Contacts of the helix formed by residues 58 - 67 (chain O) in PDB entry 5GJQ
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 58 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6O GLY 6.0 1.6 - - - +
10O GLN* 5.7 4.9 - - + -
57O ILE* 1.3 80.5 - - - +
59O LEU* 1.3 67.4 + - + +
61O GLU* 3.1 2.3 - - - -
62O ASN* 2.6 43.8 + - - +
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Residues in contact with LEU 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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3O ASP 5.5 0.8 + - - +
6O GLY 4.6 2.2 - - - +
7O PHE* 3.8 42.5 - - + +
10O GLN* 4.3 19.7 - - + -
57O ILE 3.5 0.6 - - - +
58O LYS* 1.3 81.9 - - + +
60O TYR* 1.3 59.1 + - - +
62O ASN* 2.9 20.7 + - - +
63O PHE* 3.2 15.2 + - - +
64O ILE 4.1 0.3 + - - -
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Residues in contact with TYR 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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41O VAL* 5.4 12.6 - - + -
45O VAL* 5.8 7.9 - - + -
57O ILE* 3.7 9.9 + - - +
58O LYS 3.5 0.2 - - - -
59O LEU* 1.3 78.5 - - - +
61O GLU* 1.3 57.2 + - - +
62O ASN 3.4 0.2 - - - -
63O PHE* 5.8 0.2 - - - -
64O ILE* 1.9 50.4 - - + +
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Residues in contact with GLU 61 (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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57O ILE* 1.9 66.9 + - + +
58O LYS* 3.1 3.6 - - - +
60O TYR* 1.3 74.5 - - - +
62O ASN* 1.3 57.6 + - - +
65O SER* 2.9 30.2 + - - +
83O VAL* 5.3 0.7 - - + -
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Residues in contact with ASN 62 (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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3O ASP* 5.1 11.7 - - - +
58O LYS* 2.6 21.0 + - - +
59O LEU* 2.9 3.8 + - - +
61O GLU* 1.3 73.1 - - - +
63O PHE* 1.4 59.9 + - - +
65O SER* 3.5 3.6 - - - -
66O GLU* 3.2 29.1 + - - +
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Residues in contact with PHE 63 (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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3O ASP 4.9 12.3 - - - +
7O PHE* 5.1 6.7 - - + -
59O LEU 3.2 9.6 + - - +
60O TYR* 5.8 0.2 - - - -
62O ASN* 1.4 76.2 - - - +
64O ILE* 1.3 54.4 + - - +
65O SER 3.2 1.3 - - - -
66O GLU* 2.9 14.8 - - + +
67O PHE* 2.6 35.4 + - - +
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Residues in contact with ILE 64 (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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41O VAL* 5.8 8.7 - - + -
60O TYR* 1.9 42.0 + - + +
63O PHE* 1.3 74.0 - - - +
65O SER* 1.3 63.4 + - - +
67O PHE* 2.9 18.9 + - + -
68O GLU* 3.1 15.1 + - - +
76O LEU* 6.1 5.2 - - + -
79O ILE* 4.9 20.6 - - + -
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Residues in contact with SER 65 (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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60O TYR 3.5 3.6 + - - -
61O GLU* 2.9 31.4 + - - +
62O ASN* 3.5 5.4 + - - -
64O ILE* 1.3 79.3 - - - +
66O GLU* 1.3 62.0 + - - +
67O PHE 3.2 0.9 + - - -
68O GLU* 3.5 17.4 + - - +
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Residues in contact with GLU 66 (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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62O ASN 3.2 17.2 + - - +
63O PHE* 2.9 17.6 + - + +
65O SER* 1.3 79.2 - - - +
67O PHE* 1.3 57.6 + - - +
68O GLU* 3.5 2.1 + - - +
69O HIS* 4.0 12.0 + - - +
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Residues in contact with PHE 67 (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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63O PHE 2.6 17.1 + - - +
64O ILE* 2.9 17.5 + - + +
66O GLU* 1.3 72.6 - - - +
68O GLU* 1.3 56.9 + - - +
69O HIS* 2.8 18.7 + - - +
70O ARG* 2.9 38.0 + - + +
76O LEU* 5.0 0.7 - - - +
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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