Contacts of the strand formed by residues 220 - 227 (chain A) in PDB entry 1A7C
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 TYR 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLU* 3.9 24.0 - - + +
213A PHE 3.2 11.2 - - - +
214A THR* 4.1 17.3 - - + -
218A GLY 4.3 10.3 - - - -
219A HIS* 1.3 74.5 - - - +
221A TYR* 1.3 61.7 + - - +
240A PRO* 3.7 4.2 - - - +
241A TYR* 3.0 44.3 + + + +
242A GLU* 3.5 27.8 + - + +
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.4 6.5 - - - +
213A PHE* 2.9 62.3 + - + +
214A THR 3.9 11.9 + - - -
215A THR* 4.0 4.0 - - + -
219A HIS 3.9 9.6 - - - -
220A TYR* 1.3 75.7 - - - +
222A ASP* 1.3 67.9 + - - +
223A ILE* 3.6 23.8 - - + -
238A ALA* 4.4 1.3 - - + -
239A ALA 3.2 17.0 - - - +
240A PRO* 3.6 8.3 - - + -
241A TYR* 4.0 2.7 - - - +
250A LEU* 3.4 36.8 - - + -
253A ILE* 4.2 7.6 - - + +
258A LEU* 3.9 15.4 - - - +
262A TRP* 3.1 33.8 + + - -
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Residues in contact with ASP 222 (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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210A TYR* 2.8 34.9 + - + -
211A THR 3.9 4.0 - - - -
212A GLU* 3.5 12.1 - - - +
221A TYR* 1.3 74.4 - - - +
223A ILE* 1.3 61.9 + - - +
224A LEU* 6.0 0.7 - - + -
237A ILE 4.3 0.9 - - - -
238A ALA* 3.1 26.3 - - - +
239A ALA 3.0 15.0 + - - +
240A PRO 5.0 0.5 - - - +
241A TYR* 4.1 25.1 - - - -
350A GLU* 5.5 1.6 - - - +
352A ILE* 4.5 23.0 - - + +
354A MET* 5.0 6.6 - - + +
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Residues in contact with ILE 223 (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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210A TYR* 3.5 5.5 - - - -
211A THR* 3.0 53.9 + - + +
213A PHE* 3.7 17.3 - - + +
221A TYR* 3.6 40.8 - - + +
222A ASP* 1.3 77.7 - - - +
224A LEU* 1.3 63.6 + - - +
236A PHE* 4.3 10.5 - - + -
237A ILE 3.4 8.1 - - - +
238A ALA* 4.2 3.4 - - + -
262A TRP* 3.6 39.5 - - + -
266A MET* 3.3 17.6 - - + +
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Residues in contact with LEU 224 (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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208A PHE* 4.0 32.1 - - + -
209A ASN 3.7 3.4 - - - +
210A TYR* 4.5 5.4 - - + +
222A ASP* 5.7 0.9 - - + -
223A ILE* 1.3 76.9 - - - +
225A GLU* 1.3 67.6 + - - +
226A LEU* 3.7 32.5 + - + -
235A MET 3.7 0.7 - - - +
236A PHE* 3.3 5.6 - - - -
237A ILE* 2.9 45.9 + - + +
266A MET* 4.2 2.5 - - - -
271A ARG* 4.8 2.7 - - + -
273A LEU* 3.8 25.6 - - + -
352A ILE* 3.6 32.1 - - + -
354A MET* 5.8 0.9 - - + -
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Residues in contact with GLU 225 (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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208A PHE* 4.0 8.8 - - - +
209A ASN* 3.0 38.3 + - + +
224A LEU* 1.3 81.7 - - - +
226A LEU* 1.3 65.7 + - - +
227A PRO* 3.5 9.6 - - + +
234A SER* 2.7 35.8 + - - +
235A MET 3.6 2.7 - - - +
236A PHE* 3.9 11.5 - - + -
263A LYS* 2.9 45.0 + - - +
266A MET* 3.8 16.0 - - - +
365A ASN* 3.7 2.6 + - - -
954A NAG 4.2 7.1 - - - -
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Residues in contact with LEU 226 (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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175A TRP* 3.6 36.5 - - + -
179A PHE* 4.3 12.8 - - + -
204A GLN* 5.5 0.9 - - - +
208A PHE* 3.6 29.8 - - + -
224A LEU* 3.7 17.5 - - + +
225A GLU* 1.3 73.8 - - - +
227A PRO* 1.3 66.6 - - + +
228A TYR* 4.4 0.3 - - - -
234A SER* 3.5 0.6 - - - -
235A MET* 2.7 41.6 + - + +
237A ILE* 4.6 13.9 - - + -
273A LEU* 3.8 12.3 - - + -
275A LEU* 4.1 24.0 - - + -
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Residues in contact with PRO 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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175A TRP* 3.9 7.4 - - - +
176A LYS* 3.1 41.0 + - + +
177A THR* 4.9 1.1 + - - +
208A PHE* 5.6 3.4 - - + -
225A GLU* 3.5 11.9 - - + +
226A LEU* 1.3 88.4 - - + +
228A TYR* 1.3 66.4 - - - +
231A ASP* 4.9 7.6 - - - +
233A LEU 4.3 0.9 - - - +
234A SER* 3.6 18.6 - - - +
954A NAG 3.4 32.3 - - + +
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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