Contacts of the helix formed by residues 81 - 92 (chain F) in PDB entry 1TKK
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 GLY 81 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E GLY 3.5 6.1 - - - -
125E GLY 3.6 13.5 - - - -
126E TYR* 5.5 0.2 - - - -
78F SER* 3.3 10.0 + - - +
79F LEU 3.2 0.2 - - - -
80F ALA* 1.3 76.7 - - - +
82F TYR* 1.3 60.0 + - - -
83F GLU 3.5 2.5 - - - -
84F ALA* 3.6 12.9 - - - +
85F ILE* 3.5 22.2 + - - +
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Residues in contact with TYR 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E GLN 3.3 23.8 - - - -
122E MET 3.1 16.6 + - - -
123E LEU* 3.9 6.9 + - - -
124E GLY* 3.1 20.4 + - - -
79F LEU* 3.7 31.0 - - + +
81F GLY* 1.3 73.5 - - - +
83F GLU* 1.3 66.0 + - - +
84F ALA 3.2 1.1 - - - -
85F ILE* 3.7 11.7 - - + +
86F LEU* 2.9 60.2 + - + +
107F LEU* 4.9 8.1 - - + -
108F TYR* 4.7 13.2 - + - -
111F TRP* 3.2 43.8 - + + -
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Residues in contact with GLU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E LEU 4.7 1.6 - - - +
124E GLY* 3.1 20.1 + - - +
126E TYR* 4.1 7.4 - - + -
282E ASN* 5.3 0.5 - - - +
286E GLU* 4.4 11.5 - - - +
313E SER 3.8 9.6 - - - +
314E LYS* 3.3 26.7 + - - +
315E ARG* 2.9 45.0 + - + +
316E ASN 4.5 0.2 + - - -
82F TYR* 1.3 80.6 - - - +
84F ALA* 1.3 56.6 + - - +
86F LEU* 3.3 12.0 + - - +
87F HIS* 2.8 29.7 + - + +
280F LYS* 5.3 7.3 + - - -
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Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E TYR* 4.3 25.1 - - + +
81F GLY* 3.6 13.6 + - - +
82F TYR 3.2 0.4 - - - -
83F GLU* 1.3 79.1 - - - +
85F ILE* 1.3 62.9 + - + +
87F HIS* 3.3 6.8 + - - +
88F ASP* 3.0 25.5 + - - +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F ILE* 4.7 1.8 - - + -
74F LEU* 3.6 28.2 - - + +
77F LYS* 3.9 32.1 - - + -
78F SER 3.4 29.6 - - - +
79F LEU* 4.1 14.4 - - + -
81F GLY 3.5 9.8 + - - +
82F TYR* 3.3 14.2 + - + +
84F ALA* 1.3 75.6 - - + +
86F LEU* 1.3 64.4 + - - +
88F ASP* 3.1 9.7 + - - +
89F ILE* 3.0 24.6 + - + +
107F LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TYR* 2.9 52.7 + - + +
83F GLU* 3.6 11.2 - - - +
85F ILE* 1.3 75.3 - - - +
87F HIS* 1.3 61.9 + - - +
89F ILE* 3.4 6.6 + - + +
90F GLN* 3.2 29.2 + - - +
104F GLU* 3.4 38.4 - - + +
107F LEU* 4.1 14.6 - - + -
108F TYR* 3.9 19.7 - - + +
276F SER* 4.0 14.1 - - - +
280F LYS* 6.0 2.0 - - - +
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Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E GLU* 5.3 8.4 + - - -
315E ARG* 2.9 61.5 + - + -
83F GLU* 2.8 18.6 + - + +
84F ALA* 3.5 7.0 - - - +
86F LEU* 1.3 74.5 - - - +
88F ASP* 1.3 66.2 + - - +
90F GLN* 3.4 0.8 + - - -
91F HIS* 2.9 82.4 + + + +
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Residues in contact with ASP 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F ALA* 3.4 28.4 - - - +
74F LEU* 4.9 7.9 - - + -
77F LYS* 5.3 3.8 - - - -
84F ALA 3.0 14.0 + - - +
85F ILE* 3.4 11.9 - - - +
87F HIS* 1.3 76.5 + - - +
89F ILE* 1.3 57.9 + - - +
91F HIS* 5.2 0.9 - - - -
92F LEU* 2.8 58.6 + - + +
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LEU* 3.8 13.6 - - + +
74F LEU* 4.2 15.5 - - + -
85F ILE* 3.0 34.5 + - + +
86F LEU* 3.5 11.9 - - - +
87F HIS 3.3 0.2 - - - -
88F ASP* 1.3 76.6 - - - +
90F GLN* 1.3 79.5 + - - +
93F LEU* 3.6 9.4 - - - +
100F LYS* 3.2 44.1 - - + +
103F VAL* 4.0 23.8 - - + -
104F GLU* 4.1 16.8 - - + -
107F LEU* 4.5 6.3 - - + -
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Residues in contact with GLN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F LEU 3.2 14.8 + - - +
87F HIS* 5.0 0.4 - - - -
88F ASP 3.2 0.4 - - - -
89F ILE* 1.3 90.0 - - - +
91F HIS* 1.3 77.3 + - + +
92F LEU 3.6 0.2 - - - -
93F LEU 3.1 4.9 - - - +
94F THR* 5.1 0.2 - - - -
97F MET* 4.1 8.5 - - - +
100F LYS* 3.1 36.8 + - - +
104F GLU* 3.0 19.3 + - - +
272F ALA 3.8 13.9 + - - +
273F GLY 2.7 27.7 + - - -
276F SER* 4.3 7.3 + - - +
277F GLY* 6.1 1.1 - - - -
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Residues in contact with HIS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 5.1 4.9 - - - +
223A HIS* 6.2 4.9 - + - -
87F HIS* 2.9 67.6 + + + +
88F ASP* 3.7 0.9 - - - -
90F GLN* 1.3 91.3 - - + +
92F LEU* 1.3 62.8 + - - +
93F LEU* 3.2 4.9 + - - -
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 5.3 0.9 - - - +
53A VAL* 3.5 17.8 - - - +
69F VAL* 3.7 30.0 - - + +
70F LEU* 4.9 4.9 - - + -
73F ALA* 3.3 33.4 - - + -
74F LEU* 5.8 0.7 - - + -
88F ASP* 2.8 48.4 + - + +
89F ILE 4.4 0.4 + - - -
90F GLN 3.6 0.2 - - - -
91F HIS* 1.3 75.0 - - - +
93F LEU* 1.3 65.0 + - + +
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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