Contacts of the strand formed by residues 226 - 236 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A SER* 3.6 9.4 + - - -
223A VAL 2.7 28.0 + - - +
224A LEU 3.0 2.9 + - - -
225A LYS* 1.3 75.4 - - - +
227A PHE* 1.3 70.3 + - - +
277A ALA 3.2 14.6 - - - -
278A ILE* 4.6 0.7 - - - -
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Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A THR* 4.5 10.5 - - + -
221A GLN 3.2 12.8 - - - +
222A SER* 4.9 0.7 - - - -
223A VAL* 3.7 6.8 + - - -
226A GLY* 1.3 80.3 - - - +
228A ASN* 1.3 66.6 + - - +
229A LYS* 3.7 39.5 - - + -
275A HIS* 4.4 9.4 - + - -
276A GLY* 3.1 21.2 - - - -
277A ALA* 2.9 37.0 + - + +
278A ILE* 4.2 2.2 - - - +
288A TYR* 3.8 2.9 + - - -
358A TRP* 3.8 40.8 - + - -
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Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A HIS* 3.7 2.3 + - - +
220A THR* 3.5 3.5 - - - +
221A GLN* 2.9 38.8 + - + +
223A VAL* 4.0 16.2 - - + -
227A PHE* 1.3 74.5 - - - +
229A LYS* 1.3 66.7 + - - +
230A PHE* 4.0 5.0 + - - +
274A ASP* 2.6 41.7 + - - +
275A HIS 3.6 3.6 + - - -
288A TYR* 2.6 24.2 + - - +
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A HIS* 5.1 1.8 + - - -
119A TYR* 4.2 3.8 - - - +
218A GLU* 2.9 35.1 + - + +
219A HIS 3.3 3.8 - - - +
220A THR* 3.0 30.2 + - + +
227A PHE* 3.7 29.4 - - + -
228A ASN* 1.3 77.4 - - - +
230A PHE* 1.3 61.1 + - - +
231A VAL* 4.1 2.5 - - + -
273A LEU 4.5 0.2 - - - -
274A ASP* 3.2 7.1 - - - +
275A HIS* 2.6 65.7 + - + +
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Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA 3.8 0.9 - - - +
218A GLU* 3.4 2.4 - - - -
219A HIS* 2.8 49.2 + - + +
228A ASN* 4.0 4.4 + - - +
229A LYS* 1.3 73.1 - - - +
231A VAL* 1.3 60.6 + - - +
232A VAL* 3.6 31.4 - - + -
272A ILE* 4.0 22.0 - - + -
273A LEU 3.5 5.8 - - - -
274A ASP* 3.3 23.3 - - + +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.7 43.7 - - + +
216A THR* 4.7 4.5 - - + -
217A ALA 3.3 9.9 - - - +
218A GLU* 3.7 17.0 - - + +
229A LYS* 4.5 5.2 - - + -
230A PHE* 1.3 83.4 - - - +
232A VAL* 1.3 68.9 + - - +
233A GLN* 4.1 19.5 - - + +
271A ARG* 4.4 1.6 - - - +
272A ILE* 3.5 4.3 - - - +
273A LEU* 2.6 57.0 + - + +
275A HIS* 4.8 0.7 - - + -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE 4.0 0.3 - - - +
216A THR* 3.7 0.5 - - - -
217A ALA* 2.9 41.6 + - + +
230A PHE* 3.6 30.3 - - + -
231A VAL* 1.3 79.3 - - - +
233A GLN* 1.3 71.3 + - - +
234A TYR* 5.9 1.6 - - + -
270A LEU* 4.5 12.6 - - + -
271A ARG 3.3 8.5 - - - +
272A ILE* 4.6 10.3 - - + -
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.0 30.7 + - - +
120A TRP* 3.9 8.7 - - - +
214A LEU* 4.0 17.2 - - + +
215A PHE 3.1 5.6 - - - +
216A THR* 3.1 38.4 + - + +
231A VAL* 4.1 8.7 - - + +
232A VAL* 1.3 81.9 - - - +
234A TYR* 1.3 61.4 + - - +
269A MET* 4.0 2.6 - - + +
270A LEU* 3.6 6.4 - - - +
271A ARG* 2.8 76.3 + - + +
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Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.4 2.3 - - - -
215A PHE* 2.8 62.2 + + + +
232A VAL* 5.9 1.6 - - + -
233A GLN* 1.3 76.0 - - - +
235A ALA* 1.3 63.1 + - - +
236A THR* 4.0 17.8 + - - -
268A HIS* 3.6 41.1 + + + +
269A MET 3.3 11.4 - - - -
270A LEU* 4.5 15.0 - - + -
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TRP 3.2 10.8 - - - +
214A LEU* 3.7 17.7 - - + -
233A GLN 4.3 0.2 - - - -
234A TYR* 1.3 78.1 - - - +
236A THR* 1.3 64.3 + - - +
239A MET* 3.9 23.8 - - + +
240A THR* 4.0 0.9 - - + -
268A HIS* 3.1 7.3 - - - +
269A MET* 2.7 53.8 + - + +
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLY* 3.5 13.5 - - - -
213A TRP* 2.9 39.5 + - + +
215A PHE* 5.8 1.5 - - - -
234A TYR* 4.0 18.8 + - - -
235A ALA* 1.3 76.7 + - - +
237A ASP* 1.3 80.1 + - - +
238A SER 3.1 1.4 + - - -
239A MET* 3.1 14.4 + - - +
240A THR* 3.7 2.2 - - - -
267A GLY 3.6 7.4 + - - -
268A HIS* 4.7 0.5 - - - +
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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