Contacts of the strand formed by residues 183 - 189 (chain A) in PDB entry 6AF6
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 VAL 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TYR* 4.4 14.6 - - + -
139A MET* 4.2 13.9 - - + -
171A TYR* 4.0 20.6 - - + -
172A ALA 3.4 8.5 - - - +
173A LYS* 3.8 19.1 - - + -
179A GLY 3.5 16.2 - - - +
180A PHE 3.6 3.5 + - - +
181A LEU 3.5 1.4 - - - -
182A GLY* 1.3 78.1 - - - +
184A SER* 1.4 68.4 + - - +
231A GLY* 3.1 13.0 - - - +
233A GLY* 2.7 41.7 + - - -
234A GLY* 3.8 10.3 + - - +
237A PHE* 6.0 0.2 - - + -
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Residues in contact with SER 184 (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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171A TYR* 3.4 3.8 - - - -
172A ALA 2.8 31.9 + - - +
174A THR* 2.8 39.0 + - - +
183A VAL* 1.4 71.5 - - - +
185A ALA* 1.3 60.3 + - - +
186A PHE* 3.6 17.1 - - - -
226A ARG* 4.5 9.6 - - - -
229A MET 4.8 2.0 - - - -
230A GLU* 3.8 4.3 - - - -
231A GLY 2.9 20.1 + - - +
233A GLY* 3.8 8.7 - - - +
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Residues in contact with ALA 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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169A ILE* 5.0 1.3 - - + -
170A ILE 3.2 5.6 - - - +
171A TYR* 3.8 26.9 - - + -
184A SER* 1.3 74.4 - - - +
186A PHE* 1.3 68.7 + - - +
226A ARG* 3.5 6.1 - - - +
227A ILE* 2.8 50.4 + - + +
229A MET 5.5 0.2 + - - -
233A GLY* 4.0 2.4 - - - +
236A ILE* 4.2 14.1 - - + -
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Residues in contact with PHE 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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143A ALA* 3.6 32.1 - - + -
150A TYR* 3.6 28.9 - + - -
168A PHE 3.4 0.5 - - - +
169A ILE* 3.3 3.8 - - - -
170A ILE* 2.8 54.6 + - + +
172A ALA* 4.4 4.3 - - + -
174A THR* 3.8 7.6 - - + -
184A SER* 3.6 35.9 - - - -
185A ALA* 1.3 79.1 - - - +
187A LEU* 1.3 63.1 + - - +
188A ILE* 4.7 0.4 - - + -
221A ILE* 3.7 33.7 - - + -
225A GLN 3.4 5.4 - - - +
226A ARG* 3.7 21.8 - - + -
227A ILE* 3.8 6.7 - - - +
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Residues in contact with LEU 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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100A LEU* 4.5 16.4 - - + -
108A LEU* 4.7 6.1 - - + -
112A TYR* 3.7 59.7 - - + +
116A LEU* 5.1 1.3 - - + -
167A VAL* 4.1 14.8 - - + -
168A PHE 3.3 4.5 - - - +
169A ILE* 3.9 24.5 - - + -
186A PHE* 1.3 74.2 - - - +
188A ILE* 1.3 78.4 + - - +
189A GLU* 4.5 0.9 - - + -
225A GLN* 2.8 40.1 + - - +
227A ILE* 3.9 6.5 - - + +
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Residues in contact with ILE 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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152A LEU* 4.5 3.1 - - + -
167A VAL* 3.3 3.6 - - - +
168A PHE* 2.8 51.9 + - + +
170A ILE* 4.3 10.1 - - + -
186A PHE* 4.7 4.0 - - + -
187A LEU* 1.3 82.6 - - - +
189A GLU* 1.3 64.6 + - - +
192A THR* 4.8 5.6 - - + +
195A LEU* 3.9 32.5 - - + -
216A PHE* 4.3 11.2 - - + -
219A ILE* 4.1 22.0 - - + -
221A ILE* 4.2 34.3 - - + -
225A GLN* 4.0 5.8 - - - +
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Residues in contact with GLU 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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111A LYS* 4.2 9.8 + - - -
112A TYR* 2.5 44.5 + - + +
166A ASP 3.7 6.3 - - - +
167A VAL* 4.3 6.3 - - + +
187A LEU* 4.5 0.9 - - + -
188A ILE* 1.3 78.5 - - - +
190A LYS* 1.3 71.0 + - - +
191A GLY 3.3 0.2 + - - -
192A THR* 2.7 33.0 + - - +
195A LEU* 3.7 10.1 - - - +
225A GLN* 4.7 8.2 + - - +
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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