Contacts of the helix formed by residues 115 - 124 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E ASP* 1.3 75.5 - - - +
116E GLN* 1.3 64.2 + - - +
117E PHE* 3.2 19.2 + - - +
118E GLU* 3.0 39.1 + - - +
119E HIS* 3.0 27.1 + - - -
141E SER* 3.4 7.2 - - - -
143E LEU* 3.6 22.2 - - - +
81I LEU* 4.3 10.0 - - - +
82I ASP 4.6 2.4 + - - -
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Residues in contact with GLN 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E THR* 4.0 31.4 + - + +
56E VAL* 3.4 17.9 - - + +
61E PHE* 3.5 39.3 - - + -
115E SER* 1.3 77.4 - - - +
117E PHE* 1.3 83.4 + - + +
119E HIS* 3.4 3.8 + - - -
120E LEU 3.0 23.0 + - - -
141E SER* 3.6 21.2 + - - -
143E LEU* 4.5 7.0 - - - +
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Residues in contact with PHE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PRO* 4.5 6.7 - - + -
61E PHE* 3.6 29.8 - + - -
115E SER* 3.1 11.2 - - - +
116E GLN* 1.3 104.7 - - + +
118E GLU* 1.3 59.0 + - - +
120E LEU* 3.9 3.2 - - - +
121E ALA* 3.1 27.5 + - - +
81I LEU* 4.0 17.0 - - + -
82I ASP 4.3 0.4 - - - +
83I PHE* 3.9 24.1 - - + +
84I THR* 3.6 27.4 - - + -
85I PHE* 3.6 30.5 - + - -
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Residues in contact with GLU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E ASP* 3.4 8.2 - - + +
83E PHE* 4.0 4.0 - - + -
114E ASP* 3.7 2.3 - - - +
115E SER* 3.0 36.9 + - - +
117E PHE* 1.3 76.2 - - - +
119E HIS* 1.3 65.4 + - - +
121E ALA* 3.3 6.6 + - - +
122E TRP* 2.9 25.5 + - - +
143E LEU* 5.1 0.7 - - - +
82I ASP* 3.6 7.0 - - - +
83I PHE* 3.9 20.4 - - + -
114I ASP* 2.4 34.4 - - - +
118I GLU* 2.8 48.5 - - + +
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Residues in contact with HIS 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E VAL* 3.6 10.3 - - + -
79E TYR* 3.1 22.8 + - - -
82E ASP* 2.6 27.9 + - - -
112E SER* 3.2 19.1 - - - -
114E ASP* 3.7 9.6 + - + -
115E SER 3.0 14.6 + - - -
116E GLN* 3.5 14.4 - - - +
118E GLU* 1.3 76.1 - - - +
120E LEU* 1.3 57.7 + - - +
122E TRP* 3.2 5.3 + - - +
123E ILE* 2.9 33.4 + - - +
139E LEU* 3.3 42.9 - - + +
140E LEU 3.0 25.2 + - - -
141E SER* 3.9 6.2 - - - -
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PRO* 3.6 37.9 - - + -
56E VAL* 4.1 7.1 - - + +
59E GLY* 3.8 36.1 - - - +
61E PHE* 4.1 14.6 - - + -
116E GLN 3.0 17.2 + - - +
117E PHE 3.9 4.3 - - - +
119E HIS* 1.3 72.9 - - - +
121E ALA* 1.3 61.0 + - - +
123E ILE* 3.3 12.7 + - + +
124E ASN* 2.9 53.1 + - - +
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Residues in contact with ALA 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E PHE* 4.0 4.4 - - + -
117E PHE 3.1 19.4 + - - +
118E GLU 3.3 4.7 + - - +
120E LEU* 1.3 76.5 - - - +
122E TRP* 1.3 55.1 + - - +
124E ASN* 3.3 10.9 + - - +
125E THR* 2.8 32.3 + - - -
83I PHE* 3.7 38.8 - - + -
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Residues in contact with TRP 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E TYR* 3.7 4.0 - + - -
82E ASP* 3.2 36.6 - - - +
83E PHE* 3.2 52.1 - + + +
84E THR 4.3 0.4 - - - -
87E CYS* 4.1 6.1 - - + -
88E PRO* 3.5 48.5 - - + -
91E ILE* 3.5 25.4 - - + -
118E GLU 2.9 17.0 + - - +
119E HIS 3.4 3.6 - - - +
121E ALA* 1.3 74.2 - - - +
123E ILE* 1.3 67.4 + - - +
125E THR* 3.0 13.8 + - - -
130E GLY 2.9 18.9 + - - -
131E GLY* 3.7 8.5 - - - -
132E LEU* 3.2 38.8 + - + -
139E LEU* 4.9 2.5 - - + -
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Residues in contact with ILE 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E VAL* 3.6 32.5 - - + +
59E GLY* 5.3 6.3 - - - +
119E HIS 2.9 17.7 + - - +
120E LEU* 3.4 13.2 - - + +
122E TRP* 1.3 75.9 - - - +
124E ASN* 1.3 66.0 + - - +
125E THR 3.2 3.1 + - - -
132E LEU* 4.1 6.3 - - + -
133E GLY* 3.2 42.1 + - - +
134E PRO* 4.1 9.0 - - + +
135E ILE* 3.9 25.8 - - + +
139E LEU* 3.9 19.7 - - + -
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Residues in contact with ASN 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E LEU* 2.9 43.4 + - - +
121E ALA* 3.5 10.9 - - - +
122E TRP 3.1 0.4 - - - -
123E ILE* 1.3 81.7 - - - +
125E THR* 1.3 58.4 + - - +
126E PRO* 3.9 5.5 - - - +
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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