Contacts of the strand formed by residues 187 - 193 (chain A) in PDB entry 2CX9
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 ILE 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ALA* 3.8 27.6 - - - +
139A LEU* 4.1 28.3 - - + -
171A MET* 4.2 10.5 - - + -
172A ALA 3.6 13.0 - - - +
173A ARG* 4.1 12.1 - - - +
183A LYS 3.9 14.6 - - - +
184A HIS 4.0 8.9 + - - +
186A GLY* 1.3 80.9 - - - +
188A SER* 1.3 66.4 + - - +
235A GLY 3.0 9.1 + - - -
237A GLY 2.7 28.3 + - - -
238A PHE* 3.9 33.9 - - + +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL 3.8 0.7 - - - +
171A MET* 3.3 2.9 - - - -
172A ALA 2.8 33.4 + - - +
174A THR* 3.1 28.5 + - - +
186A GLY 4.2 0.4 + - - -
187A ILE* 1.3 74.4 - - - +
189A ALA* 1.3 61.1 + - - +
190A PHE* 3.7 12.1 - - - -
230A LEU* 4.0 11.7 - - - -
233A GLU 4.9 1.3 - - - -
234A ARG* 3.4 6.4 - - - -
235A GLY 2.6 29.3 + - - -
237A GLY* 4.2 5.6 - - - +
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Residues in contact with ALA 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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99A HIS* 3.5 36.3 - - + +
169A VAL* 4.7 1.1 - - + -
170A VAL 3.4 4.3 - - - -
171A MET* 3.6 11.7 - - + -
188A SER* 1.3 73.2 - - - +
190A PHE* 1.3 64.7 + - - +
230A LEU* 3.7 3.6 - - - +
231A LEU* 2.8 49.5 + - + +
237A GLY* 4.5 6.7 - - - -
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Residues in contact with PHE 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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143A ALA* 3.8 22.2 - - + -
150A TRP* 3.5 46.7 - + + -
152A LEU* 4.4 14.4 - - + -
168A TYR 3.4 2.1 - - - +
169A VAL* 3.2 5.6 - - - -
170A VAL* 2.8 44.1 + - + +
172A ALA* 4.7 4.0 - - + -
174A THR* 4.0 2.0 - - + -
188A SER* 3.7 29.4 - - - -
189A ALA* 1.3 77.6 - - - +
191A ALA* 1.3 60.6 + - - +
192A PHE* 3.6 19.6 - - + -
225A VAL* 4.1 14.1 - - + -
229A ALA* 3.3 8.1 - - + +
230A LEU* 3.8 30.1 - - + -
231A LEU* 4.9 0.2 - - - -
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Residues in contact with ALA 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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100A ILE* 4.0 26.2 - - + -
108A GLN* 5.7 0.7 - - - +
112A PHE* 3.4 29.8 - - + -
167A VAL* 5.3 0.2 - - + -
168A TYR 3.2 7.0 - - - +
169A VAL* 4.2 4.9 - - + +
189A ALA 4.4 0.2 - - - -
190A PHE* 1.3 71.0 - - - +
192A PHE* 1.3 65.0 + - - +
229A ALA* 2.9 28.1 + - - +
231A LEU* 4.3 13.1 - - + +
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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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112A PHE* 4.0 12.4 - - - -
152A LEU* 3.8 16.8 - - + -
167A VAL* 3.6 1.0 - - - -
168A TYR* 2.9 53.8 + + + +
170A VAL* 3.9 19.7 - - + -
190A PHE* 3.6 21.1 - - + -
191A ALA* 1.3 78.6 - - - +
193A PHE* 1.3 80.3 + - - +
195A PRO* 3.9 16.2 - - + -
199A LEU* 4.8 2.7 - - + -
220A LEU* 5.1 2.9 - - + -
223A LEU* 3.4 27.6 - - + -
225A VAL* 3.6 28.7 - - + -
226A PRO* 5.4 4.9 - - + -
229A ALA* 4.8 1.3 - - + -
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Residues in contact with PHE 193 (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 ALA* 3.2 30.3 - - + -
112A PHE* 3.3 27.1 - + - -
115A LYS* 4.2 30.7 - - + -
166A GLY 3.3 16.4 - - - +
167A VAL* 4.1 14.6 - - + +
168A TYR* 4.8 0.4 - - - -
192A PHE* 1.3 82.8 - - - +
194A ARG* 1.3 69.4 + - - +
195A PRO* 2.9 13.0 - - - +
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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