Contacts of the helix formed by residues 115 - 124 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D ASP* 1.3 75.0 - - - +
116D GLN* 1.3 61.6 + - - +
117D PHE* 3.2 15.6 + - - +
118D GLU* 2.9 39.5 + - - +
119D HIS* 2.9 27.4 + - - -
141D SER* 3.4 6.7 - - - -
143D LEU* 3.5 25.3 - - - +
81J LEU* 4.2 13.0 - - - +
82J ASP 4.6 2.3 + - - -
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D THR* 4.0 31.7 + - + +
56D VAL* 3.4 12.5 - - + +
61D PHE* 3.3 44.7 - - + -
115D SER* 1.3 76.6 - - - +
117D PHE* 1.3 83.6 + - + +
119D HIS* 4.1 3.1 - - - -
120D LEU* 3.1 22.3 + - - +
141D SER* 3.5 21.8 + - - -
143D LEU* 4.4 8.0 - - - +
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D PHE* 3.6 30.7 - + - -
115D SER* 3.1 11.8 - - - +
116D GLN* 1.3 104.9 - - + +
118D GLU* 1.3 57.8 + - - +
120D LEU* 3.6 3.5 + - - +
121D ALA* 3.0 27.2 + - - +
223E PRO* 4.5 7.0 - - + -
81J LEU* 3.9 16.8 - - + -
82J ASP 4.3 0.7 - - - +
83J PHE* 3.9 23.9 - - + +
84J THR* 3.5 28.3 - - + -
85J PHE* 3.6 32.1 - + - -
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ASP* 3.4 8.2 - - + +
83D PHE* 3.9 3.9 - - + -
114D ASP* 3.7 2.6 - - - +
115D SER* 2.9 37.4 + - - +
117D PHE* 1.3 75.4 - - - +
119D HIS* 1.3 65.0 + - - +
121D ALA* 3.3 6.8 + - - +
122D TRP* 2.9 24.8 + - - +
143D LEU* 5.0 0.9 - - - +
82J ASP* 3.7 6.3 - - - +
83J PHE* 3.9 20.0 - - + -
114J ASP* 2.5 34.8 - - - +
118J GLU* 2.8 49.3 - - + +
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Residues in contact with HIS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 3.6 16.8 - - + -
79D TYR* 3.1 22.3 + - - -
82D ASP* 2.6 28.5 + - - -
112D SER* 3.2 19.5 - - - -
114D ASP* 3.7 9.4 - - + -
115D SER 2.9 13.9 + - - -
116D GLN* 3.6 5.4 - - - +
117D PHE 3.4 0.2 - - - -
118D GLU* 1.3 75.1 - - - +
120D LEU* 1.3 57.6 + - - +
122D TRP* 3.2 5.6 + - - +
123D ILE* 3.0 33.7 + - - +
139D LEU* 3.2 41.3 - - + +
140D LEU 2.9 25.1 + - - -
141D SER* 3.9 10.2 - - - -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 4.1 7.2 - - + +
59D GLY* 3.9 36.1 - - - +
61D PHE* 4.2 13.0 - - + -
116D GLN 3.1 17.6 + - - +
117D PHE* 3.9 4.0 - - - +
118D GLU 3.2 0.2 - - - -
119D HIS* 1.3 73.6 - - - +
121D ALA* 1.3 60.2 + - - +
123D ILE* 3.2 13.1 + - + -
124D ASN* 2.9 53.7 + - - +
223E PRO* 3.7 36.8 - - + -
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 3.9 4.4 - - + -
117D PHE 3.0 18.6 + - - +
118D GLU 3.3 4.2 + - - +
120D LEU* 1.3 75.6 - - - +
122D TRP* 1.3 52.3 + - - +
124D ASN* 3.4 11.4 + - - +
125D THR* 2.7 31.4 + - - -
83J PHE* 3.7 40.2 - - + -
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Residues in contact with TRP 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TYR* 3.6 3.8 - + - -
82D ASP* 3.3 36.3 - - - +
83D PHE* 3.2 50.1 - + + +
84D THR 4.3 0.2 - - - -
87D CYS* 4.0 7.4 - - + -
88D PRO* 3.5 46.0 - - + -
91D ILE* 3.5 28.0 - - + -
118D GLU 2.9 18.0 + - - +
119D HIS 3.4 4.9 - - - +
120D LEU 3.1 0.2 - - - -
121D ALA* 1.3 74.5 - - - +
123D ILE* 1.3 65.7 + - - +
124D ASN 3.2 0.2 - - - -
125D THR* 3.1 9.9 + - - +
130D GLY 3.0 19.3 + - - -
131D GLY* 3.7 9.6 - - - -
132D LEU* 3.0 41.7 + - + -
139D LEU* 5.1 1.8 - - + -
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 3.7 31.0 - - + +
59D GLY* 5.5 5.8 - - - +
119D HIS 3.0 18.4 + - - +
120D LEU* 3.5 14.1 - - + +
122D TRP* 1.3 76.7 - - - +
124D ASN* 1.3 64.5 + - - +
125D THR 3.2 2.9 + - - -
132D LEU* 4.1 6.3 - - + -
133D GLY* 3.1 40.1 - - - +
134D PRO* 3.9 16.4 - - + +
135D ILE* 3.7 28.5 - - + +
139D LEU* 3.8 17.0 - - + -
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 2.9 42.0 + - - +
121D ALA* 3.5 11.9 - - - +
122D TRP 3.2 0.6 - - - -
123D ILE* 1.3 81.9 - - - +
125D THR* 1.3 58.0 + - - +
126D PRO* 4.0 5.2 - - - +
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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