Contacts of the helix formed by residues 145 - 151 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B LEU 3.2 16.6 + - - -
144B THR* 4.6 1.0 + - - -
145B HIS* 3.2 33.5 + + - -
113G VAL* 3.4 33.5 + - + +
142G ASP* 2.9 21.3 + - - -
143G LEU 3.3 9.6 + - - -
144G THR* 1.3 77.9 + - - +
146G GLN* 1.3 62.4 + - - +
147G ILE 3.3 2.9 - - - -
148G SER* 3.4 1.9 + - - -
149G LYS* 2.9 43.8 + - - +
154G TYR* 3.2 40.4 + + + -
159G GLY 3.9 2.6 + - - -
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Residues in contact with GLN 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LYS* 4.2 6.9 - - - +
142G ASP* 3.3 1.6 + - - +
144G THR* 3.1 19.5 + - - +
145G HIS* 1.3 79.0 - - - +
147G ILE* 1.3 67.1 + - + +
149G LYS* 3.9 9.7 - - - +
150G ASP* 3.0 61.6 + - - +
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Residues in contact with ILE 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G TRP* 3.8 29.4 - - + -
52G GLU 3.8 22.4 - - - +
53G GLY* 5.1 0.7 - - - -
76G PHE* 4.0 10.5 - - + -
78G PHE* 3.9 20.2 - - + -
111G CYS* 4.6 1.1 - - - -
140G LEU* 3.9 24.9 - - + -
141G SER 4.5 7.4 - - - +
142G ASP* 3.0 20.7 + - + +
146G GLN* 1.3 77.5 - - + +
148G SER* 1.3 67.9 + - - +
150G ASP* 3.2 7.7 + - - +
151G TYR* 3.1 28.6 + - + -
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Residues in contact with SER 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G PHE* 3.7 15.7 - - - -
112G SER 5.4 0.2 - - - -
113G VAL* 4.0 4.9 + - - +
142G ASP* 2.6 30.0 + - - +
145G HIS* 3.7 5.8 - - - -
147G ILE* 1.3 74.0 - - - +
149G LYS* 1.3 57.6 + - - +
151G TYR 3.2 1.7 + - - -
152G GLY 3.0 21.8 + - - -
153G VAL* 3.0 14.2 + - - +
154G TYR* 3.9 17.7 - - - -
161G THR* 3.1 33.0 - - - +
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Residues in contact with LYS 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 5.3 8.9 - - - +
40G SER* 4.0 9.9 + - - -
144G THR 5.0 3.0 + - - +
145G HIS* 2.9 34.2 + - - +
146G GLN* 3.9 10.5 - - - +
148G SER* 1.3 73.5 - - - +
150G ASP* 1.3 67.5 + - - +
152G GLY* 3.0 14.1 + - - +
154G TYR* 3.7 41.3 - - + -
156G GLU* 3.7 15.6 + - - +
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Residues in contact with ASP 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LYS* 2.7 66.5 + - + +
42G ALA 3.4 5.2 + - - -
49G PRO* 3.8 12.5 - - + +
50G TYR 4.3 11.8 - - - +
146G GLN* 3.0 41.9 + - - +
147G ILE* 3.2 8.3 + - - +
149G LYS* 1.3 76.8 - - - +
151G TYR* 1.3 66.1 + - + +
152G GLY 3.3 0.2 - - - -
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Residues in contact with TYR 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G SER* 3.6 8.9 + - - -
42G ALA* 4.1 8.3 - - + +
48G ALA* 3.6 15.0 - - + +
49G PRO* 2.7 48.0 + - + -
50G TYR 5.0 0.2 - - - -
51G TRP* 3.4 23.6 + + + -
66G LEU* 3.9 1.9 - - - +
76G PHE* 3.7 17.7 - + - -
78G PHE* 3.6 29.6 - + + -
147G ILE* 3.1 21.9 + - + +
148G SER 4.0 1.8 - - - +
150G ASP* 1.3 80.8 - - + +
152G GLY* 1.3 62.9 + - - +
153G VAL* 3.3 3.1 + - + +
166G PHE* 3.4 55.7 - + + -
168G ILE* 4.0 6.6 - - + +
174G LEU* 5.5 1.1 - - + -
179G 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