Contacts of the helix formed by residues 61 - 72 (chain R) in PDB entry 1TQE
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 ASP 61 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58R ALA* 3.7 6.9 - - - +
60R THR* 1.3 87.9 + - - +
62R MET* 1.3 67.0 + - - +
63R ASP* 3.2 18.9 - - - +
64R ARG* 2.5 70.3 + - - +
65R VAL* 3.4 13.4 + - - +
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Residues in contact with MET 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R ALA* 3.9 15.0 - - + -
45R LEU 4.5 2.2 - - - +
46R ILE* 4.8 7.9 - - + -
56R GLN* 3.7 28.9 - - + +
57R TYR 2.8 32.8 - - - +
58R ALA* 3.4 14.3 - - + +
61R ASP* 1.3 71.9 - - - +
63R ASP* 1.3 64.4 + - - +
65R VAL* 3.4 1.9 + - - +
66R LEU* 2.8 65.0 + - + +
69S TYR* 3.1 28.3 - - + +
109Y ALA* 4.0 10.5 - - + +
110Y SER* 4.5 2.7 - - - +
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Residues in contact with ASP 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R ASP* 3.0 16.5 - - - +
62R MET* 1.3 78.8 + - - +
64R ARG* 1.3 64.9 + - - +
67R LEU* 2.9 31.5 + - + +
109Y ALA 3.5 10.2 - - - +
110Y SER* 2.8 32.2 + - - -
113Y VAL* 3.5 25.8 - - + +
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Residues in contact with ARG 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R GLU* 3.7 23.8 - - - +
60R THR* 4.2 8.1 + - - +
61R ASP* 2.5 47.2 + - - +
63R ASP* 1.3 72.7 - - - +
65R VAL* 1.3 51.2 + - - +
67R LEU* 3.2 7.2 + - - +
68R LYS* 2.8 38.9 + - + +
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Residues in contact with VAL 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R GLU* 3.9 35.0 - - + +
43R ILE* 4.6 13.2 - - - +
44R ALA* 3.6 28.7 - - + +
58R ALA* 5.8 1.3 - - + -
59R SER* 5.3 2.5 - - - +
60R THR* 5.3 2.0 - - - +
61R ASP 3.4 10.9 + - - +
62R MET* 3.4 6.0 + - - +
63R ASP 3.3 0.4 - - - -
64R ARG* 1.3 75.0 - - - +
66R LEU* 1.3 70.7 + - + +
67R LEU 2.9 1.3 - - - -
68R LYS* 2.9 8.7 + - - +
69R TYR* 2.8 21.8 + - - +
46S ILE* 3.7 22.9 - - + +
48S PHE* 4.0 7.1 - - + -
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Residues in contact with LEU 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R ALA* 4.5 3.4 - - + -
46R ILE* 4.9 2.5 - - + -
62R MET* 2.8 62.6 + - + +
63R ASP* 5.4 0.2 - - - -
65R VAL* 1.3 79.1 - - + +
67R LEU* 1.3 62.4 + - - +
69R TYR* 3.3 20.3 + - + +
70R THR* 3.6 11.1 + - - +
46S ILE* 5.3 5.8 - - + -
66S LEU* 4.7 13.5 - - + -
69S TYR* 4.2 18.4 - - + -
110Y SER* 5.5 1.6 - - - +
113Y VAL* 4.0 17.0 - - + -
114Y LYS* 6.4 0.7 - - + -
117Y LEU* 3.1 37.5 - - + +
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Residues in contact with LEU 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R ASP* 2.9 19.9 + - + +
64R ARG* 3.2 5.8 - - - +
65R VAL 2.9 0.6 - - - -
66R LEU* 1.3 73.5 - - - +
68R LYS* 1.3 57.7 + - - +
69R TYR 2.9 4.7 - - - -
70R THR* 2.5 38.2 + - + +
71R GLU* 3.5 4.0 - - - +
113Y VAL* 3.7 27.1 - - + -
116Y LYS* 3.9 30.3 - - + -
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Residues in contact with LYS 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R GLU* 2.7 26.9 + - - +
64R ARG* 2.8 24.3 + - + +
65R VAL* 2.9 3.7 + - - +
67R LEU* 1.3 70.9 - - - +
69R TYR* 1.3 59.1 + - - +
70R THR 3.3 0.8 + - - -
71R GLU* 3.6 17.3 + - - +
72R TYR* 3.8 23.0 + - + -
48S PHE* 3.3 44.0 - - + +
49S ASN 5.5 0.6 + - - -
52S ASN* 3.2 36.8 + - - +
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Residues in contact with TYR 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R VAL 2.8 10.4 + - - +
66R LEU* 3.3 17.7 - - + +
67R LEU 2.9 0.6 - - - -
68R LYS* 1.3 77.7 - - - +
70R THR* 1.3 61.6 + - - +
71R GLU 3.4 0.2 - - - -
72R TYR 3.7 10.1 - - - +
73R SER* 3.7 21.3 + - - -
46S ILE* 3.5 29.8 - - + -
48S PHE* 3.9 7.2 - + + -
54S LEU* 3.6 27.1 - - + -
56S GLN* 3.1 29.0 + - - -
62S MET* 3.5 14.6 - - - +
63S ASP* 4.6 1.2 + - - -
66S LEU* 3.8 22.6 - - + +
117Y LEU* 4.7 7.4 - - + -
120Y PHE* 3.9 12.1 - + - -
121Y LEU* 4.8 5.8 - - + -
124Y LYS* 4.4 13.7 + - - -
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Residues in contact with THR 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R LEU 3.8 10.5 - - - +
67R LEU* 2.5 30.0 + - + +
69R TYR* 1.3 78.3 - - - +
71R GLU* 1.3 76.5 + - - +
116Y LYS* 4.5 25.1 - - + -
117Y LEU* 4.4 20.0 - - + -
120Y PHE* 3.7 45.8 - - + -
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Residues in contact with GLU 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R LEU 3.5 12.2 - - - +
68R LYS* 3.6 13.8 + - - +
69R TYR 3.4 0.2 - - - -
70R THR* 1.3 93.4 + - - +
72R TYR* 1.3 79.0 + - + +
73R SER* 2.5 22.2 + - - -
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Residues in contact with TYR 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P GLU* 3.7 30.5 - - - +
68R LYS* 3.8 33.0 + - + +
69R TYR 3.7 7.3 - - - +
71R GLU* 1.3 92.0 - - + +
73R SER* 1.3 59.6 + - - +
74R GLU 3.5 2.2 - - - -
48S PHE* 4.1 11.2 - + + -
52S ASN* 3.1 48.1 + - + +
54S LEU* 3.5 16.4 - - + +
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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