Contacts of the helix formed by residues 239 - 250 (chain A) in PDB entry 1TQ6
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 ASP 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 3.2 30.4 + - - -
227A ILE 4.6 2.4 - - - +
228A PHE* 3.7 18.4 - - + -
229A LEU* 2.6 41.3 + - - +
230A LEU* 4.6 1.8 - - - -
238A TYR* 1.3 80.2 - - - +
240A PHE* 1.3 52.5 + - - +
241A PRO* 3.4 1.1 - - - -
242A VAL* 3.7 17.0 - - + +
243A LEU* 2.6 37.1 + - - +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.4 9.6 - + - -
88A THR* 3.9 22.7 - - + -
89A LEU* 4.1 30.7 - - + -
230A LEU* 3.4 37.2 - - + +
231A SER 4.6 0.7 - - - -
232A ASN* 4.5 6.1 - - - -
235A VAL* 3.8 31.2 - - + -
236A CYS 3.8 13.2 - - - +
237A HIS 5.0 0.4 - - - +
238A TYR 3.1 1.9 - - - +
239A ASP* 1.3 74.3 - - - +
241A PRO* 1.3 76.4 - - + +
243A LEU* 3.0 24.0 + - + +
244A MET* 3.0 30.8 + - + +
264A PRO* 4.8 3.8 - - + -
266A ILE* 3.9 16.2 - - + -
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Residues in contact with PRO 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A CYS* 4.3 11.7 - - - +
238A TYR 3.1 15.7 - - - +
240A PHE* 1.3 95.5 - - + +
242A VAL* 1.3 63.7 + - + +
244A MET* 3.3 13.2 + - + +
245A ASP* 3.1 30.8 + - - +
266A ILE* 4.3 2.2 - - + -
267A THR* 4.1 29.2 - - + +
269A SER* 6.4 1.6 - - - -
270A VAL* 5.4 2.0 - - + -
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 4.1 8.5 - - + -
238A TYR 4.3 4.3 - - - +
239A ASP* 3.6 34.1 - - + +
241A PRO* 1.3 75.1 - - + +
243A LEU* 1.3 64.3 + - - +
245A ASP* 3.3 10.8 + - + +
246A LYS* 3.0 26.7 + - + +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.0 25.1 - - + -
89A LEU* 6.0 1.1 - - + -
153A ILE* 5.4 2.7 - - + -
179A TYR* 5.2 1.8 - - + -
181A VAL* 4.4 12.3 - - + -
228A PHE* 3.5 38.6 - - + -
230A LEU* 3.9 25.1 - - + -
239A ASP 2.6 21.5 + - - +
240A PHE* 3.0 14.8 + - + +
242A VAL* 1.3 74.7 - - - +
244A MET* 1.3 59.8 + - + +
246A LYS* 3.4 1.6 + - - +
247A LEU* 3.0 57.2 + - + +
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Residues in contact with MET 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.9 3.1 - - + -
240A PHE* 3.0 23.3 + - + +
241A PRO* 3.8 7.0 - - + +
243A LEU* 1.3 77.9 - - + +
245A ASP* 1.3 62.9 + - - +
247A LEU* 3.8 11.0 - - + +
248A ILE* 3.0 35.1 + - - +
259A PHE* 5.1 0.2 - - - -
263A LEU* 3.7 48.0 - - + -
264A PRO* 4.2 13.7 - - + +
266A ILE* 3.1 36.6 - - + -
270A VAL* 3.4 26.0 - - + -
273A LYS* 5.6 0.2 - - - -
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 5.4 6.0 + - - -
241A PRO* 3.1 19.0 + - - +
242A VAL* 3.3 13.3 + - + +
244A MET* 1.3 79.1 - - - +
246A LYS* 1.3 58.8 + - - +
248A ILE* 3.9 1.6 - - - +
249A SER* 3.0 30.1 + - - -
270A VAL* 6.2 0.5 - - - +
273A LYS* 3.8 28.5 + - - +
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 4.8 4.1 + - - -
179A TYR* 4.0 7.0 - - + -
226A PRO* 4.1 22.5 - - + +
228A PHE* 3.8 24.9 - - + -
242A VAL* 3.0 18.3 + - + +
243A LEU 3.6 4.3 - - - +
245A ASP* 1.3 75.5 - - - +
247A LEU* 1.3 66.6 + - - +
249A SER* 2.6 24.9 + - - +
250A ASP* 3.0 45.4 + - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 6.1 3.4 - - + -
89A LEU* 5.9 4.5 - - + -
151A PHE* 3.0 57.8 - - + -
153A ILE* 4.3 13.9 - - + -
179A TYR* 4.0 20.9 - - + -
243A LEU* 3.0 42.6 + - + +
244A MET* 3.8 7.9 - - + +
246A LYS* 1.3 79.2 - - + +
248A ILE* 1.3 62.1 + - - +
250A ASP* 3.4 6.6 + - - -
251A LEU* 3.7 2.9 + - - +
259A PHE* 3.8 31.9 - - + -
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 4.9 6.7 - - - +
244A MET 3.0 20.9 + - - +
245A ASP 3.9 3.1 - - - +
247A LEU* 1.3 75.4 - - - +
249A SER* 1.3 65.9 + - - +
251A LEU* 3.0 16.6 + - + +
256A ARG* 3.2 44.7 + - + +
259A PHE* 3.3 29.8 - - + -
260A MET* 4.0 34.3 - - + +
263A LEU* 4.4 5.6 - - + -
273A LYS* 4.2 20.6 - - - +
277A PHE* 5.0 4.5 - - + -
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ASP 3.0 15.5 + - - -
246A LYS* 2.6 29.8 + - - +
248A ILE* 1.3 79.4 - - - +
250A ASP* 1.3 64.9 + - - +
251A LEU 3.2 1.1 + - - +
256A ARG* 3.0 24.0 + - - +
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 4.4 4.4 - - + -
177A GLU* 4.0 3.4 - - - +
179A TYR* 2.5 31.0 + - - +
246A LYS* 3.0 52.4 + - - +
247A LEU 3.9 6.1 - - - +
248A ILE 3.1 0.8 + - - -
249A SER* 1.3 80.5 + - - +
251A LEU* 1.3 63.9 + - - +
252A PRO* 4.2 2.4 - - - +
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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