Contacts of the helix formed by residues 145 - 151 (chain C) 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 HIS 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C VAL* 3.5 26.9 + - + +
142C ASP* 3.0 19.1 + - - -
143C LEU 3.4 10.1 + - - -
144C THR* 1.3 78.0 + - - +
146C GLN* 1.3 65.1 + - - +
147C ILE 3.3 2.9 - - - -
148C SER* 3.4 1.9 + - - -
149C LYS* 3.0 44.6 + - - +
154C TYR* 3.1 41.6 + + + -
159C GLY 3.9 6.5 + - - -
143F LEU 3.3 16.4 + - - -
144F THR 4.6 0.6 + - - -
145F HIS* 3.1 34.5 + + - -
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Residues in contact with GLN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 5.9 1.2 - - - +
142C ASP* 3.3 2.1 + - - +
144C THR* 3.1 19.7 + - - +
145C HIS* 1.3 77.9 - - - +
147C ILE* 1.3 63.9 + - + +
149C LYS* 3.4 6.8 + - - +
150C ASP* 3.0 50.2 + - - +
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TYR 5.8 0.2 - - - +
51C TRP* 3.8 28.9 - - + -
52C GLU 3.8 22.0 - - - +
53C GLY* 5.1 0.2 - - - -
76C PHE* 4.1 10.5 - - + -
78C PHE* 3.8 20.4 - - + -
111C CYS* 4.7 0.7 - - - -
140C LEU* 4.0 20.9 - - + -
141C SER 4.4 6.5 - - - +
142C ASP* 3.0 26.6 + - + +
146C GLN* 1.3 81.9 - - + +
148C SER* 1.3 64.0 + - - +
150C ASP* 3.1 8.2 + - - +
151C TYR* 3.0 29.1 + - + -
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.7 15.9 - - - -
113C VAL* 3.9 6.1 + - - +
142C ASP* 2.6 29.5 + - - +
145C HIS* 3.8 4.9 - - - -
147C ILE* 1.3 74.4 - - - +
149C LYS* 1.3 56.8 + - - +
151C TYR 3.2 1.2 + - - -
152C GLY 3.0 22.0 + - - -
153C VAL* 3.0 14.5 + - - +
154C TYR* 3.9 18.2 - - - -
161C THR* 3.1 32.7 - - - +
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Residues in contact with LYS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU 4.6 1.9 - - - +
40C SER* 4.2 7.6 - - - -
144C THR 4.8 3.6 + - - -
145C HIS* 3.0 36.6 + - + +
146C GLN* 3.9 6.1 - - - +
148C SER* 1.3 72.7 - - - +
150C ASP* 1.3 69.0 + - - +
152C GLY* 3.0 15.4 + - - +
154C TYR* 3.7 32.8 - - + -
156C GLU* 3.6 24.8 + - - +
149F LYS* 5.4 7.9 - - - +
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Residues in contact with ASP 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 2.9 71.5 + - + +
42C ALA 3.4 5.9 + - - -
49C PRO* 3.9 9.0 - - + +
50C TYR 4.3 12.2 - - - +
146C GLN* 3.0 37.1 + - - +
147C ILE* 3.1 11.8 + - - +
149C LYS* 1.3 79.0 - - - +
151C TYR* 1.3 66.6 + - + +
152C GLY 3.3 0.2 - - - -
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Residues in contact with TYR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C SER* 3.4 10.0 + - - -
42C ALA* 4.0 7.6 - - + +
48C ALA* 3.6 16.1 - - + +
49C PRO* 2.7 49.1 + - + -
50C TYR 5.0 0.2 - - - -
51C TRP* 3.4 24.0 + + + -
66C LEU* 4.1 0.5 - - - +
76C PHE* 3.8 16.8 - + - -
78C PHE* 3.5 28.9 - + + -
147C ILE* 3.0 21.1 + - + +
148C SER 3.2 2.2 + - - +
149C LYS 3.1 0.2 - - - -
150C ASP* 1.3 80.5 - - + +
152C GLY* 1.3 61.6 + - - +
153C VAL* 3.3 1.7 - - + +
166C PHE* 3.3 57.1 - + + -
168C ILE* 4.0 6.5 - - + +
174C LEU* 4.8 1.8 - - + -
179C LEU* 5.7 0.2 - - - +
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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