Contacts of the strand formed by residues 50 - 53 (chain A) in PDB entry 3BSQ
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 TRP 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.6 4.4 - - - +
46A VAL* 2.9 48.0 + - + -
47A ASN* 3.0 32.5 + - - +
48A GLU 3.7 0.2 - - - -
49A ARG* 1.3 100.8 - - + +
51A VAL* 1.3 61.4 + - - +
85A PHE* 3.9 20.0 - + - -
101A LEU* 3.9 25.6 - - + -
102A VAL 3.3 19.7 - - - -
103A LYS* 3.6 46.1 - - + +
104A LEU* 4.3 1.4 - - - +
234A THR* 4.3 4.9 - - + -
235A MET* 3.5 29.9 - - + +
237A HIS* 3.7 32.6 + - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.8 27.8 - - + -
33A LEU* 4.6 7.2 - - + -
43A GLY* 4.1 1.8 - - - -
44A VAL 3.2 16.8 - - - +
45A LEU* 4.4 11.7 - - + -
50A TRP* 1.3 75.2 - - - +
52A LEU* 1.3 72.6 + - - +
53A THR* 3.5 11.7 - - - +
64A VAL* 4.6 7.0 - - + -
101A LEU* 3.2 5.9 - - - +
102A VAL* 2.2 44.7 + - + +
104A LEU* 4.3 21.1 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLY* 3.3 1.4 - - - -
44A VAL* 2.8 50.7 + - + +
46A VAL* 3.6 22.4 - - + -
51A VAL* 1.3 67.2 + - - +
53A THR* 1.3 62.8 + - - +
99A LEU* 4.3 18.6 - - + -
100A MET 3.1 25.3 + - - +
101A LEU* 3.6 18.9 - - + +
119A LEU* 5.3 0.7 - - + -
192A GLY 4.1 0.2 - - - +
201A LEU* 4.3 11.7 - - + -
204A LEU* 3.7 32.8 - - + -
224A VAL* 4.5 7.2 - - + -
231A ILE* 4.8 15.7 - - + -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.5 26.4 - - + +
41A CYS* 4.0 0.2 - - + -
42A GLY 2.8 28.0 - - - +
51A VAL* 3.5 9.4 - - - +
52A LEU* 1.3 75.4 - - - +
54A ALA* 1.3 67.0 + - - +
57A CYS* 3.8 19.7 - - + -
99A LEU* 3.3 5.4 - - - +
100A MET* 2.8 33.8 + - - +
102A VAL* 3.9 9.4 - - - +
192A GLY* 3.9 9.6 - - - -
204A LEU* 3.5 12.9 - - - +
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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