Contacts of the strand formed by residues 213 - 217 (chain B) in PDB entry 2J0U
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 GLN 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 3.0 20.9 + - - +
75B GLY* 2.9 30.6 - - - +
76B ARG 2.9 27.9 + - - +
77B ASP* 3.6 5.2 - - - +
99B CYS* 5.4 5.0 - - - +
182B LYS* 2.5 24.9 + - + +
183B MET* 3.6 36.9 - - + +
184B LEU 2.5 34.0 + - - -
211B ALA 3.6 2.7 + - - +
212B THR* 1.3 74.2 - - - +
214B VAL* 1.3 61.0 + - - +
215B VAL* 4.7 0.4 - - + -
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG 4.1 0.2 - - - +
77B ASP* 2.6 42.5 + - - +
78B VAL 3.0 4.7 + - - -
184B LEU* 3.3 17.0 - - + +
186B LEU* 4.3 14.4 - - + -
205B TYR* 4.3 14.4 - - + -
212B THR* 3.8 9.2 - - + +
213B GLN* 1.3 80.7 - - - +
215B VAL* 1.3 65.6 + - - +
232B PHE* 3.4 41.7 - - + +
233B MET* 3.4 20.7 - - + +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.0 32.3 - - + -
78B VAL* 3.4 16.6 - - + +
80B ALA* 5.5 0.9 - - + -
92B PHE* 4.9 0.7 - - + -
183B MET* 3.4 30.7 - - + -
184B LEU 3.0 6.5 + - - +
185B VAL* 3.3 11.1 - - + -
186B LEU* 2.7 34.1 + - - +
213B GLN* 4.7 3.4 - - + -
214B VAL* 1.3 77.7 - - - +
216B LEU* 1.3 57.7 + - - +
217B ILE* 3.3 31.6 + - + -
233B MET* 4.0 0.9 - - - -
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Residues in contact with LEU 216 (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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78B VAL 2.8 9.9 + - - +
79B ILE* 3.4 4.9 - - + -
80B ALA 2.8 26.8 + - - -
186B LEU* 3.5 27.6 - - + -
189B ALA* 3.2 36.6 - - + -
215B VAL* 1.3 72.2 - - - +
217B ILE* 1.3 65.9 + - - +
218B SER* 3.8 8.2 + - - -
221B LEU* 4.1 12.6 - - + -
225B VAL* 5.1 10.1 - - + -
229B THR* 4.4 15.3 - - + -
232B PHE* 4.5 10.3 - - + -
233B MET* 3.4 19.7 - - + +
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Residues in contact with ILE 217 (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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80B ALA* 3.6 19.1 - - + +
82B SER* 4.2 17.0 - - - +
88B LYS 5.2 6.1 - - - +
92B PHE* 3.4 36.8 - - + -
185B VAL* 3.5 16.6 - - + -
186B LEU 2.9 10.2 + - - +
187B ASP* 3.6 18.2 - - - +
188B GLU* 2.9 12.2 + - + +
189B ALA 2.9 22.7 + - - -
215B VAL* 3.3 30.1 - - + -
216B LEU* 1.3 75.2 - - - +
218B SER* 1.3 63.4 + - - +
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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