Contacts of the strand formed by residues 43 - 47 (chain J) in PDB entry 6ATU
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 LYS 43 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J THR* 4.5 5.5 - - - -
12J LYS* 3.1 22.6 + - + +
13J PRO 3.8 16.2 - - - +
14J GLY* 3.8 28.6 + - - +
15J SER 4.3 1.3 - - - -
16J CYS* 4.2 22.2 - - - +
35J ASP* 2.8 34.1 + - - +
38J CYS* 4.0 2.9 - - - -
41J ILE 3.5 3.5 + - - +
42J LYS* 1.3 76.1 - - - +
44J CYS* 1.3 62.0 + - - +
45J CYS* 3.6 14.0 - - - -
52J ALA 3.5 1.2 - - - +
53J CYS* 3.3 3.3 - - - -
54J PHE 2.7 35.3 + - - +
56J PRO* 4.4 6.5 - - + -
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Residues in contact with CYS 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J CYS* 3.5 9.5 - - - -
32J CYS* 2.1 63.3 - - + -
33J LEU 3.7 2.2 - - - +
34J LYS* 3.4 28.5 - - - +
35J ASP* 2.7 14.5 + - - +
38J CYS* 4.0 2.3 - - - -
43J LYS* 1.3 71.2 - - - +
45J CYS* 1.3 59.5 + - - +
51J MET* 3.7 24.2 - - + +
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Residues in contact with CYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J CYS* 2.0 57.2 - - + -
17J PRO* 4.0 11.4 - - - +
43J LYS* 3.6 18.2 - - - -
44J CYS* 1.3 77.1 - - - +
46J GLU* 1.3 68.3 + - - +
47J GLY* 3.3 0.5 + - - -
51J MET* 3.0 9.6 - - - -
52J ALA 2.8 30.9 + - - +
54J PHE* 3.7 18.6 - - + -
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Residues in contact with GLU 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J PRO 4.5 5.7 - - - +
19J ILE* 3.1 19.5 - - + +
22J ARG* 3.9 40.3 + - - +
28J PRO* 4.9 6.1 - - - +
30J ASN* 5.0 0.3 - - - +
45J CYS* 1.3 78.9 - - - +
47J GLY* 1.3 58.9 + - - +
50J GLY* 3.7 27.0 + - - -
51J MET* 3.7 16.4 + - - +
54J PHE* 4.3 2.6 - - - -
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Residues in contact with GLY 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ILE* 3.6 19.7 - - - +
22J ARG* 3.7 5.7 - - - +
45J CYS 3.3 1.8 + - - -
46J GLU* 1.3 79.3 - - - +
48J SER* 1.3 66.6 + - - +
49J CYS* 3.3 4.9 + - - -
50J GLY 3.2 19.5 + - - +
52J ALA* 5.1 1.6 - - - -
54J PHE* 4.0 21.8 - - - -
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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