Contacts of the helix formed by residues 52 - 61 (chain J) in PDB entry 6QXT
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 THR 52 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43I LEU* 5.5 5.8 - - - -
45I THR 3.9 17.9 - - - -
46I THR* 3.7 11.0 + - - -
48I ILE* 3.1 27.3 + - - -
67I PHE* 6.1 4.9 - - - -
68I CYS 5.0 5.1 - - - +
50J LEU 4.4 0.2 + - - -
51J THR* 1.3 72.5 - - - +
53J MET* 1.3 57.4 + - - +
55J VAL* 3.3 10.7 + - - +
56J LYS* 2.9 27.4 + - - +
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Residues in contact with MET 53 (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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46I THR* 3.0 34.0 + - - +
17J TYR* 4.7 7.4 - - + +
51J THR* 3.2 6.0 - - - -
52J THR* 1.3 75.6 - - - +
54J LEU* 1.3 60.1 + - - +
56J LYS* 3.2 5.6 + - - +
57J ARG* 2.9 28.6 + - - +
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Residues in contact with LEU 54 (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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15J LEU* 4.9 4.3 - - + +
16J SER* 4.4 6.7 - - - +
17J TYR* 3.8 33.2 - - + +
50J LEU* 5.7 2.7 - - + -
51J THR* 3.1 19.3 + - - +
53J MET* 1.3 79.5 - - - +
55J VAL* 1.3 57.0 + - - +
57J ARG* 3.5 3.5 + - - +
58J LEU* 2.9 28.6 + - - +
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Residues in contact with VAL 55 (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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67I PHE* 5.5 11.4 - - + -
76I ALA* 6.0 0.2 - - - +
50J LEU* 6.4 0.4 - - + -
51J THR 3.1 12.2 + - - +
52J THR* 3.5 13.2 - - - +
53J MET 3.2 0.4 - - - -
54J LEU* 1.3 75.8 - - - +
56J LYS* 1.3 59.7 + - - +
58J LEU* 3.3 6.7 + - - +
59J VAL* 2.9 27.9 + - - +
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Residues in contact with LYS 56 (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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46I THR* 5.4 3.6 - - - -
68I CYS 4.6 4.0 - - - +
69I ASP* 4.5 27.1 - - + -
70I ASP 5.5 0.4 - - - +
75I THR* 5.7 4.0 - - - -
52J THR 2.9 13.5 + - - +
53J MET* 3.2 10.7 + - - +
55J VAL* 1.3 77.5 - - - +
57J ARG* 1.3 56.1 + - - +
59J VAL* 3.2 7.9 + - - +
60J ASP* 2.9 29.6 + - - +
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Residues in contact with ARG 57 (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 TYR* 4.8 10.1 - - + -
53J MET 2.9 16.9 + - - +
54J LEU* 3.8 8.1 - - - +
56J LYS* 1.3 76.3 - - - +
58J LEU* 1.3 57.2 + - - +
60J ASP* 3.5 6.3 + - - +
61J GLU* 2.9 29.5 + - - +
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Residues in contact with LEU 58 (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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54J LEU 2.9 17.9 + - - +
55J VAL* 3.6 8.7 - - - +
56J LYS 3.2 0.2 - - - -
57J ARG* 1.3 75.9 - - - +
59J VAL* 1.3 59.2 + - - +
61J GLU* 3.4 5.1 + - - -
62J ASN 3.0 20.8 + - - -
63J ILE* 3.0 34.0 + - + +
65J VAL* 5.6 7.4 - - + -
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Residues in contact with VAL 59 (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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75I THR* 4.4 21.1 - - - -
76I ALA* 4.6 15.5 - - + -
55J VAL 2.9 16.7 + - - +
56J LYS* 3.2 7.8 + - - +
58J LEU* 1.3 74.8 - - - +
60J ASP* 1.3 63.5 + - - +
62J ASN* 3.2 13.3 + - - +
63J ILE 5.5 0.4 - - - -
80J PRO* 4.9 15.7 - - + +
83J ALA* 6.2 0.3 - - - -
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Residues in contact with ASP 60 (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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56J LYS 2.9 15.6 + - - +
57J ARG* 3.9 7.4 - - - +
59J VAL* 1.3 77.5 - - - +
61J GLU* 1.3 60.0 + - - +
62J ASN* 3.2 3.0 + - - +
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Residues in contact with GLU 61 (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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35J LEU* 5.1 20.2 - - + +
57J ARG 2.9 19.1 + - - +
58J LEU* 3.9 7.2 - - - +
59J VAL 3.3 0.4 - - - -
60J ASP* 1.3 75.4 - - - +
62J ASN* 1.3 70.2 + - - +
63J ILE* 4.4 8.0 - - + +
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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