Contacts of the strand formed by residues 63 - 67 (chain B) in PDB entry 3BWB
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 3.9 18.4 - - + -
52B ILE* 3.9 7.9 - - + -
53B PHE 3.5 10.8 - - - +
54B GLU* 2.6 28.5 + - - +
62B GLY* 1.3 71.3 - - - -
64B VAL* 1.3 61.2 + - - +
74B THR* 3.4 1.4 - - - -
75B ASP* 3.0 41.2 + - - -
138B HIS* 4.3 13.0 + - + +
139B PHE* 3.4 29.2 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.0 19.5 - - + -
51B THR 3.8 0.7 - - - +
52B ILE* 3.4 5.5 - - - +
53B PHE* 2.8 62.3 + - + +
55B SER* 4.0 11.2 - - - -
61B TRP* 4.2 6.1 - - + -
62B GLY 3.6 12.1 - - - +
63B THR* 1.3 77.1 - - - +
65B MSE 1.3 64.8 + - - +
71B ILE* 4.1 21.1 - - + -
73B VAL 3.5 4.0 - - - +
74B THR* 3.9 24.2 - - + -
139B PHE* 4.0 2.2 - - - -
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Residues in contact with MSE 65 (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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50B LEU* 3.8 25.1 - - + -
51B THR 3.3 4.5 - - - +
52B ILE* 3.4 20.6 - - + +
64B VAL* 1.3 76.9 - - - +
66B ALA* 1.3 64.9 + - - +
67B LEU* 5.0 7.6 - - + -
71B ILE* 3.5 4.5 - - - +
72B GLN* 2.8 26.6 + - + -
73B VAL* 2.7 33.2 + - + +
106B ASP* 5.4 2.7 - - + +
131B VAL* 4.3 15.3 - - - +
135B SER* 3.3 31.2 - - - +
139B PHE* 3.2 39.7 - - + -
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Residues in contact with ALA 66 (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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20B PHE* 3.7 36.1 - - + -
49B HIS 3.5 2.3 - - - +
50B LEU* 3.7 2.6 - - - +
51B THR* 2.7 49.5 + - + +
53B PHE* 5.3 2.9 - - + -
64B VAL* 4.9 0.2 - - - +
65B MSE 1.3 76.5 - - - +
67B LEU* 1.3 62.6 + - - +
69B GLY* 4.6 1.3 - - - -
70B CYS 3.3 17.3 - - - +
71B ILE* 4.1 3.4 - - + +
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Residues in contact with LEU 67 (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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48B GLN* 4.0 31.9 - - + +
49B HIS 3.3 6.7 - - - +
50B LEU* 3.6 30.7 - - + -
65B MSE 5.0 5.2 - - - -
66B ALA* 1.3 71.6 - - - +
68B ASP* 1.3 72.0 - - + +
69B GLY 3.2 0.7 - - - -
70B CYS* 2.9 23.6 + - - +
72B GLN* 3.8 32.2 + - + +
131B VAL* 3.8 29.2 - - + -
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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