Contacts of the helix formed by residues 115 - 124 (chain F) in PDB entry 3TKR
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 SER 115 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C LEU* 4.1 10.4 - - - +
82C ASP 4.6 2.6 + - - -
114F ASP* 1.3 76.7 - - - +
116F GLN* 1.3 65.7 + - - +
117F PHE* 3.2 20.6 + - - +
118F GLU* 3.0 37.3 + - - +
119F HIS* 3.0 22.4 + - - -
141F SER* 3.4 7.2 - - - -
143F LEU* 3.7 25.3 - - - +
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Residues in contact with GLN 116 (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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54F THR* 4.1 31.3 + - + +
56F VAL* 3.5 8.4 - - + +
61F PHE* 3.4 46.4 - - + -
115F SER* 1.3 76.9 - - - +
117F PHE* 1.3 83.4 + - + +
119F HIS* 4.2 7.6 - - - -
120F LEU 3.0 23.2 + - - -
141F SER* 3.6 22.0 + - - -
143F LEU* 4.4 6.8 - - - +
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Residues in contact with PHE 117 (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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81C LEU* 3.8 17.0 - - + -
82C ASP 4.3 0.7 - - - +
83C PHE* 3.7 25.9 - - + +
84C THR* 3.5 27.8 - - + -
85C PHE* 3.8 30.7 - + - -
61F PHE* 3.5 31.9 - + - -
115F SER* 3.1 12.7 - - - +
116F GLN* 1.3 105.9 - - + +
118F GLU* 1.3 57.4 + - - +
120F LEU* 3.5 2.9 + - - +
121F ALA* 3.0 28.4 + - - +
221G PRO 5.7 0.4 - - - -
223G PRO* 4.6 4.7 - - + -
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Residues in contact with GLU 118 (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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82C ASP* 3.6 7.6 - - - +
83C PHE* 3.8 19.3 - - + -
114C ASP* 2.5 35.0 - - - +
118C GLU* 2.8 50.2 - - + +
82F ASP* 3.4 8.2 - - - +
83F PHE* 3.9 4.3 - - + -
114F ASP* 3.6 2.4 - - - +
115F SER* 3.0 34.8 + - - +
117F PHE* 1.3 74.5 - - - +
119F HIS* 1.3 65.1 - - - +
121F ALA* 3.2 7.0 + - - +
122F TRP* 2.9 25.1 + - - +
143F LEU* 5.3 0.2 - - - +
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Residues in contact with HIS 119 (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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56F VAL* 3.7 10.8 - - + -
79F TYR* 3.1 16.5 + - - -
82F ASP* 2.6 28.2 + - - -
112F SER* 3.1 26.4 + - - -
114F ASP* 3.8 8.7 - - + -
115F SER 3.0 13.5 + - - -
116F GLN* 3.4 13.0 + - - +
118F GLU* 1.3 76.1 - - - +
120F LEU* 1.3 56.1 + - - +
122F TRP* 3.2 4.6 + - - +
123F ILE* 2.9 33.8 + - - +
139F LEU* 3.3 42.7 - - + +
140F LEU 3.0 24.1 + - - -
141F SER* 3.9 7.2 - - - -
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Residues in contact with LEU 120 (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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56F VAL* 4.2 7.9 - - + -
59F GLY* 3.8 39.0 - - - +
61F PHE* 4.2 12.1 - - + -
116F GLN 3.0 17.1 + - - +
117F PHE* 3.9 4.0 - - - +
119F HIS* 1.3 77.9 - - - +
121F ALA* 1.3 57.4 + - - +
123F ILE* 3.2 14.0 + - + +
124F ASN* 3.0 53.2 + - - +
223G PRO* 3.6 37.7 - - + -
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Residues in contact with ALA 121 (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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83C PHE* 3.6 40.6 - - + -
83F PHE* 4.0 4.0 - - + -
117F PHE 3.0 19.0 + - - +
118F GLU 3.2 4.9 + - - +
120F LEU* 1.3 76.1 - - - +
122F TRP* 1.3 53.4 + - - +
124F ASN* 3.4 11.0 + - - +
125F THR* 2.7 31.2 + - - -
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Residues in contact with TRP 122 (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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79F TYR* 3.6 4.5 - + - -
82F ASP* 3.2 35.9 - - - +
83F PHE* 3.2 52.2 - + + +
87F CYS* 4.0 6.3 - - + -
88F PRO* 3.4 50.7 - - + -
91F ILE* 3.5 24.7 - - + -
118F GLU 2.9 18.3 + - - +
119F HIS 3.5 3.6 - - - +
120F LEU 3.1 0.2 - - - -
121F ALA* 1.3 75.7 - - - +
123F ILE* 1.3 66.3 + - - +
125F THR* 3.1 13.5 + - - -
130F GLY 3.0 18.5 + - - -
131F GLY* 3.7 9.1 - - - -
132F LEU* 3.1 39.2 + - + -
139F LEU* 5.1 1.8 - - + -
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Residues in contact with ILE 123 (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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56F VAL* 3.7 28.5 - - + +
59F GLY* 5.5 4.5 - - - +
119F HIS 2.9 18.4 + - - +
120F LEU* 3.2 15.5 + - + +
122F TRP* 1.3 77.1 - - - +
124F ASN* 1.3 64.6 + - - +
125F THR 3.2 1.9 + - - -
132F LEU* 4.0 6.3 - - + -
133F GLY* 3.2 41.9 + - - +
134F PRO* 4.2 8.8 - - + +
135F ILE* 3.6 29.6 - - + +
139F LEU* 3.7 19.5 - - + -
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Residues in contact with ASN 124 (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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120F LEU* 3.0 41.9 + - - +
121F ALA* 3.6 11.2 - - - +
122F TRP 3.2 0.4 - - - -
123F ILE* 1.3 82.1 - - - +
125F THR* 1.3 59.3 + - - +
126F PRO* 3.9 5.9 - - - +
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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