Contacts of the strand formed by residues 230 - 239 (chain A) in PDB entry 5E6J
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A CYS* 5.6 1.1 - - - -
222A SER* 4.5 19.6 - - - -
223A ILE 3.6 8.7 - - - +
224A PRO* 3.6 22.8 - - - +
228A GLY 4.0 7.3 - - - +
229A ARG* 1.3 76.1 - - - +
231A ALA* 1.3 61.4 + - - +
232A THR* 4.2 2.8 + - - -
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Residues in contact with ALA 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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188A VAL* 3.9 21.1 - - + -
189A VAL 3.2 20.2 - - - +
190A CYS* 4.3 4.9 - - - +
221A VAL 3.2 1.7 - - - +
222A SER* 3.4 4.6 - - - -
223A ILE* 2.7 42.1 + - + +
225A CYS* 3.8 20.2 - - + -
229A ARG 3.5 1.8 + - - -
230A ASP* 1.3 74.5 - - - +
232A THR* 1.3 62.0 + - - +
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Residues in contact with THR 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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187A ASN 3.5 3.8 - - - +
188A VAL* 4.7 1.1 - - - -
189A VAL* 3.1 43.5 + - + +
219A THR 4.7 3.6 - - - +
220A GLY* 3.7 26.5 - - - -
221A VAL 3.4 5.6 - - - +
222A SER* 5.0 1.0 - - - +
230A ASP 4.9 2.1 + - - -
231A ALA* 1.3 74.0 - - - +
233A GLN* 1.3 62.5 + - - +
234A TYR* 4.0 6.4 + - + -
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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
----------------------------------------------------------
186A LEU* 4.2 23.8 - - + +
187A ASN 3.6 8.7 - - - +
188A VAL* 4.3 18.8 - - + +
208A TYR* 2.6 38.8 + - - -
217A LEU* 4.3 5.2 - - + +
220A GLY* 3.3 3.3 - - - -
221A VAL* 2.7 49.1 + - + +
223A ILE* 4.4 15.3 - - + +
231A ALA 3.9 0.8 + - - -
232A THR* 1.3 72.3 - - - +
234A TYR* 1.3 69.1 + - - +
46B ALA* 3.6 30.7 + - - +
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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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186A LEU* 3.7 5.0 - - - +
187A ASN* 3.2 66.4 + - + +
189A VAL* 4.8 10.8 - - + -
217A LEU* 3.3 6.7 - - - +
218A LYS 3.8 14.1 - - - +
219A THR 3.9 11.9 - - - +
220A GLY* 4.3 0.9 - - - -
232A THR* 4.3 9.2 - - + -
233A GLN* 1.3 79.4 - - - +
235A LEU* 1.3 72.6 + - - +
236A VAL* 3.3 18.0 + - + +
313A THR* 4.5 4.3 - - + -
315A ILE* 3.4 54.0 + - + +
317A PRO* 4.9 12.0 - - - +
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Residues in contact with LEU 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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184A ARG* 4.0 2.7 - - + +
185A VAL 3.8 0.2 - - - +
186A LEU* 3.6 22.8 - - + +
214A TYR* 3.8 27.6 - - + +
217A LEU* 2.6 32.0 + - + +
218A LYS* 4.2 8.5 - - + +
234A TYR* 1.3 72.3 - - - +
236A VAL* 1.3 59.3 + - - +
237A GLN 3.3 28.5 - - - +
238A GLN* 3.7 29.8 - - + +
311A TYR* 3.7 23.3 + - + -
313A THR* 2.9 22.3 - - - +
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Residues in contact with VAL 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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185A VAL* 2.9 25.4 + - + +
186A LEU 3.7 10.3 - - - +
187A ASN* 3.4 34.1 - - + +
197A THR* 5.3 2.5 - - - +
234A TYR* 3.3 13.9 + - + +
235A LEU* 1.3 72.5 - - - +
237A GLN* 1.3 61.6 + - + +
311A TYR* 3.9 2.9 - - - +
312A THR* 4.1 0.9 - - - -
313A THR* 3.1 41.5 + - - +
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Residues in contact with GLN 237 (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 LYS* 4.5 10.6 + - - -
184A ARG* 3.4 3.0 - - - -
185A VAL* 2.8 51.2 + - + +
235A LEU* 3.3 8.7 - - - +
236A VAL* 1.3 81.7 - - + +
238A GLN* 1.3 60.0 + - - +
239A GLU* 2.3 44.0 + - + +
310A SER* 4.6 4.2 + - - -
311A TYR* 3.1 20.9 - - - +
312A THR* 4.5 15.5 - - + +
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Residues in contact with GLN 238 (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 LYS 3.6 1.7 + - - -
184A ARG* 2.7 40.8 + - - +
205A ALA 2.7 26.0 + - - -
214A TYR* 3.4 25.8 - - - +
235A LEU* 3.7 15.1 - - + +
237A GLN* 1.3 76.0 - - - +
239A GLU* 1.3 59.5 + - - +
240A SER* 3.1 26.5 + - - +
242A PHE 4.3 0.2 + - - -
243A VAL* 3.3 20.0 - - + +
308A GLU* 3.8 7.8 - - + +
310A SER* 3.7 3.6 - - - -
311A TYR* 3.4 27.5 + - + -
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Residues in contact with GLU 239 (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 SER 3.6 7.1 - - - +
182A ALA* 3.3 5.2 - - - -
183A LYS* 2.7 61.1 + - + +
237A GLN* 2.3 42.8 + - + +
238A GLN* 1.3 69.6 - - - +
240A SER* 1.3 59.4 + - - +
309A THR 4.1 8.1 - - - +
310A SER* 4.0 13.7 - - - +
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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