Contacts of the helix formed by residues 56 - 60 (chain O) in PDB entry 6T9L
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 LEU 56 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1O MET* 5.3 6.5 - - + -
3O ILE* 4.7 11.7 - - + -
17O VAL* 3.7 30.3 - - + -
18O GLU 4.9 2.0 - - - +
19O PRO* 4.3 6.5 + - + +
21O ASP 3.4 13.1 + - - +
22O THR 4.8 2.2 - - - +
23O ILE* 3.8 31.4 - - + +
26O VAL* 4.7 13.2 - - + -
50O LEU* 4.6 7.9 - - + -
55O THR* 1.3 73.6 - - - +
57O SER* 1.3 65.2 + - - +
58O ASP 3.2 0.7 - - - -
59O TYR* 3.2 11.5 + - + +
61O ILE* 3.2 57.4 + - + +
67O LEU* 6.0 3.6 - - + -
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Residues in contact with SER 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O PRO* 2.6 43.2 + - - +
55O THR* 3.3 6.2 - - - -
56O LEU* 1.3 79.0 - - - +
58O ASP* 1.3 62.6 + - - +
60O ASN* 3.6 12.5 + - - +
61O ILE 4.7 7.2 - - - +
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Residues in contact with ASP 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O ARG* 3.3 43.0 - - + +
55O THR* 3.0 20.4 + - - +
56O LEU 3.2 1.0 - - - -
57O SER* 1.3 78.5 - - - +
59O TYR* 1.3 59.1 + - - +
60O ASN* 3.2 13.3 + - - +
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Residues in contact with TYR 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O ILE* 5.3 3.1 - - + -
45O PHE* 4.2 11.7 - + + -
48O LYS* 4.3 31.9 - - + +
49O GLN 4.2 7.7 + - - -
50O LEU* 4.0 25.8 - - + -
51O GLU* 3.2 42.5 + - - +
54O ARG* 3.6 37.9 - - + +
55O THR 3.4 18.8 - - - -
56O LEU* 3.2 10.0 + - + +
58O ASP* 1.3 77.0 - - - +
60O ASN* 1.3 69.4 + - - +
61O ILE* 3.1 17.7 + - + +
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Residues in contact with ASN 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K LYS* 4.8 20.0 - - - +
45O PHE* 4.6 7.4 - - + -
57O SER 3.6 11.1 + - - +
58O ASP 3.2 13.1 - - - +
59O TYR* 1.3 79.2 - - - +
61O ILE* 1.3 61.7 + - - +
62O GLN* 3.5 21.9 + - - +
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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