Contacts of the helix formed by residues 115 - 124 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E LEU* 4.2 10.8 - - - +
82E ASP 4.6 2.1 + - - -
114I ASP* 1.3 75.3 - - - +
116I GLN* 1.3 62.4 + - - +
117I PHE* 3.2 18.8 + - - +
118I GLU* 2.9 39.2 + - - +
119I HIS* 2.9 27.1 + - - -
141I SER* 3.5 6.3 - - - -
143I LEU* 3.6 25.3 - - - +
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Residues in contact with GLN 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I THR* 4.1 32.0 + - + +
55I ALA 5.3 0.2 - - - -
56I VAL* 3.5 8.3 - - + +
61I PHE* 3.4 46.6 - - + -
115I SER* 1.3 77.7 - - - +
117I PHE* 1.3 84.4 + - + +
119I HIS* 3.5 9.6 + - - -
120I LEU* 3.0 22.2 + - - +
141I SER* 3.6 18.8 + - - -
143I LEU* 4.4 7.6 - - - +
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Residues in contact with PHE 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 3.8 17.0 - - + -
82E ASP 4.3 0.9 - - - +
83E PHE* 3.8 26.7 - - + +
84E THR* 3.5 27.1 - - + -
85E PHE* 3.8 29.2 - + - -
61I PHE* 3.7 29.8 - + - -
115I SER* 3.1 12.5 - - - +
116I GLN* 1.3 104.4 - - + +
118I GLU* 1.3 57.8 + - - +
120I LEU* 3.4 3.9 + - - +
121I ALA* 2.9 28.6 + - - +
221J PRO 5.8 0.2 - - - -
223J PRO* 4.5 5.8 - - + -
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Residues in contact with GLU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E ASP* 3.8 6.3 - - - +
83E PHE* 3.9 18.6 - - + -
114E ASP* 2.5 33.7 - - - +
118E GLU* 2.8 48.5 - - + +
82I ASP* 3.4 8.5 - - + +
83I PHE* 4.0 3.5 - - + -
114I ASP* 3.6 2.4 - - - +
115I SER* 2.9 34.2 + - - +
117I PHE* 1.3 73.6 - - - +
119I HIS* 1.3 65.3 + - - +
121I ALA* 3.2 7.1 + - - +
122I TRP* 2.8 26.2 + - - +
143I LEU* 5.1 0.9 - - - +
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Residues in contact with HIS 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I VAL* 3.7 10.5 - - + -
79I TYR* 3.1 15.3 + - - -
82I ASP* 2.6 28.6 + - - -
112I SER* 3.1 26.2 - - - -
114I ASP* 3.7 9.6 - - + -
115I SER 2.9 13.9 + - - -
116I GLN* 3.6 10.3 - - - +
118I GLU* 1.3 75.3 - - - +
120I LEU* 1.3 58.8 + - - +
122I TRP* 3.2 3.9 + - - +
123I ILE* 2.9 33.8 + - - +
139I LEU* 3.3 43.3 - - + +
140I LEU 2.9 24.5 + - - -
141I SER* 3.8 10.0 - - - -
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Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I VAL* 4.1 7.8 - - + +
59I GLY* 4.0 35.0 - - - +
61I PHE* 4.3 11.2 - - + -
116I GLN 3.0 18.1 + - - +
117I PHE* 3.8 4.7 - - - +
118I GLU 3.2 0.2 - - - -
119I HIS* 1.3 77.6 - - - +
121I ALA* 1.3 63.0 + - - +
123I ILE* 3.3 12.4 + - + -
124I ASN* 3.0 44.6 + - - +
223J PRO* 3.6 36.8 - - + -
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Residues in contact with ALA 121 (chain I).
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* 3.7 39.5 - - + -
83I PHE* 4.1 4.2 - - + -
117I PHE 2.9 17.5 + - - +
118I GLU* 3.7 4.9 - - - +
120I LEU* 1.3 75.7 - - - +
122I TRP* 1.3 60.9 + - - +
124I ASN* 3.3 11.6 + - - +
125I THR* 2.8 25.0 + - - -
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Residues in contact with TRP 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I TYR* 3.6 3.8 - + - -
82I ASP* 3.2 38.4 - - - +
83I PHE* 3.1 53.7 - + + +
84I THR 4.3 0.2 - - - -
87I CYS* 4.1 7.0 - - + -
88I PRO* 3.5 46.7 - - + -
91I ILE* 3.4 26.5 - - + -
118I GLU 2.8 16.3 + - - +
119I HIS* 3.5 3.8 - - - +
121I ALA* 1.3 75.7 - - - +
123I ILE* 1.3 64.4 + - - +
125I THR* 3.1 13.9 + - - -
130I GLY 3.0 18.6 + - - -
131I GLY* 3.7 9.8 - - - -
132I LEU* 3.1 38.4 + - + -
139I LEU* 5.1 1.8 - - + -
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Residues in contact with ILE 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I VAL* 3.6 31.9 - - + +
59I GLY* 5.7 4.3 - - - +
119I HIS 2.9 19.8 + - - +
120I LEU* 3.5 12.6 - - + +
122I TRP* 1.3 77.2 - - - +
124I ASN* 1.3 64.9 + - - +
125I THR 3.2 4.0 + - - -
132I LEU* 4.1 12.1 - - + +
133I GLY* 3.4 34.5 + - - +
135I ILE* 3.8 27.6 - - + -
139I LEU* 3.7 24.2 - - + -
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Residues in contact with ASN 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I LEU* 3.0 38.5 + - - +
121I ALA* 3.6 10.5 - - - +
122I TRP 3.2 0.6 - - - -
123I ILE* 1.3 82.3 - - - +
125I THR* 1.3 59.4 + - - +
126I PRO* 3.8 6.6 - - - +
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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