Contacts of the helix formed by residues 52 - 61 (chain Z) in PDB entry 6QY3
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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43Y LEU* 5.5 6.3 - - - -
45Y THR 3.9 17.9 - - - -
46Y THR* 3.7 10.8 + - - -
48Y ILE* 3.1 26.7 + - - -
50Y LEU 5.9 0.2 - - - +
67Y PHE* 6.1 4.5 - - - -
68Y CYS 5.0 5.0 - - - +
50Z LEU 4.4 0.2 + - - -
51Z THR* 1.3 72.3 - - - +
53Z MET* 1.3 57.4 + - - +
55Z VAL* 3.2 10.1 + - - +
56Z LYS* 2.9 27.9 + - - +
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Residues in contact with MET 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Y THR* 3.0 33.4 + - - +
17Z TYR* 4.7 7.7 - - + +
51Z THR* 3.2 6.0 - - - -
52Z THR* 1.3 77.6 - - - +
54Z LEU* 1.3 57.9 + - - +
56Z LYS* 3.3 5.8 + - - +
57Z ARG* 2.9 27.5 + - - +
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Residues in contact with LEU 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Z LEU* 5.0 4.0 - - + +
16Z SER* 4.3 7.6 - - - +
17Z TYR* 3.8 32.8 - - + +
50Z LEU* 5.7 3.1 - - + -
51Z THR* 3.2 19.5 + - - +
53Z MET* 1.3 77.4 - - - +
55Z VAL* 1.3 58.5 + - - +
57Z ARG* 3.8 3.0 - - - +
58Z LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Y PHE* 5.5 11.0 - - + -
76Y ALA* 5.9 0.5 - - - +
50Z LEU* 6.4 0.4 - - + -
51Z THR 3.1 11.9 + - - +
52Z THR* 3.5 12.6 - - - +
53Z MET 3.2 0.2 - - - -
54Z LEU* 1.3 76.8 - - - +
56Z LYS* 1.3 59.0 + - - +
58Z LEU* 3.3 7.1 + - - +
59Z VAL* 2.9 27.9 + - - +
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Residues in contact with LYS 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Y THR* 5.4 3.4 - - - -
68Y CYS 4.6 4.7 - - - +
69Y ASP* 4.4 27.4 - - + -
70Y ASP 5.5 0.4 - - - +
75Y THR* 5.7 4.9 - - - -
52Z THR 2.9 15.6 + - - +
53Z MET* 3.3 8.3 + - - +
55Z VAL* 1.3 74.2 - - - +
57Z ARG* 1.3 59.9 + - - +
59Z VAL* 3.2 7.5 + - - +
60Z ASP* 2.9 29.0 + - - +
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Residues in contact with ARG 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z TYR* 4.8 10.1 - - + -
53Z MET 2.9 17.3 + - - +
54Z LEU* 3.8 8.7 - - - +
56Z LYS* 1.3 76.2 - - - +
58Z LEU* 1.3 56.2 + - - +
60Z ASP* 3.8 6.5 - - - +
61Z GLU* 2.9 30.0 + - - +
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Residues in contact with LEU 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Z LEU 2.9 18.5 + - - +
55Z VAL* 3.6 8.1 - - - +
56Z LYS 3.2 0.2 - - - -
57Z ARG* 1.3 75.1 - - - +
59Z VAL* 1.3 59.3 + - - +
61Z GLU* 3.4 5.2 + - - -
62Z ASN 3.0 21.3 + - - -
63Z ILE* 3.0 33.1 + - + +
65Z VAL* 5.6 8.1 - - + -
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Residues in contact with VAL 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Y THR* 4.4 21.1 - - - -
76Y ALA* 4.6 15.7 - - + -
55Z VAL 2.9 16.6 + - - +
56Z LYS* 3.2 8.2 + - - +
58Z LEU* 1.3 74.6 - - - +
60Z ASP* 1.3 64.3 + - - +
62Z ASN* 3.3 13.2 + - - +
63Z ILE 5.5 0.4 - - - -
80Z PRO* 4.9 15.8 - - + +
83Z ALA* 6.2 0.2 - - - -
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Residues in contact with ASP 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Z LYS 2.9 16.1 + - - +
57Z ARG* 3.9 7.0 - - - +
59Z VAL* 1.3 77.0 - - - +
61Z GLU* 1.3 60.3 + - - +
62Z ASN* 3.2 3.0 + - - +
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Residues in contact with GLU 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z LEU* 5.1 20.2 - - + +
57Z ARG 2.9 18.4 + - - +
58Z LEU* 3.4 7.2 + - - +
59Z VAL 3.3 0.2 - - - -
60Z ASP* 1.3 75.7 - - - +
62Z ASN* 1.3 70.4 + - - +
63Z ILE* 3.5 7.9 + - + +
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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