Contacts of the strand formed by residues 228 - 235 (chain A) in PDB entry 4II9
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 MET 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLY 5.0 0.2 - - - -
187A ASN* 3.3 49.9 - - - +
192A LEU* 5.5 0.4 - - + -
216A PHE* 4.2 7.6 - - + +
219A MET* 3.5 52.7 - - + +
220A GLN* 3.7 13.7 - - + +
223A PHE* 3.9 8.7 - - + -
224A ASP 2.8 9.3 + - - +
225A ALA 3.6 7.8 - - - +
227A THR* 1.3 78.3 - - - +
229A ARG* 1.3 66.1 + - - +
230A ILE* 4.3 11.2 - - + -
244A ILE* 4.1 26.0 - - + -
245A ALA 3.6 3.6 - - - -
246A LEU* 3.7 13.0 - - + -
278A TRP* 4.5 0.2 - - - -
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Residues in contact with ARG 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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185A SER* 3.5 29.4 + - - -
186A GLY* 3.8 14.3 - - - +
225A ALA 3.0 25.6 + - - +
226A ASP* 4.2 9.1 + - - +
227A THR 4.2 0.2 + - - -
228A MET* 1.3 75.9 - - - +
230A ILE* 1.3 66.2 + - - +
231A PHE* 3.6 32.1 - - + -
244A ILE* 3.6 1.8 - - - +
245A ALA 2.9 32.1 + - - -
278A TRP* 3.4 50.8 - - + +
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Residues in contact with ILE 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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184A HIS 4.0 0.2 - - - +
185A SER* 3.2 4.4 - - - -
186A GLY 2.8 34.5 + - - +
187A ASN* 3.9 8.1 - - - +
191A GLU* 3.7 24.5 - - + +
192A LEU* 3.8 34.3 - - + +
195A PHE* 3.8 15.5 - - + -
220A GLN* 3.6 24.0 - - - +
228A MET* 4.3 8.3 - - + -
229A ARG* 1.3 73.5 - - - +
231A PHE* 1.3 64.8 + - - +
232A VAL* 4.0 10.9 + - + -
242A THR* 4.8 0.4 - - - -
243A GLY 3.4 10.1 - - - +
244A ILE* 4.0 15.5 - - + -
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Residues in contact with PHE 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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183A VAL* 4.0 9.6 - - + -
184A HIS 3.4 4.7 - - - -
185A SER* 3.8 16.4 - - - -
229A ARG* 3.6 44.2 - - + -
230A ILE* 1.3 76.6 - - - +
232A VAL* 1.3 60.6 + - - +
233A ALA 4.2 0.4 - - - -
242A THR* 3.1 7.6 - - - -
243A GLY 2.8 32.7 + - - +
245A ALA* 4.3 0.9 - - + -
271A VAL* 4.0 18.1 - - + +
274A GLU* 3.7 42.2 - - + -
275A MET* 3.7 33.4 - - + -
278A TRP* 3.9 22.7 - + + -
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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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182A GLU 3.6 0.7 - - - +
183A VAL* 3.2 5.3 - - - +
184A HIS* 2.8 68.5 + - + +
191A GLU* 4.2 10.1 - - + +
194A GLU* 3.6 24.7 - - + +
230A ILE* 4.0 16.4 - - + -
231A PHE* 1.3 78.6 - - - +
233A ALA* 1.3 59.5 - - - +
234A GLU* 4.3 2.9 - - + +
239A LEU* 3.6 28.3 - - + -
241A SER 3.9 2.2 - - - -
242A THR* 4.0 12.1 - - + -
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Residues in contact with ALA 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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181A VAL* 3.9 11.0 - - + -
182A GLU 3.4 4.7 - - - -
183A VAL* 4.1 6.1 - - + +
231A PHE 4.2 0.4 - - - -
232A VAL* 1.3 71.7 - - - +
234A GLU* 1.3 63.2 + - - +
239A LEU* 4.1 2.1 - - - +
240A LEU* 2.9 25.0 + - - +
241A SER 2.8 21.0 + - - +
267A ALA* 3.6 26.9 - - + +
271A VAL* 3.8 16.6 - - + +
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Residues in contact with GLU 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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180A GLY 3.8 0.2 - - - +
181A VAL* 3.3 1.6 - - - -
182A GLU* 2.8 37.2 + - + +
184A HIS* 3.2 35.0 + - + +
194A GLU* 3.6 12.3 - - - +
232A VAL* 4.3 5.6 - - + +
233A ALA* 1.3 79.5 - - - +
235A ARG* 1.4 62.6 + - - +
236A GLU 5.2 0.2 - - - +
237A GLY* 4.2 18.1 + - - +
238A LYS 3.1 17.7 - - - +
239A LEU* 4.1 12.6 - - - +
240A LEU* 4.2 4.5 - - - -
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Residues in contact with ARG 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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179A ASP 2.8 24.3 + - - -
180A GLY* 3.7 22.6 - - - +
181A VAL* 4.3 0.7 - - - -
234A GLU* 1.4 74.5 - - - +
236A GLU* 1.3 106.8 + - + +
237A GLY 3.2 0.7 - - - -
238A LYS* 2.9 25.0 + - + +
240A LEU* 3.7 17.9 - - + +
265A TYR* 3.5 49.2 + - + -
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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