Contacts of the helix formed by residues 145 - 151 (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 HIS 145 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143E LEU 3.3 15.7 + - - -
144E THR 4.7 0.8 + - - -
145E HIS* 3.2 33.5 + + - -
113I VAL* 3.5 31.7 + - + +
142I ASP* 3.0 20.4 + - - -
143I LEU 3.3 9.7 + - - -
144I THR* 1.3 77.6 + - - +
146I GLN* 1.3 58.2 + - - +
147I ILE 3.3 2.2 - - - -
148I SER* 3.4 1.8 + - - -
149I LYS* 2.9 47.9 + - - +
154I TYR* 3.1 45.6 + + + -
159I GLY 4.0 2.0 + - - -
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Residues in contact with GLN 146 (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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41I LYS* 5.9 1.0 - - - +
142I ASP* 3.3 1.9 + - - +
144I THR* 3.1 20.0 + - - +
145I HIS* 1.3 77.6 - - - +
147I ILE* 1.3 68.8 + - + +
149I LYS* 3.9 6.6 - - - +
150I ASP* 3.0 47.9 + - - +
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Residues in contact with ILE 147 (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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51I TRP* 3.9 29.8 - - + -
52I GLU 3.8 21.3 - - - +
53I GLY* 5.1 0.4 - - - -
76I PHE* 4.0 9.6 - - + -
78I PHE* 3.8 22.0 - - + -
111I CYS* 4.6 1.1 - - - -
140I LEU* 3.9 22.4 - - + -
141I SER 4.2 7.6 - - - +
142I ASP* 3.0 25.1 + - + +
146I GLN* 1.3 80.9 - - + +
148I SER* 1.3 64.2 + - - +
150I ASP* 3.2 8.4 + - - +
151I TYR* 3.1 28.3 + - + -
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Residues in contact with SER 148 (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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78I PHE* 3.8 16.2 - - - -
111I CYS* 5.2 0.2 - - - -
112I SER 5.3 0.2 - - - -
113I VAL* 3.9 5.5 + - - +
142I ASP* 2.6 29.6 + - - +
145I HIS* 3.8 5.2 - - - -
147I ILE* 1.3 73.4 - - - +
149I LYS* 1.3 60.3 + - - +
151I TYR 3.3 1.2 + - - -
152I GLY 3.0 3.8 + - - -
153I VAL* 3.0 29.5 + - - +
154I TYR* 3.9 17.3 - - - -
161I THR* 3.0 33.0 - - - +
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Residues in contact with LYS 149 (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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149E LYS* 5.3 8.9 - - - +
39I LEU 4.5 1.9 - - - +
40I SER* 4.2 7.6 - - - -
144I THR 4.9 2.8 + - - +
145I HIS* 2.9 34.0 + - + +
146I GLN* 3.9 5.6 - - - +
148I SER* 1.3 74.0 - - - +
150I ASP* 1.3 68.8 + - - +
152I GLY* 3.0 14.1 + - - -
154I TYR* 3.8 39.4 - - + -
156I GLU* 3.8 17.1 + - - +
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Residues in contact with ASP 150 (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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41I LYS* 2.8 70.1 + - + +
42I ALA 3.5 3.1 + - - -
49I PRO* 4.0 12.4 - - + +
50I TYR 4.3 12.2 - - - +
146I GLN* 3.0 38.9 + - - +
147I ILE* 3.2 10.8 + - - +
149I LYS* 1.3 77.4 - - - +
151I TYR* 1.3 66.4 + - + +
152I GLY 3.3 0.2 - - - -
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Residues in contact with TYR 151 (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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40I SER* 3.5 10.1 + - - -
42I ALA* 4.1 7.4 - - + +
48I ALA* 3.6 17.6 - - + +
49I PRO* 2.6 49.6 + - + -
50I TYR 4.9 0.4 - - - -
51I TRP* 3.4 24.3 + + + -
66I LEU* 4.0 1.6 - - - +
76I PHE* 3.7 17.7 - + - -
78I PHE* 3.6 29.6 - + + -
147I ILE* 3.1 20.7 + - + +
148I SER 3.3 2.4 + - - +
149I LYS 3.1 0.4 - - - -
150I ASP* 1.3 78.9 - - + +
152I GLY* 1.3 62.8 + - - +
153I VAL* 3.3 1.9 + - + +
166I PHE* 3.4 57.9 - + + -
168I ILE* 4.1 2.9 - - + +
174I LEU* 5.5 0.7 - - + -
179I 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