Contacts of the strand formed by residues 236 - 243 (chain N) in PDB entry 1A14
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 VAL 236 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N CYS* 3.1 1.9 - - - -
233N HIS* 2.9 40.9 + - - +
234N ASN* 3.9 9.0 - - + +
235N GLY* 1.3 78.5 - - - +
237N CYS* 1.3 62.9 + - - +
238N PRO* 3.4 9.8 - - + +
256N TYR* 4.5 18.6 - - + -
257N PHE 3.5 8.3 - - - +
258N LYS* 4.5 13.2 - - + +
263N LEU* 4.7 1.6 - - + -
307N PRO* 3.7 27.2 - - + +
310N MET* 4.1 24.5 - - + -
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Residues in contact with CYS 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N CYS* 4.1 5.2 - - - -
185N ASP* 3.9 14.4 - - - -
190N MET* 3.5 30.1 - - + -
207N TYR* 6.2 1.1 - - - -
231N VAL 3.8 0.9 - - - +
232N CYS* 2.0 47.6 - - - -
235N GLY 3.9 6.5 - - - -
236N VAL* 1.3 73.4 - - - +
238N PRO* 1.3 67.3 - - - +
239N VAL* 3.5 8.5 + - - +
257N PHE* 3.0 29.9 + - - +
259N GLU 6.2 0.7 - - - -
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Residues in contact with PRO 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226N GLN* 4.6 3.3 - - - +
230N CYS* 3.9 12.3 - - - +
231N VAL 3.1 24.1 + - - +
236N VAL* 3.4 13.4 - - + +
237N CYS* 1.3 80.4 - - - +
239N VAL* 1.3 62.0 + - - +
254N ILE* 4.2 1.3 - - + -
255N TYR 3.1 8.3 - - - +
256N TYR* 3.6 29.8 - - + -
280N CYS* 5.9 1.4 - - - -
287N ILE* 3.4 26.6 - - + +
305N ILE* 3.8 28.5 - - + +
307N PRO* 4.6 2.0 - - + -
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Residues in contact with VAL 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N THR* 4.0 4.9 - - + +
190N MET* 3.7 29.4 - - + -
192N ILE* 3.8 19.1 - - + -
225N THR* 3.5 22.4 - - - +
226N GLN* 4.2 6.5 - - - +
230N CYS* 4.3 9.9 - - + -
237N CYS 3.8 4.5 - - - +
238N PRO* 1.3 79.7 - - - +
240N VAL* 1.3 62.8 + - - +
241N PHE* 3.9 13.1 + - + -
253N ARG 3.6 0.9 - - - +
254N ILE* 3.5 2.6 - - - -
255N TYR* 2.8 32.5 + - - +
257N PHE* 3.8 17.9 - - + -
305N ILE* 5.9 0.2 - - - -
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Residues in contact with VAL 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N THR* 3.7 17.0 + - - -
226N GLN* 3.1 28.2 + - - +
239N VAL* 1.3 77.9 - - - +
241N PHE* 1.3 60.7 + - - +
242N THR* 4.8 2.1 + - - +
252N THR* 3.8 26.5 - - + -
253N ARG 3.5 4.9 - - - +
254N ILE* 4.4 13.2 - - + -
275N ILE* 4.3 4.3 - - + -
278N CYS* 3.5 34.0 - - + -
280N CYS* 4.6 5.2 - - - -
289N CYS* 4.8 4.0 - - - -
303N ILE* 4.7 7.6 - - + -
305N ILE* 5.1 7.6 - - + -
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Residues in contact with PHE 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N ILE* 4.3 9.9 - - + -
194N ILE* 4.1 8.7 - - + -
203N ALA* 3.9 22.4 - - + -
215N ILE* 4.2 16.8 - - + -
218N TRP* 3.4 25.4 - + + -
223N LEU* 4.5 7.6 - - + -
224N ARG 3.4 9.9 - - - +
225N THR* 4.0 21.8 - - - -
239N VAL* 3.9 19.3 - - + -
240N VAL* 1.3 75.5 - - - +
242N THR* 1.3 65.5 + - - +
252N THR* 3.2 8.8 - - - +
253N ARG 2.9 30.5 + - - +
255N TYR* 3.5 42.8 - + + -
257N PHE* 4.1 9.0 - + - -
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Residues in contact with THR 242 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218N TRP* 4.6 1.6 - - - -
223N LEU* 3.5 4.9 - - - +
224N ARG* 3.0 63.3 + - - +
240N VAL* 4.8 3.5 + - - +
241N PHE* 1.3 79.5 + - - +
243N ASP* 1.3 62.8 + - - +
250N ALA* 3.8 14.1 - - + -
251N GLU 3.6 6.1 - - - +
252N THR* 3.2 21.7 + - - +
274N HIS* 5.0 1.3 - - - +
275N ILE 2.8 26.0 + - - +
276N GLU* 4.2 8.0 - - + +
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Residues in contact with ASP 243 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217N THR* 2.5 30.3 + - - -
218N TRP* 3.2 32.9 + - + +
219N ALA* 3.0 22.5 - - - +
221N ASN 2.9 27.3 + - - -
222N ILE 4.2 0.7 - - - -
223N LEU* 3.9 9.5 - - + +
224N ARG* 3.7 4.0 - - - +
242N THR* 1.3 76.6 - - - +
244N GLY* 1.3 64.3 + - - +
250N ALA* 3.2 0.7 - - - +
251N GLU* 2.7 34.9 + - - +
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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