Contacts of the strand formed by residues 42 - 48 (chain B) in PDB entry 5BOU
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ALA* 2.7 37.3 + - - +
40B SER 3.5 0.8 - - - -
41B ASP* 1.3 80.9 - - - +
43B ILE* 1.3 59.7 + - - +
145B TYR* 3.5 16.6 - - - -
185B VAL* 3.3 12.9 - - - +
215B ILE 3.1 13.9 - - - -
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Residues in contact with ILE 43 (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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37B ILE 3.4 11.9 - - - +
38B MET* 4.1 6.5 - - + -
42B GLY* 1.3 78.8 - - - +
44B VAL* 1.3 73.4 + - - +
137B ALA* 3.7 22.7 - - + -
138B GLY 3.4 26.9 - - - +
145B TYR* 3.7 18.4 - - + -
146B GLN 3.3 34.5 - - - +
147B LEU* 3.8 14.6 - - + -
185B VAL* 4.3 1.5 - - - +
214B THR* 3.4 6.1 - - - -
215B ILE* 2.9 39.9 + - + +
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Residues in contact with VAL 44 (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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35B ILE 3.9 0.2 - - - +
36B GLY* 3.3 6.2 - - - -
37B ILE* 2.9 36.5 + - + +
43B ILE* 1.3 82.4 - - - +
45B LEU* 1.3 67.6 + - - +
46B ALA 4.2 0.2 - - - -
185B VAL* 3.9 10.8 - - + +
188B ALA* 3.8 17.0 - - + +
189B ILE* 3.7 33.7 - - + +
192B ALA* 4.2 18.6 - - + -
212B PHE* 3.6 32.8 - - + -
213B ALA 3.7 2.9 - - - +
214B THR* 4.4 2.5 - - + +
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Residues in contact with LEU 45 (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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35B ILE 3.5 9.0 - - - +
36B GLY* 4.1 2.7 - - - -
44B VAL* 1.3 79.5 - - - +
46B ALA* 1.3 60.8 + - - +
65B LEU* 4.0 15.3 - - + +
73B ALA* 4.2 25.1 - - + +
74B VAL 4.3 14.1 - - - +
75B ALA* 4.1 11.7 - - + +
135B ILE* 3.9 28.7 - - + +
137B ALA* 3.7 30.5 - - + -
147B LEU* 4.6 0.2 - - + -
212B PHE* 3.5 4.9 - - - -
213B ALA* 2.7 52.9 + - + +
215B ILE* 5.5 1.8 - - + -
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Residues in contact with ALA 46 (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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34B ALA* 3.4 0.5 - - - +
35B ILE* 2.6 41.9 + - + +
44B VAL* 4.2 0.6 - - - +
45B LEU* 1.3 74.3 - - - +
47B ALA* 1.3 61.4 + - - +
65B LEU* 5.1 0.2 - - - -
192B ALA* 4.0 19.1 - - + -
196B LEU* 3.7 21.6 - - + +
211B GLU 3.7 4.9 - - - -
212B PHE* 3.6 26.0 - - + -
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Residues in contact with ALA 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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33B THR 3.4 8.7 - - - +
34B ALA* 4.0 8.7 - - + -
46B ALA* 1.3 77.7 - - - +
48B GLU* 1.3 60.0 + - - +
64B LYS* 3.7 35.2 - - + -
65B LEU* 3.8 13.5 - - + -
196B LEU* 4.1 3.2 - - - +
210B LEU* 3.5 9.6 - - - +
211B GLU 2.8 37.4 + - - +
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Residues in contact with GLU 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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32B GLY* 3.6 10.4 - - - -
33B THR* 2.9 31.1 + - - +
47B ALA* 1.3 72.0 - - - +
49B ARG* 1.3 76.1 + - - +
50B LYS* 5.5 8.9 - - + +
64B LYS* 3.5 20.5 - - - -
196B LEU* 4.8 9.2 - - + +
200B THR* 2.6 40.1 + - - -
201B ASP 4.6 1.9 + - - -
202B SER* 3.6 13.0 + - - -
205B LEU* 4.5 10.0 - - + +
209B ARG* 3.5 19.6 - - - +
210B LEU* 4.3 6.3 - - + -
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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