 4.1 8.6 - - + +
232C VAL* 1.3 83.0 - - - +
234C TYR* 1.3 61.0 + - - +
269C MET* 4.5 2.5 - - + -
270C LEU* 3.6 6.4 - - - +
271C ARG* 2.8 77.9 + - + +
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Residues in contact with TYR 234 (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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214C LEU* 3.4 2.6 - - - -
215C PHE* 2.8 63.7 + + + +
232C VAL* 5.9 1.3 - - + -
233C GLN* 1.3 77.4 - - - +
235C ALA* 1.3 61.2 + - - +
236C THR* 4.0 18.0 + - - -
268C HIS* 3.6 41.8 + + + +
269C MET 3.3 10.8 - - - -
270C LEU* 4.5 16.6 - - + -
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Residues in contact with ALA 235 (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 TRP 3.2 10.3 - - - +
214C LEU* 3.8 15.5 - - + -
234C TYR* 1.3 78.8 - - - +
236C THR* 1.3 63.7 + - - +
239C MET* 3.9 21.1 - - + +
240C THR* 4.0 0.7 - - + -
268C HIS* 3.1 7.3 - - - +
269C MET* 2.7 58.9 + - + +
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Residues in contact with THR 236 (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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212C GLY* 3.6 10.4 - - - -
213C TRP* 2.9 39.7 + - + +
215C PHE* 5.7 1.8 - - - -
234C TYR* 4.0 19.2 + - - -
235C ALA* 1.3 75.5 + - - +
237C ASP* 1.3 79.2 + - - +
238C SER 3.1 1.2 + - - -
239C MET* 3.1 17.5 + - - +
240C THR* 3.8 2.5 - - - -
267C GLY 3.7 6.9 + - - -
268C HIS* 4.8 0.9 - - - +
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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