Contacts of the strand formed by residues 240 - 244 (chain X) in PDB entry 2DE0
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 THR 240 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198X LEU* 3.0 20.0 + - - +
199X GLN* 3.4 35.2 - - - +
201X PRO* 3.3 21.7 - - + +
207X ALA* 4.7 1.0 - - - +
208X LYS 3.0 13.8 + - - -
209X LYS* 3.4 11.4 - - - +
210X LEU 3.0 23.4 + - - +
234X ALA* 4.7 0.2 - - - -
239X ARG* 1.3 70.0 - - - +
241X LEU* 1.3 75.0 + - - +
242X ILE* 3.4 11.5 + - + -
263X SER* 4.9 0.2 - - - +
266X CYS* 4.3 7.6 - - + +
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Residues in contact with LEU 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199X GLN* 2.9 31.7 + - - +
210X LEU* 3.6 13.9 - - + +
212X CYS* 3.6 30.7 - - + -
227X VAL* 4.3 13.7 - - + -
230X CYS* 4.3 2.7 - - + -
231X PHE* 3.7 50.9 - - + -
234X ALA* 4.3 7.8 - - + +
239X ARG 3.4 2.8 + - - -
240X THR* 1.3 77.6 - - - +
242X ILE* 1.3 74.5 - - - +
243X LEU* 4.5 3.8 - - + +
262X VAL* 3.6 25.8 - - + +
263X SER* 5.2 0.7 - - - -
266X CYS 4.8 1.2 - - - +
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Residues in contact with ILE 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209X LYS* 3.8 30.5 - - + -
210X LEU 2.9 13.7 + - - +
211X VAL* 3.6 14.0 - - + +
212X CYS 3.0 27.0 + - - +
240X THR* 3.9 10.8 - - + +
241X LEU* 1.3 81.7 - - - +
243X LEU* 1.3 63.5 + - - +
244X GLU* 3.8 12.0 + - - +
262X VAL* 5.2 0.2 - - - -
266X CYS* 3.3 28.9 - - - +
267X THR* 3.6 23.8 - - - +
268X ASP 3.7 23.3 - - - +
269X ARG* 4.1 7.0 - - + +
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Residues in contact with LEU 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212X CYS* 3.8 16.8 - - + +
214X ILE* 4.1 22.7 - - + +
227X VAL* 4.0 31.2 - - + -
241X LEU* 4.1 4.8 + - + -
242X ILE* 1.3 78.6 - - - +
244X GLU* 1.3 60.7 + - - +
245X SER* 3.4 15.2 + - - +
255X TRP* 3.6 48.9 - - + +
256X GLU* 4.6 9.5 - - - +
262X VAL* 4.6 24.0 - - + +
267X THR 5.8 0.2 - - - +
335X LEU* 5.4 0.2 - - + -
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Residues in contact with GLU 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X VAL* 4.1 12.6 - - + -
212X CYS 2.8 13.6 + - - +
213X ASN* 3.2 24.0 + - + +
214X ILE* 3.0 27.4 + - - +
215X ASN* 4.2 0.2 + - - -
242X ILE* 4.7 9.0 - - - +
243X LEU* 1.3 70.7 - - - +
245X SER* 1.3 61.5 + - - +
246X GLN* 3.7 11.4 - - - +
269X ARG* 3.0 50.0 + - - +
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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