Contacts of the strand formed by residues 184 - 190 (chain A) in PDB entry 1T9A
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 MET 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLY* 3.9 22.9 - - - +
146A ALA* 4.2 8.3 - - + -
147A GLU* 4.1 10.1 - - - +
156A PRO* 4.5 0.4 - - - +
157A GLY* 3.2 19.7 - - - +
159A VAL* 4.3 7.2 - - + -
173A PRO* 3.6 28.3 - - + +
174A MET* 3.6 24.9 - - + +
177A ALA* 3.7 10.1 - - + -
182A ILE* 3.3 6.0 + - + +
183A PRO* 1.3 76.7 - - - +
185A VAL* 1.3 62.4 + - - +
186A VAL* 3.9 16.2 - - + -
237A ALA* 4.0 2.9 - - - +
243A GLY 3.3 7.2 + - - +
244A PRO* 3.1 11.9 - - + +
245A VAL* 2.8 30.0 + - - +
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Residues in contact with VAL 185 (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 PRO* 4.6 5.4 - - + -
157A GLY 2.9 10.5 + - - +
158A VAL* 3.5 5.4 - - + +
159A VAL 3.0 24.4 + - - +
184A MET* 1.3 77.1 - - - +
186A VAL* 1.3 61.9 + - - +
187A PHE* 3.4 36.7 + - + -
233A ALA* 4.0 9.6 - - + -
234A PHE* 3.8 45.3 - - + -
237A ALA* 4.2 5.8 - - + -
245A VAL* 3.7 21.8 - - + -
247A VAL* 4.6 3.1 - - + -
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Residues in contact with VAL 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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159A VAL* 3.8 20.9 - - + -
161A VAL* 4.9 0.7 - - + -
170A VAL* 4.0 20.0 - - + -
174A MET* 3.9 29.6 - - + -
184A MET* 3.9 24.0 - - + +
185A VAL* 1.3 75.3 - - - +
187A PHE* 1.3 62.8 + - - +
188A THR* 4.0 21.1 - - + -
244A PRO* 5.3 0.7 - - + -
245A VAL 2.8 17.8 + - - +
246A LEU* 3.3 5.1 - - + +
247A VAL 2.8 27.2 + - - +
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Residues in contact with PHE 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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98A PHE* 3.6 34.5 - + - -
102A MET* 4.1 13.2 - - + -
158A VAL* 3.9 19.1 - - + -
159A VAL 2.8 20.5 + - - +
160A LEU* 3.4 17.5 - - + +
161A VAL* 3.0 28.9 + - - +
185A VAL* 3.4 28.0 - - + -
186A VAL* 1.3 71.4 - - - +
188A THR* 1.3 61.5 + - - +
230A ILE* 4.0 22.2 - - + -
234A PHE* 4.1 8.1 - + - -
247A VAL* 3.5 31.4 - - + -
249A LEU* 3.9 17.0 - - + -
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Residues in contact with THR 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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118A ILE* 4.7 0.7 - - - -
161A VAL* 3.5 25.1 - - + -
162A THR 4.4 0.4 - - - -
167A ALA* 3.7 25.4 - - + -
170A VAL* 4.7 1.1 - - + -
186A VAL* 3.8 15.4 + - + -
187A PHE* 1.3 74.6 - - - +
189A GLY* 1.3 61.8 + - - +
206A VAL* 3.8 6.2 - - + +
246A LEU* 3.8 15.9 - - + +
247A VAL 3.1 4.6 + - - -
248A ASP* 2.7 30.8 + - - +
249A LEU* 2.7 35.3 + - - +
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Residues in contact with GLY 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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117A ALA* 4.0 4.5 - - - -
118A ILE* 3.8 26.3 - - - +
161A VAL 2.9 14.6 + - - -
162A THR 3.8 1.6 - - - -
163A SER* 2.9 28.8 - - - -
167A ALA* 5.4 0.2 - - - +
188A THR* 1.3 79.7 - - - +
190A GLN* 1.3 60.0 + - - +
206A VAL* 5.8 0.7 - - - +
248A ASP* 4.0 3.1 - - - +
249A LEU 3.5 8.3 - - - -
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Residues in contact with GLN 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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117A ALA* 3.4 15.6 - - - +
163A SER* 3.7 7.6 - - - -
189A GLY* 1.3 74.6 - - - +
191A VAL* 1.3 102.9 + - - +
196A ILE* 4.2 19.0 - - + +
203A GLU* 4.2 2.1 - - - +
204A ALA 3.1 35.0 + - - +
205A ASP* 5.2 0.4 - - - +
206A VAL* 4.7 2.8 - - - +
219A MET* 4.7 6.7 - - - +
248A ASP* 2.8 34.7 + - - +
249A LEU 2.8 6.8 + - - -
250A PRO* 3.7 20.0 - - + -
251A LYS* 2.9 21.3 + - - +
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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