Contacts of the strand formed by residues 234 - 240 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M TYR 2.9 8.4 + - - +
155M MET* 3.3 8.9 - - + -
156M VAL 2.9 21.3 + - - -
227M LEU 3.4 10.3 - - - +
228M ARG* 4.5 10.5 - - + -
229M TRP* 3.7 6.9 - - - -
232M GLY 3.7 6.7 - - - +
233M ALA* 1.3 77.5 - - - +
235M GLY* 1.3 59.7 + - - +
209N TYR* 3.7 25.1 - - + +
210N THR* 3.6 30.1 - - - +
211N ALA* 3.8 14.4 - - + +
213N LEU* 3.6 31.4 - - + -
222N THR* 3.7 22.9 - - + +
223N GLY* 4.2 0.9 - - - -
224N VAL* 3.6 16.6 - - + -
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Residues in contact with GLY 235 (chain M).
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* 4.6 1.3 - - - -
156M VAL 2.7 14.8 - - - -
227M LEU* 2.9 30.6 + - - -
229M TRP* 3.8 11.2 - - - -
234M MET* 1.3 80.2 - - - +
236M SER* 1.3 60.6 + - - -
224N VAL* 3.3 21.8 - - - +
238N ASN* 4.6 0.2 - - - -
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Residues in contact with SER 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156M VAL 3.0 5.7 + - - +
157M THR* 3.2 17.3 - - - +
158M VAL* 2.9 25.9 + - - +
196M LEU* 5.3 0.2 - - - +
224M VAL* 5.0 0.2 - - - -
225M ALA 3.1 13.2 - - - -
226M ALA* 4.7 0.2 - - - -
227M LEU* 3.8 8.0 - - - +
235M GLY* 1.3 75.5 - - - -
237M ILE* 1.3 61.6 + - - +
238M ASN* 3.2 9.7 + - - -
224N VAL* 3.8 7.6 - - - -
236N SER* 3.2 14.8 + - - -
238N ASN* 2.7 25.3 + - - -
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Residues in contact with ILE 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158M VAL* 3.2 33.0 - - + +
185M PHE* 3.8 12.2 - - + -
189M ALA 4.8 0.9 - - - +
192M TYR* 4.0 6.1 - - + +
193M VAL* 3.8 37.7 - - + +
196M LEU* 4.4 13.5 - - + -
224M VAL* 3.4 4.0 - - - -
225M ALA* 3.0 44.2 + - + -
227M LEU* 4.6 6.7 - - + -
236M SER* 1.3 75.9 - - - +
238M ASN* 1.3 64.1 + - - +
239M VAL* 4.0 18.2 - - + -
335M ILE* 4.9 4.0 - - + -
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Residues in contact with ASN 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157M THR* 3.6 6.1 - - - +
158M VAL 2.6 11.1 + - - -
159M ASN* 3.2 25.0 + - - +
160M VAL 2.8 26.9 + - - +
161M PHE* 3.6 14.3 - - + -
223M GLY 3.9 4.7 - - - -
224M VAL* 3.3 21.5 - - - +
236M SER* 3.2 21.2 + - - -
237M ILE* 1.3 74.4 - - - +
239M VAL* 1.3 61.3 + - - +
155N MET* 4.0 8.5 - - - -
157N THR* 3.9 9.0 + - - +
236N SER* 2.7 25.4 + - - -
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Residues in contact with VAL 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M VAL* 3.3 10.1 - - + +
161M PHE* 4.9 0.2 - - - -
184M ALA* 3.7 29.4 - - + +
185M PHE* 3.7 30.1 - - + +
189M ALA* 3.7 31.9 - - + -
222M THR* 3.3 0.3 - - - -
223M GLY 2.8 33.8 + - - +
237M ILE* 4.0 10.3 - - + -
238M ASN* 1.3 79.6 - - - +
240M THR* 1.3 68.5 + - - +
241M MET* 4.0 10.8 - - + -
155N MET* 3.4 6.8 - - - +
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Residues in contact with THR 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M VAL 2.9 9.1 + - - +
161M PHE* 4.2 3.8 - - + -
162M TRP 2.9 25.6 + - - +
221M ASP 3.4 5.4 - - - -
222M THR* 2.9 29.8 + - - +
239M VAL* 1.3 77.6 - - - +
241M MET* 1.3 66.0 + - - +
242M LEU* 3.1 21.5 + - + +
243M THR* 3.7 19.7 - - - +
154N TYR* 4.6 3.0 - - + +
155N MET* 4.1 9.6 - - + -
255N LEU* 4.0 23.3 - - + -
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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