Contacts of the helix formed by residues 115 - 124 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B LEU* 4.2 10.0 - - - +
82B ASP 4.6 2.4 + - - -
114G ASP* 1.3 76.2 - - - +
116G GLN* 1.3 62.8 + - - +
117G PHE* 3.3 18.8 + - - +
118G GLU* 3.0 38.3 + - - +
119G HIS* 3.0 26.3 + - - -
141G SER* 3.4 7.9 - - - -
143G LEU* 3.6 26.2 - - - +
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Residues in contact with GLN 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G THR* 4.1 31.5 + - + +
55G ALA 5.3 0.7 - - - -
56G VAL* 3.5 5.5 - - + +
61G PHE* 3.5 47.4 - - + -
115G SER* 1.3 75.2 - - - +
117G PHE* 1.3 90.9 + - + +
119G HIS* 3.4 11.8 + - + +
120G LEU* 3.0 19.2 + - - +
141G SER* 3.7 16.2 + - - -
143G LEU* 4.3 7.8 - - - +
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Residues in contact with PHE 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.9 16.4 - - + -
82B ASP 4.3 0.7 - - - +
83B PHE* 3.8 25.2 - - + +
84B THR* 3.5 27.4 - - + -
85B PHE* 3.7 31.2 - + - -
61G PHE* 3.7 28.7 - + - -
115G SER* 3.2 11.6 - - - +
116G GLN* 1.3 102.5 - - + +
118G GLU* 1.3 57.2 + - - +
120G LEU* 3.5 4.0 + - - +
121G ALA* 3.0 28.1 + - - +
221H PRO 5.8 0.2 - - - -
223H PRO* 4.4 7.2 - - + -
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Residues in contact with GLU 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP* 3.6 7.1 - - - +
83B PHE* 3.9 20.6 - - + -
114B ASP* 2.3 36.5 - - - +
118B GLU* 2.9 48.0 - - + +
82G ASP* 3.4 7.9 - - + +
83G PHE* 3.9 3.9 - - + -
114G ASP* 3.7 2.3 - - - +
115G SER* 3.0 36.9 + - - +
117G PHE* 1.3 73.8 - - - +
119G HIS* 1.3 65.9 + - - +
121G ALA* 3.3 6.8 + - - +
122G TRP* 2.9 24.9 + - - +
143G LEU* 5.1 0.9 - - - +
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Residues in contact with HIS 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G VAL* 3.8 11.0 - - + -
79G TYR* 3.1 23.5 + - - -
82G ASP* 2.6 27.8 + - - -
112G SER* 3.1 19.5 + - - -
114G ASP* 3.8 8.3 - - + -
115G SER 3.0 14.6 + - - -
116G GLN* 3.4 11.4 + - - +
118G GLU* 1.3 75.4 - - - +
120G LEU* 1.3 57.1 + - - +
122G TRP* 3.1 6.1 + - - +
123G ILE* 2.9 33.7 + - - +
139G LEU* 3.2 41.2 + - + +
140G LEU 3.0 25.0 + - - -
141G SER* 3.9 9.2 - - - -
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Residues in contact with LEU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 4.1 7.4 - - + +
59G GLY* 3.8 35.2 - - - +
61G PHE* 4.2 12.6 - - + -
116G GLN 3.0 17.3 + - - +
117G PHE* 3.8 4.0 - - - +
119G HIS* 1.3 74.1 - - - +
121G ALA* 1.3 65.4 + - - +
123G ILE* 3.3 11.1 + - + +
124G ASN* 3.0 47.1 + - - +
223H PRO* 3.6 38.1 - - + -
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Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 3.7 38.8 - - + -
83G PHE* 4.0 4.0 - - + -
117G PHE 3.0 18.2 + - - +
118G GLU 3.3 4.7 + - - +
120G LEU* 1.3 75.8 - - - +
122G TRP* 1.3 55.2 + - - +
124G ASN* 3.3 10.4 + - - +
125G THR* 2.8 31.7 + - - -
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Residues in contact with TRP 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G TYR* 3.6 4.0 - + - -
82G ASP* 3.3 34.5 - - - +
83G PHE* 3.2 54.6 - + + +
87G CYS* 4.1 6.7 - - + -
88G PRO* 3.5 49.8 - - + -
91G ILE* 3.4 25.1 - - + -
118G GLU 2.9 14.1 + - - +
119G HIS 3.3 8.1 - - - +
121G ALA* 1.3 74.9 - - - +
123G ILE* 1.3 65.5 + - - +
125G THR* 3.1 13.4 + - - -
130G GLY 3.0 18.9 + - - -
131G GLY* 3.7 8.0 - - - -
132G LEU* 3.2 38.8 + - + -
139G LEU* 4.9 2.2 - - + -
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Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 3.6 32.5 - - + +
59G GLY* 5.4 6.3 - - - +
119G HIS 2.9 18.3 + - - +
120G LEU* 3.3 12.5 + - + +
122G TRP* 1.3 75.2 - - - +
124G ASN* 1.3 66.1 + - - +
125G THR 3.2 2.3 + - - -
132G LEU* 4.2 5.8 - - + -
133G GLY* 3.1 46.2 + - - +
134G PRO* 4.1 9.6 - - + +
135G ILE* 3.9 26.9 - - + +
139G LEU* 4.0 17.0 - - + -
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Residues in contact with ASN 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G LEU* 3.0 44.4 + - - +
121G ALA* 3.3 9.9 + - - +
122G TRP 3.1 0.4 - - - -
123G ILE* 1.3 81.1 - - - +
125G THR* 1.3 58.1 + - - +
126G 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