Contacts of the strand formed by residues 240 - 245 (chain R) in PDB entry 5G04
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 TYR 240 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234R TRP* 3.5 10.9 - - - -
235R ILE* 3.0 53.7 + - + +
237R GLU* 4.2 6.7 - - - -
239R ASN* 1.3 121.7 + - - +
241R LEU* 1.3 60.9 + - - +
242R ALA 4.3 0.2 - - - -
252R LEU* 4.3 16.8 - - + -
253R TRP 3.3 4.5 - - - +
254R ASP* 3.5 35.2 + - - -
256R GLN* 5.1 1.4 + - - -
261R LEU* 3.6 22.6 - - + +
276R TRP* 5.4 4.5 - - + -
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Residues in contact with LEU 241 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199R ALA* 3.8 26.0 - - + -
206R VAL* 3.7 29.4 - - + -
208R LEU* 4.2 3.4 - - + -
219R LEU* 3.8 21.8 - - + -
232R VAL* 4.2 4.9 - - + -
233R ALA 3.6 31.6 - - - +
234R TRP* 3.8 22.2 - - + +
240R TYR* 1.3 74.7 - - - +
242R ALA* 1.3 64.6 + - - +
243R VAL* 3.9 11.7 + - + +
251R GLN 3.8 0.7 - - - +
252R LEU* 3.5 3.5 - - - -
253R TRP* 2.8 43.0 + - - +
255R VAL* 4.7 0.9 - - + +
276R TRP* 5.4 0.4 - - - -
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Residues in contact with ALA 242 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232R VAL* 3.3 5.9 - - - -
233R ALA 2.8 41.4 + - - +
240R TYR 4.3 0.4 - - - -
241R LEU* 1.3 73.7 - - - +
243R VAL* 1.3 62.7 + - - +
250R VAL* 5.2 0.2 - - + -
251R GLN 3.3 6.7 - - - +
252R LEU* 4.5 1.6 - - + +
274R LEU* 3.4 16.8 - - + +
276R TRP* 3.6 20.0 - - + +
281R LEU* 3.8 24.9 - - + -
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Residues in contact with VAL 243 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206R VAL* 4.1 1.8 - - + -
220R LEU* 3.9 28.5 - - + -
229R ILE* 3.8 33.4 - - + -
231R SER 3.4 2.7 - - - -
232R VAL* 4.1 8.3 - - + -
241R LEU* 4.0 26.0 - - + +
242R ALA* 1.3 79.6 - - - +
244R GLY* 1.3 63.2 + - - +
245R THR* 4.1 9.4 + - + +
249R GLU 3.6 1.4 - - - +
250R VAL* 3.6 3.0 - - - +
251R GLN* 2.8 49.9 + - + +
253R TRP* 4.4 3.1 - - + -
274R LEU* 4.1 1.8 - - - -
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Residues in contact with GLY 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229R ILE* 3.5 8.1 - - - +
230R SER* 2.8 28.8 + - - -
231R SER* 2.8 27.8 + - - -
243R VAL* 1.3 73.4 - - - +
245R THR* 1.3 58.8 + - - +
249R GLU 3.4 7.6 - - - -
250R VAL* 4.7 1.3 - - - -
271R VAL* 4.0 11.4 - - - -
274R LEU* 3.7 4.2 - - - +
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Residues in contact with THR 245 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222R MET* 3.9 27.6 - - + -
228R TYR 3.6 4.3 - - - -
229R ILE* 4.7 0.7 - - + -
230R SER* 3.3 6.7 - - - -
243R VAL* 4.3 16.2 - - + +
244R GLY* 1.3 77.7 - - - +
246R SER* 1.3 62.8 + - - +
247R SER* 3.0 21.6 + - - -
248R ALA* 3.2 11.1 + - - -
249R GLU* 3.0 37.6 + - - +
251R GLN* 4.1 11.7 - - - +
271R VAL* 3.3 18.0 + - - +
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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