Contacts of the helix formed by residues 118 - 123 (chain D) in PDB entry 1TKK
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 PRO 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D GLY 4.7 1.3 - - - +
117D LEU* 1.3 89.0 - - + +
119D LEU* 1.3 66.5 + - - +
120D TYR* 3.5 26.9 - - + -
121D GLN* 3.1 29.6 + - - +
122D MET* 3.1 16.8 + - - +
309D HIS* 4.6 2.0 - - + -
347D PRO 4.0 7.9 - - - +
348D GLY* 3.6 22.4 - - - +
349D LYS 3.4 25.3 - - - +
350D PRO* 4.6 0.4 - - + -
351D GLY 3.6 4.0 - - - +
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Residues in contact with LEU 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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105D MET 5.4 0.2 - - - +
108D TYR* 3.5 49.4 - - + +
111D TRP* 4.5 1.8 - - + -
112D ALA* 3.6 15.0 - - + -
117D LEU 3.5 1.6 + - - -
118D PRO* 1.3 70.3 - - - +
120D TYR* 1.3 64.7 + - - +
122D MET* 2.9 17.2 + - + +
123D LEU* 3.0 36.7 + - + +
275D ILE* 4.1 15.5 - - + -
306D ALA 4.9 0.7 - - - +
309D HIS* 3.4 18.4 + - + +
351D GLY 3.0 17.2 + - - +
352D LEU* 3.7 24.7 - - + -
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Residues in contact with TYR 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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118D PRO* 3.2 32.0 - - + -
119D LEU* 1.3 79.5 - - - +
121D GLN* 1.3 83.1 + - + +
124D GLY 3.3 0.7 + - - -
125D GLY* 2.6 40.3 + - - -
127D ARG 3.2 27.6 - - - -
128D ASP* 3.6 21.3 + - - -
309D HIS* 3.1 41.0 + + - +
312D ALA* 4.1 5.4 - - + -
313D SER* 3.3 11.2 - - - -
346D MET* 3.5 40.8 + - + +
347D PRO 3.8 8.2 + - - -
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Residues in contact with GLN 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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79C LEU 4.6 1.0 - - - +
80C ALA* 3.3 43.4 - - + +
82C TYR* 3.6 10.2 - - - -
117D LEU* 3.3 27.4 - - + +
118D PRO* 3.1 20.5 + - - +
120D TYR* 1.3 118.8 + - + +
122D MET* 1.3 68.1 + - - +
123D LEU 3.3 0.4 - - - -
124D GLY 3.2 9.4 + - - -
125D GLY* 3.7 2.9 - - - +
128D ASP* 5.3 0.8 + - - -
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Residues in contact with MET 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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82C TYR* 3.1 20.1 + - - -
111C TRP* 3.8 20.2 - - + +
114C MET* 4.7 0.7 - - + -
115C CYS* 3.6 17.7 - - - -
122C MET* 4.8 0.7 - - - -
111D TRP* 3.3 41.2 - - + -
112D ALA* 4.1 13.5 - - + -
115D CYS* 3.4 33.7 - - - -
117D LEU* 3.4 34.5 - - + -
118D PRO 3.1 10.9 + - - +
119D LEU* 3.3 15.3 - - + +
121D GLN* 1.3 78.4 - - - +
123D LEU* 1.3 57.3 + - - +
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Residues in contact with LEU 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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82C TYR* 3.5 10.1 + - - -
83C GLU* 4.8 1.2 - - - +
108D TYR* 3.9 27.4 - - + -
111D TRP* 4.0 15.9 - - + -
119D LEU* 3.0 37.9 + - + +
122D MET* 1.3 75.7 - - - +
124D GLY* 1.3 56.6 + - - +
275D ILE* 4.0 22.0 - - + -
279D GLU* 4.4 12.3 - - - +
309D HIS 4.4 2.0 - - - +
310D PHE* 4.2 22.0 - - + -
313D SER* 3.5 17.2 + - - +
314D LYS* 2.7 35.0 + - - +
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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