Contacts of the strand formed by residues 234 - 240 (chain N) in PDB entry 3Q2K
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 234 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209M TYR* 3.8 21.1 - - + +
210M THR* 3.7 28.9 - - - +
211M ALA* 3.6 22.7 - - + -
213M LEU* 3.9 6.3 - - + -
222M THR* 3.8 26.2 - - + +
223M GLY* 4.1 2.5 - - - -
224M VAL* 4.2 15.9 - - + -
154N TYR 3.2 6.3 + - - +
155N MET* 3.3 12.8 - - + +
156N VAL 3.1 20.3 + - - -
227N LEU 3.3 13.9 - - - +
228N ARG* 4.4 11.2 - - + -
229N TRP* 3.8 6.3 - - - -
232N GLY 3.5 19.5 + - - +
233N ALA* 1.3 77.3 - - - +
235N GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 235 (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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224M VAL* 3.5 19.7 - - - +
155N MET* 4.4 1.1 - - - -
156N VAL 2.8 15.7 - - - -
226N ALA* 3.5 0.2 - - - -
227N LEU* 3.0 31.9 + - - -
229N TRP* 3.9 9.1 - - - -
234N MET* 1.3 78.3 - - - +
236N SER* 1.3 63.8 + - - -
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Residues in contact with SER 236 (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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224M VAL* 4.0 7.6 - - - -
236M SER* 3.2 17.3 + - - -
238M ASN* 2.7 28.1 + - - -
156N VAL 3.1 6.0 + - - +
157N THR* 3.4 4.5 - - - +
158N VAL* 2.8 25.6 + - - +
196N LEU* 5.5 0.9 - - - +
224N VAL* 4.9 0.4 - - - -
225N ALA 3.1 13.0 - - - -
227N LEU* 4.0 6.0 - - - +
235N GLY* 1.3 77.1 - - - -
237N ILE* 1.3 61.9 + - - +
238N ASN* 3.2 18.3 + - - -
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Residues in contact with ILE 237 (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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158N VAL* 3.2 33.2 - - + +
160N VAL* 5.4 0.4 - - + -
185N PHE* 3.9 14.0 - - + -
189N ALA 4.8 0.7 - - - +
192N TYR* 4.2 5.2 - - + +
193N VAL* 3.8 38.6 - - + +
196N LEU* 4.4 19.3 - - + -
224N VAL* 3.6 1.9 - - - -
225N ALA* 2.9 50.7 + - + +
227N LEU* 4.1 3.8 - - + +
236N SER* 1.3 75.0 - - - +
238N ASN* 1.3 67.4 + - - +
239N VAL* 4.0 15.0 - - + -
335N ILE* 4.7 3.6 - - + -
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Residues in contact with ASN 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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155M MET* 4.1 9.3 - - - +
157M THR* 4.1 8.4 + - - +
236M SER* 2.7 31.1 + - - -
157N THR* 3.9 5.1 - - - +
158N VAL 2.9 9.9 + - - -
159N ASN* 2.9 25.3 + - - +
160N VAL 2.8 31.0 + - - -
161N PHE* 3.7 15.0 - - + -
223N GLY 3.7 5.2 - - - -
224N VAL* 3.5 13.0 - - - +
236N SER* 3.2 20.2 + - - -
237N ILE* 1.3 75.8 - - - +
239N VAL* 1.3 55.4 + - - +
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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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155M MET* 3.6 6.8 - - - +
160N VAL* 3.3 10.8 - - + +
161N PHE* 4.9 0.2 - - - -
184N ALA* 3.6 29.8 - - + +
185N PHE* 3.5 36.1 - - + +
189N ALA* 3.7 28.7 - - + -
223N GLY 2.9 31.9 + - - +
237N ILE* 4.0 10.1 - - + -
238N ASN* 1.3 78.9 - - - +
240N THR* 1.3 64.9 + - - +
241N MET* 3.9 10.1 - - + -
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Residues in contact with THR 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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154M TYR* 4.6 2.4 - - + +
155M MET* 4.3 8.7 - - + -
255M LEU* 3.8 22.9 - - + -
160N VAL 2.9 8.7 + - - +
161N PHE* 4.4 4.9 - - + -
162N TRP 2.9 24.9 + - - -
221N ASP 3.5 5.8 - - - -
222N THR* 3.0 29.4 + - - +
239N VAL* 1.3 76.4 - - - +
241N MET* 1.3 62.7 + - - +
242N LEU* 3.1 21.5 + - + +
243N THR* 3.5 20.4 - - - +
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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