Contacts of the strand formed by residues 185 - 192 (chain A) in PDB entry 1TJY
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 TRP 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A VAL* 4.4 2.9 - - + -
144A ALA* 4.0 16.8 - - + -
145A ALA* 3.7 38.8 - - + -
148A VAL* 4.0 19.3 - - + -
149A ASP 5.4 0.7 - - - -
150A LYS 3.1 20.0 + - - -
151A GLU* 3.3 15.8 + - - +
153A ALA* 3.3 19.6 - - + +
155A VAL* 3.8 23.6 - - + -
178A ILE* 4.0 43.9 - - + +
182A HIS* 2.9 47.9 + + + +
183A PRO* 3.9 8.0 - - - +
184A GLY* 1.3 79.5 - - - +
186A GLU* 1.3 59.3 + - - +
187A ILE* 4.2 1.1 + - - +
218A ILE* 5.0 0.9 - - + -
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Residues in contact with GLU 186 (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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153A ALA 2.9 6.3 + - - -
154A LYS* 2.7 48.5 + - + +
155A VAL* 2.9 26.1 + - - -
184A GLY 3.8 1.5 + - - +
185A TRP* 1.3 73.6 - - - +
187A ILE* 1.3 72.5 + - - +
188A VAL* 3.4 17.2 + - - +
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Residues in contact with ILE 187 (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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155A VAL* 3.3 22.2 - - + +
157A PHE* 3.8 20.4 - - + -
175A LYS* 3.7 42.0 - - + +
178A ILE* 4.6 16.8 - - + -
185A TRP 4.2 0.8 + - - +
186A GLU* 1.3 78.6 - - - +
188A VAL* 1.3 60.4 + - - +
189A THR 3.8 20.0 - - - +
190A THR* 4.1 8.5 - - - +
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Residues in contact with VAL 188 (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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154A LYS* 3.9 20.4 - - + -
155A VAL 2.9 17.9 + - - +
186A GLU* 3.9 33.7 - - - +
187A ILE* 1.3 73.9 - - - +
189A THR* 1.3 69.0 + - + +
211A TYR* 3.6 43.1 + - + -
213A ASP 5.2 0.9 - - - +
214A LEU* 3.8 21.8 - - + -
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Residues in contact with THR 189 (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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156A ALA* 3.4 21.7 - - + -
157A PHE 3.0 23.4 + - - -
187A ILE* 3.5 6.3 - - - +
188A VAL* 1.3 82.8 - - + +
190A THR* 1.3 67.0 + - - +
191A GLN* 2.9 34.3 + - + +
207A ILE* 4.2 10.3 - - + -
211A TYR* 3.8 27.9 + - + -
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Residues in contact with THR 190 (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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157A PHE* 3.3 12.2 - - + +
159A TYR* 3.8 31.4 - - + +
175A LYS* 2.8 33.5 + - - +
187A ILE* 4.1 3.5 - - - +
189A THR* 1.3 76.9 + - - +
191A GLN* 1.3 66.5 + - - +
192A PHE* 4.0 21.5 - - + -
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Residues in contact with GLN 191 (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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157A PHE 3.0 6.7 + - - -
158A PHE* 3.3 7.9 - - - -
159A TYR* 3.1 23.6 + - - -
189A THR* 2.9 25.6 + - + +
190A THR* 1.3 80.5 - - - +
192A PHE* 1.3 73.1 + - - +
203A THR* 3.7 26.9 - - + +
206A GLY* 5.5 1.6 - - - -
207A ILE* 3.7 28.7 + - + +
210A ALA* 6.1 0.4 - - - +
211A TYR* 4.4 8.7 + - - -
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Residues in contact with PHE 192 (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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158A PHE* 4.0 4.5 - - - -
159A TYR* 3.1 34.8 - + - -
160A SER 3.4 9.9 - - - +
161A SER* 3.5 21.3 - - - -
162A PRO* 3.5 40.4 - - + -
190A THR* 4.0 27.4 - - + -
191A GLN* 1.3 83.7 - - - +
193A GLY* 1.3 59.0 + - - +
194A TYR* 3.7 30.5 - - + -
199A LYS* 5.7 0.3 - - - +
203A THR* 3.2 18.0 + - - +
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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