Contacts of the helix formed by residues 145 - 151 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU 3.3 16.5 + - - -
144A THR* 4.6 0.9 + - - -
145A HIS* 3.2 33.5 + + - -
113H VAL* 3.6 25.8 + - + +
142H ASP* 3.0 22.0 + - - -
143H LEU 3.3 10.4 + - - -
144H THR* 1.3 76.4 + - - +
146H GLN* 1.3 64.0 + - - +
147H ILE 3.3 2.9 - - - -
148H SER* 3.4 1.5 + - - -
149H LYS* 3.0 44.7 + - - +
154H TYR* 3.1 41.9 + + + -
159H GLY 3.9 8.1 + - - -
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Residues in contact with GLN 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LYS* 4.3 6.1 + - - -
142H ASP* 3.3 2.7 + - - +
144H THR* 3.1 20.4 + - - +
145H HIS* 1.3 79.2 - - - +
147H ILE* 1.3 68.5 + - + +
149H LYS* 3.8 8.7 - - - +
150H ASP* 3.0 55.9 + - - +
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Residues in contact with ILE 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H TYR 6.1 0.2 - - - -
51H TRP* 3.8 30.1 - - + -
52H GLU 3.9 21.3 - - - +
53H GLY* 5.1 0.2 - - - -
76H PHE* 4.0 10.3 - - + -
78H PHE* 4.0 20.0 - - + -
111H CYS* 4.7 1.3 - - - -
140H LEU* 3.9 21.5 - - + -
141H SER 4.3 7.6 - - - +
142H ASP* 3.0 25.1 + - + +
146H GLN* 1.3 78.7 - - + +
148H SER* 1.3 64.2 + - - +
150H ASP* 3.2 7.7 + - - +
151H TYR* 3.1 29.3 + - + -
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Residues in contact with SER 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H PHE* 3.8 18.5 - - - -
111H CYS* 5.2 0.2 - - - -
112H SER 5.4 0.3 - - - -
113H VAL* 3.9 9.5 + - - +
142H ASP* 2.6 29.0 + - - +
145H HIS* 3.8 4.0 - - - -
147H ILE* 1.3 72.6 - - - +
149H LYS* 1.3 58.4 + - - +
151H TYR 3.4 1.0 + - - -
152H GLY 3.0 6.9 + - - -
153H VAL* 3.0 28.6 + - - +
154H TYR* 3.5 20.8 + - - -
161H THR* 3.3 24.2 + - - -
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Residues in contact with LYS 149 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LYS* 5.3 8.5 - - - +
39H LEU 4.5 2.1 - - - +
40H SER* 4.1 7.4 - - - -
144H THR 4.8 3.4 + - - -
145H HIS* 3.0 35.5 + - + +
146H GLN* 3.8 8.5 - - - +
148H SER* 1.3 75.6 - - - +
150H ASP* 1.3 67.8 + - - +
152H GLY* 3.0 14.6 + - - +
154H TYR* 3.8 40.1 - - + -
156H GLU* 3.8 15.7 + - - +
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Residues in contact with ASP 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LYS* 2.8 67.2 + - + +
42H ALA 3.4 5.5 + - - -
49H PRO* 3.9 11.9 - - + +
50H TYR 4.3 12.1 - - - +
146H GLN* 3.0 37.8 + - - +
147H ILE* 3.2 12.0 + - - +
149H LYS* 1.3 76.6 - - - +
151H TYR* 1.3 66.9 + - + +
152H GLY 3.3 0.2 - - - -
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Residues in contact with TYR 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H SER* 3.5 9.5 + - - -
42H ALA* 4.0 7.8 - - + +
48H ALA* 3.5 18.1 - - + +
49H PRO* 2.7 47.8 + - + -
50H TYR 4.9 0.4 - - - -
51H TRP* 3.4 24.7 + + + -
66H LEU* 3.8 1.6 - - - +
76H PHE* 3.7 17.3 - + - -
78H PHE* 3.6 30.1 - + + -
147H ILE* 3.1 20.2 + - + +
148H SER 4.0 1.8 - - - +
150H ASP* 1.3 79.7 - - + +
152H GLY* 1.3 62.9 + - - +
153H VAL* 3.3 2.8 + - + +
166H PHE* 3.4 56.8 - + + -
168H ILE* 4.1 3.3 - - + +
174H LEU* 5.5 1.1 - - + -
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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