Contacts of the strand formed by residues 240 - 244 (chain B) in PDB entry 2DOU
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 GLY 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.5 11.8 - - - -
93B LEU* 2.7 36.8 + - - +
95B GLY* 3.6 6.0 - - - +
226B PHE 3.3 13.0 - - - -
227B SER* 3.9 5.8 - - - -
228B LEU* 4.5 0.7 - - - -
239B LEU* 1.3 75.3 - - - +
241B PHE* 1.3 68.9 + - - +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.7 29.6 - + + -
69B LEU* 4.7 4.0 - - + -
72B ALA* 4.1 17.3 - - + -
75B TRP* 3.7 27.6 - + - -
91B LEU 3.4 11.9 - - - +
93B LEU* 3.7 6.9 - - - +
224B GLU 3.7 1.6 - - - +
226B PHE* 2.9 72.5 + + + +
227B SER 4.9 2.5 - - - -
228B LEU* 4.7 9.0 - - + -
232B TYR* 6.3 0.2 - + - -
240B GLY* 1.3 77.9 - - - +
242B ALA* 1.3 58.5 + - - +
243B LEU* 3.6 27.8 - - + -
275B LEU* 4.2 18.4 - - + -
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ALA* 3.2 6.1 - - - -
91B LEU* 2.9 33.9 + - + +
93B LEU* 3.6 19.0 - - + +
223B VAL* 4.2 1.6 - - + -
224B GLU 3.5 5.2 - - - -
225B LEU* 3.8 22.0 - - + -
241B PHE* 1.3 73.8 - - - +
243B LEU* 1.3 61.9 + - - +
249B LEU* 3.8 23.3 - - + +
252B LEU* 4.4 5.2 - - + -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 4.5 11.7 - - + +
73B ALA* 5.1 1.3 - - - +
76B TYR* 3.7 39.3 - - + -
84B LEU* 3.8 16.4 - - + -
89B GLU 3.3 4.5 - - - +
90B ALA* 3.4 30.3 - - + -
91B LEU 5.1 0.2 - - - +
213B LEU* 4.1 10.0 - - + +
223B VAL* 3.4 4.1 - - - +
224B GLU 2.8 34.8 + - - +
226B PHE* 4.0 6.5 - - + -
241B PHE* 3.6 35.7 - - + -
242B ALA* 1.3 77.6 - - - +
244B GLY* 1.3 59.4 + - - +
249B LEU* 4.2 3.1 - - - -
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 4.5 3.7 - - - +
89B GLU* 3.0 34.5 + - - +
213B LEU* 4.1 17.5 - - - +
219B LYS* 5.1 2.0 - - - -
222B VAL 3.4 8.7 - - - -
223B VAL* 4.5 0.9 - - - -
243B LEU* 1.3 76.0 - - - +
245B SER* 1.3 68.7 + - - +
246B GLU 3.0 4.0 + - - -
249B LEU* 3.7 4.9 - - - +
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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