Contacts of the strand formed by residues 250 - 254 (chain R) in PDB entry 5A31
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 250 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243R VAL 3.3 11.7 - - - +
244R GLY* 4.6 0.4 - - - -
248R GLY 3.8 3.8 - - - +
249R LEU* 1.3 80.4 - - - +
251R GLU* 1.3 64.9 + - - +
263R THR* 3.6 1.4 - - - +
264R LEU* 2.6 53.8 + - + +
271R VAL* 3.8 30.5 - - + -
274R LEU* 4.0 19.5 - - + -
281R LEU* 4.2 18.6 - - + -
283R SER* 4.2 3.6 - - - -
293R ARG* 3.9 21.3 - - - +
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Residues in contact with GLU 251 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224R ASP 5.4 0.5 - - - +
225R THR* 5.8 0.2 - - - -
229R TYR* 4.2 7.4 + - - -
241R LEU 3.8 0.5 - - - +
242R ALA* 3.5 2.6 - - - +
243R VAL* 2.8 50.0 + - + +
245R GLN* 3.3 31.9 + - - +
249R LEU* 3.8 14.7 - - + +
250R VAL* 1.3 76.6 - - - +
252R ILE* 1.3 65.4 + - - +
253R TYR* 3.0 33.3 + - + -
260R CYS* 3.7 16.5 - - - -
262R ARG 3.2 13.7 - - - +
263R THR* 4.2 8.1 + - - +
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Residues in contact with ILE 252 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240R HIS* 3.9 31.0 - - + +
241R LEU 3.5 7.2 - - - +
242R ALA* 4.5 4.0 - - - -
251R GLU* 1.3 78.3 - - - +
253R TYR* 1.3 59.7 + - - +
260R CYS* 3.6 2.8 - - - -
261R ILE* 2.8 38.4 + - + -
262R ARG* 2.9 26.6 + - + +
264R LEU* 3.7 24.5 - - + -
276R TRP* 4.2 8.1 - - + -
281R LEU* 4.2 19.5 - - + -
295R VAL* 3.3 34.1 - - + -
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Residues in contact with TYR 253 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222R LEU* 3.8 30.5 - - + -
223R CYS* 3.2 39.1 - - + +
224R ASP 5.0 1.9 + - - -
229R TYR* 4.0 1.7 + - - -
240R HIS* 3.1 11.3 - - - +
241R LEU* 2.8 43.2 + - + +
243R VAL* 4.1 21.3 - - + -
251R GLU* 3.0 39.8 + - + -
252R ILE* 1.3 78.0 - - - +
254R ASP* 1.3 61.0 + - - +
255R VAL* 3.3 1.1 + - + +
258R ARG 4.9 2.2 - - - -
259R LYS* 3.4 18.6 - - - -
260R CYS* 3.5 24.0 - - + +
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Residues in contact with ASP 254 (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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239R SER 4.4 1.0 - - - +
240R HIS* 3.5 24.5 + - + -
253R TYR* 1.3 71.9 - - - +
255R VAL* 1.3 54.4 + - - +
256R MET* 3.2 14.1 + - - +
257R LYS* 3.0 46.5 + - + +
258R ARG* 2.7 34.1 + - - -
259R LYS* 3.0 11.3 + - + +
261R ILE* 3.5 28.8 - - + +
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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
------------------------------------------------------------
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