Contacts of the helix formed by residues 145 - 158 (chain D) in PDB entry 1TW8
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 ALA 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D ILE 3.1 3.8 + - - -
144D SER* 1.3 70.5 - - - +
146D TYR* 1.3 50.2 + - - +
148D LEU* 4.3 1.6 - - - -
149D ALA* 2.7 33.8 + - - +
200D ILE* 3.5 27.1 - - + -
206D MET* 2.6 23.5 + - + +
208D ILE* 3.8 15.0 - - + -
230D TYR* 2.9 27.8 + - - +
234D PHE* 3.6 7.4 - - + -
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Residues in contact with TYR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LYS* 3.5 28.1 + - - +
249C PHE* 3.6 37.7 - + + -
253C PHE* 3.6 26.5 - + - -
144D SER* 2.8 8.9 - - - +
145D ALA* 1.3 77.1 - - - +
147D LYS* 1.3 59.8 + - - +
149D ALA 3.2 0.2 + - - -
150D GLN* 2.9 58.0 + - + +
206D MET* 3.6 23.7 + - + +
234D PHE* 3.8 13.8 - + + -
5G G 4.2 13.0 - - - -
6G T 3.5 17.7 - - - -
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.5 30.5 + - + -
88D LEU* 4.3 7.9 - - + -
110D ASN* 3.9 8.1 + - - -
112D THR* 2.5 41.5 + - + +
143D ILE* 5.2 5.4 - - + -
144D SER* 2.6 30.4 + - - +
146D TYR* 1.3 72.0 - - - +
148D LEU* 1.3 52.7 + - - +
150D GLN* 3.3 1.1 + - - +
151D THR* 2.7 39.8 + - - +
6G T 3.6 26.3 + - - +
7G C 2.9 26.5 + - - +
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ILE* 4.0 20.8 - - + +
144D SER 2.7 14.5 + - - +
145D ALA* 3.6 8.1 - - - +
147D LYS* 1.3 72.2 - - - +
149D ALA* 1.3 65.7 + - - +
151D THR* 3.0 12.1 + - + -
152D CYS* 2.9 45.2 + - - -
155D MET* 5.7 0.2 - - + -
166D ILE* 5.5 5.2 - - + -
190D LEU* 3.4 34.8 - - + -
191D PHE* 5.6 2.0 - - + -
198D LEU* 4.8 0.2 - - + -
208D ILE* 4.6 5.4 - - + -
226D TRP* 3.6 17.3 - - + -
230D TYR* 3.5 27.6 - - + +
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Residues in contact with ALA 149 (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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253C PHE* 3.8 11.6 - - + -
145D ALA 2.7 22.3 + - - +
146D TYR 3.2 6.0 + - - +
148D LEU* 1.3 75.1 - - - +
150D GLN* 1.3 62.3 + - - +
152D CYS 3.5 0.2 + - - -
153D ALA* 3.2 16.3 + - - +
230D TYR* 3.5 8.5 - - - -
231D LEU* 3.2 18.7 - - + +
234D PHE* 3.6 37.9 - - + -
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Residues in contact with GLN 150 (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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253C PHE* 4.0 13.0 - - + -
87D PHE* 3.6 37.6 - - + -
146D TYR* 2.9 63.8 + - + +
149D ALA* 1.3 73.0 - - - +
151D THR* 1.3 60.1 + - - +
153D ALA* 3.0 6.2 + - - +
154D LYS* 2.8 44.6 + - - +
6G T 4.2 5.7 + - - -
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Residues in contact with THR 151 (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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84D THR* 4.0 8.7 - - + -
87D PHE* 3.9 3.6 - - - -
88D LEU* 3.0 26.9 - - + +
147D LYS* 2.7 23.9 + - - +
148D LEU* 3.0 14.2 + - + -
150D GLN* 1.3 75.4 - - - +
152D CYS* 1.3 52.4 + - - +
154D LYS* 3.0 12.8 + - - +
155D MET* 2.8 53.7 + - + +
164D PHE* 3.5 22.2 - - + -
166D ILE* 5.3 4.7 - - + -
191D PHE* 5.4 0.2 - - + -
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Residues in contact with CYS 152 (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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148D LEU* 2.9 38.8 + - - +
149D ALA 3.8 4.5 - - - +
151D THR* 1.3 76.3 - - - +
153D ALA* 1.3 65.1 + - - +
155D MET* 2.8 29.6 + - - +
156D ILE* 3.0 18.1 + - - +
226D TRP* 3.9 8.1 - - - -
227D ALA* 3.4 32.5 - - + -
230D TYR* 4.0 8.5 - - - -
231D LEU* 3.9 14.1 - - + -
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Residues in contact with ALA 153 (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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253C PHE* 4.4 8.5 - - + -
256C TYR* 3.5 37.5 - - + +
149D ALA 3.2 10.6 + - - +
150D GLN* 3.0 14.5 + - - +
152D CYS* 1.3 78.8 - - - +
154D LYS* 1.3 63.6 + - + +
156D ILE* 3.1 2.6 + - - +
157D ASP* 2.7 31.1 + - - +
231D LEU* 4.2 4.6 - - + +
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Residues in contact with LYS 154 (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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83D PRO* 4.8 9.6 - - + +
84D THR* 3.1 34.7 + - + +
87D PHE* 4.4 28.4 - - + -
150D GLN* 2.8 36.4 + - - +
151D THR* 3.3 9.2 - - - +
153D ALA* 1.3 72.5 - - + +
155D MET* 1.3 62.8 + - - +
157D ASP* 4.8 4.0 - - - -
158D ASN* 3.1 34.6 + - - +
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Residues in contact with MET 155 (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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84D THR* 4.0 16.2 - - + -
148D LEU* 5.7 0.2 - - + -
151D THR* 2.8 35.6 + - + +
152D CYS* 2.8 32.3 + - - +
154D LYS* 1.3 78.6 - - - +
156D ILE* 1.3 56.1 + - + +
159D LYS* 2.9 6.6 + - - -
160D GLU 2.7 50.2 + - - +
161D PHE* 4.0 18.9 - - + -
164D PHE* 3.7 18.2 - - + -
191D PHE* 3.7 26.2 - - + -
223D ARG* 4.8 9.2 - - - -
227D ALA* 4.8 7.6 - - + -
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Residues in contact with ILE 156 (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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256C TYR* 3.5 32.8 - - + -
152D CYS 3.0 9.5 + - - +
153D ALA 3.1 3.6 + - - +
155D MET* 1.3 74.8 - - + +
157D ASP* 1.3 63.2 + - - +
159D LYS* 2.7 26.0 + - - +
161D PHE* 4.7 10.3 - - + -
224D GLU* 5.2 6.3 - - + +
227D ALA* 4.8 6.7 - - + -
228D LYS* 3.7 43.3 - - + +
231D LEU* 3.8 15.7 - - + -
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Residues in contact with ASP 157 (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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255C LYS* 3.9 12.2 + - - -
256C TYR* 2.7 32.5 + - - -
153D ALA 2.7 24.6 + - - +
154D LYS* 4.3 3.8 - - + +
156D ILE* 1.3 77.0 - - - +
158D ASN* 1.3 65.9 + - - +
159D LYS* 3.6 1.2 + - - +
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Residues in contact with ASN 158 (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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83D PRO* 3.4 36.0 - - - +
84D THR* 4.4 1.0 + - - -
154D LYS* 3.1 21.3 + - - +
156D ILE 3.1 0.6 - - - -
157D ASP* 1.3 80.4 - - - +
159D LYS* 1.3 73.4 + - - +
160D GLU* 3.1 30.7 + - + +
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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