Contacts of the strand formed by residues 16 - 21 (chain A) in PDB entry 3BUK
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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A CYS 4.0 2.4 + - - -
15A ASP* 1.3 75.9 - - - +
17A GLU* 1.3 63.4 + - - +
18A SER* 5.7 0.2 + - - -
55A THR* 3.9 15.0 + - - -
56A ARG 3.2 11.7 - - - -
58A LYS* 4.1 9.7 + - - +
107A SER* 5.6 0.2 - - - -
108A CYS* 3.9 18.6 - - - -
83D TYR* 5.2 3.3 - - - -
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Residues in contact with GLU 17 (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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16A SER* 1.3 75.4 - - - +
18A SER* 1.3 65.0 - - - +
19A LEU* 4.7 2.4 - - + +
55A THR* 3.2 3.3 - - - -
56A ARG* 2.6 89.0 + - + +
57A CYS 4.2 0.7 - - - +
58A LYS* 3.2 53.8 + - + +
83D TYR* 4.5 8.5 - - + -
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Residues in contact with SER 18 (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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17A GLU* 1.3 76.6 - - - +
19A LEU* 1.3 67.2 + - - +
53A TYR* 3.0 36.0 + - - -
54A GLU 3.2 5.2 - - - -
55A THR* 3.1 19.1 + - - +
83D TYR* 3.3 30.7 + - - -
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Residues in contact with LEU 19 (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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17A GLU* 4.7 5.2 - - + +
18A SER* 1.3 79.8 - - - +
20A TRP* 1.3 67.1 + - - +
21A VAL* 3.7 17.2 + - + -
52A PHE 3.5 1.4 - - - +
53A TYR* 3.7 4.6 - - - -
54A GLU* 2.8 56.2 + - + +
55A THR 4.9 0.2 - - - +
56A ARG* 4.4 32.5 - - + +
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Residues in contact with TRP 20 (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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19A LEU* 1.3 78.4 - - - +
21A VAL* 1.3 61.3 + - - +
22A THR* 3.7 13.6 + - + +
51A TYR* 3.5 26.9 - + + -
52A PHE 3.4 2.9 - - - -
53A TYR* 3.5 46.7 - + + -
30B ILE* 3.9 16.8 - - + -
85B TYR* 4.7 1.3 - - + -
101B TRP* 3.3 47.8 - + + -
67D MET* 3.5 48.3 + - + +
68D SER* 4.5 4.8 - - - +
70D PRO* 3.6 25.1 - - + -
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Residues in contact with VAL 21 (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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19A LEU* 3.8 30.5 - - + +
20A TRP* 1.3 74.3 - - - +
22A THR* 1.3 60.2 + - - +
23A ASP* 3.7 16.8 + - - +
24A LYS* 4.0 22.6 + - + -
51A TYR* 3.3 4.0 - - - +
52A PHE* 2.8 37.1 + - + +
54A GLU* 3.5 37.0 - - + +
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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