Contacts of the strand formed by residues 46 - 52 (chain B) in PDB entry 2ARB
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASP* 2.5 26.5 + - - +
34B THR* 3.7 22.0 - - - -
35B LYS* 2.9 31.3 + - + +
43B VAL* 3.3 26.2 - - - +
44B ALA 4.2 1.6 - - - +
45B SER* 1.3 74.5 - - - +
47B VAL* 1.3 68.9 + - - +
218B ALA* 3.3 1.3 - - - -
219B SER* 2.9 37.5 + - - +
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Residues in contact with VAL 47 (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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22B GLY* 3.6 5.2 - - - -
23B ASP* 2.8 26.7 + - - +
33B LEU 4.2 3.1 - - - -
34B THR* 4.6 0.4 - - - -
45B SER 5.7 0.2 - - - -
46B THR* 1.3 84.6 + - - +
48B GLY* 1.3 64.1 + - - +
49B ARG* 4.8 0.7 - - + -
99B ILE* 4.1 27.1 - - + -
103B SER* 4.6 0.7 - - - +
104B GLY* 3.4 33.0 - - - +
109B GLY* 3.6 26.9 - - - -
217B ALA 3.5 10.1 - - - +
218B ALA* 3.8 3.8 - - + -
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Residues in contact with GLY 48 (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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21B GLN 3.3 12.1 - - - -
22B GLY* 4.4 0.2 - - - -
24B ALA* 3.8 4.5 - - - -
33B LEU* 3.2 26.9 + - - +
47B VAL* 1.3 78.3 - - - +
49B ARG* 1.3 66.4 + - - +
99B ILE* 4.6 0.2 - - - -
216B SER* 3.5 0.3 - - - -
217B ALA* 3.0 31.6 + - - +
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Residues in contact with ARG 49 (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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19B ILE 4.5 0.2 - - - -
21B GLN* 2.9 63.5 + - + +
24B ALA* 3.4 9.2 - - - +
33B LEU* 4.1 2.2 - - - -
47B VAL* 4.8 1.1 - - + -
48B GLY* 1.3 80.6 - - - +
50B ILE* 1.3 64.3 + - - +
91B PHE* 3.8 18.5 - - + -
97B THR* 2.9 35.6 + - - +
98B THR 3.2 28.5 + - - +
99B ILE* 3.6 17.7 - - + +
100B PRO* 4.2 2.4 - - - +
109B GLY 2.9 23.2 + - - -
110B LEU* 4.0 11.1 + - - +
215B PHE 3.1 13.0 - - - +
216B SER* 3.2 24.0 - - - +
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Residues in contact with ILE 50 (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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11B PHE* 4.8 1.1 - - + -
18B LEU* 4.4 15.9 - - + -
19B ILE 3.2 8.3 - - - +
20B PHE* 3.6 34.5 - - + -
24B ALA* 4.0 2.9 - - + -
31B VAL* 4.0 24.9 - - + -
33B LEU* 4.2 9.4 - - + +
49B ARG* 1.3 79.3 - - - +
51B LEU* 1.3 68.0 + - - +
91B PHE* 4.4 0.5 - - - -
214B GLY* 3.2 2.7 - - - -
215B PHE* 3.0 44.8 + - + +
228B LEU* 3.7 26.5 - - + -
231B TRP* 4.4 16.2 - - + -
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Residues in contact with LEU 51 (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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18B LEU* 3.5 8.8 - - - +
19B ILE* 2.8 44.4 + - + +
21B GLN* 4.0 26.9 - - - +
50B ILE* 1.3 77.2 - - - +
52B PHE* 1.3 68.4 + - - +
91B PHE* 3.6 32.5 - - + -
95B PRO 5.0 1.8 - - - +
97B THR* 3.7 24.7 - - + +
212B ARG* 4.2 24.9 - - + -
213B VAL 3.4 20.9 - - - +
214B GLY* 4.1 0.9 - - - -
231B TRP* 5.1 0.7 - - - -
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Residues in contact with PHE 52 (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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1A GLN* 4.2 5.8 - - + -
4A LEU* 4.5 13.9 - - + -
54A ALA* 4.6 3.8 - - + -
4B LEU* 4.9 4.7 - - + -
6B PHE* 3.4 60.8 - + + -
8B PHE* 4.0 23.1 - + - -
17B ASN* 3.5 37.5 - - + -
18B LEU* 4.3 4.0 - - + -
51B LEU* 1.3 74.6 - - - +
53B SER* 1.3 65.1 + - - +
54B ALA* 3.5 47.6 + - + +
56B VAL* 6.1 0.2 - - + -
212B ARG* 3.5 18.4 - - - +
213B VAL* 3.0 17.1 + - + +
231B TRP* 4.1 8.4 - - + -
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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