Contacts of the strand formed by residues 187 - 193 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ALA* 3.7 27.4 - - - +
139D LEU* 4.2 26.7 - - + -
171D MET* 4.3 8.1 - - + -
172D ALA 3.9 8.3 - - - +
173D ARG* 4.0 14.4 - - + +
183D LYS 3.8 15.3 - - - +
184D HIS 4.7 0.4 + - - +
185D GLN* 3.6 0.6 - - - +
186D GLY* 1.3 81.6 - - - +
188D SER* 1.3 74.3 + - - +
235D GLY 2.9 10.8 + - - -
237D GLY 2.8 21.9 + - - -
238D PHE* 3.7 47.1 - - + +
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Residues in contact with SER 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL 3.9 0.3 - - - +
171D MET* 3.4 4.8 - - - -
172D ALA 2.9 31.6 + - - +
174D THR* 3.0 31.6 + - - +
187D ILE* 1.3 76.2 - - - +
189D ALA* 1.3 59.8 + - - +
190D PHE* 3.9 9.0 - - - -
230D LEU* 3.9 13.5 - - - -
233D GLU 5.1 0.9 - - - -
234D ARG* 3.7 5.1 - - - +
235D GLY 2.7 26.6 + - - -
237D GLY* 4.3 5.8 - - - +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 3.5 19.7 - - + +
169D VAL* 4.6 1.3 - - + -
170D VAL 3.5 3.8 - - - -
171D MET* 3.3 26.0 - - + -
188D SER* 1.3 75.1 - - - +
190D PHE* 1.3 63.2 + - - +
230D LEU* 3.5 4.5 - - - +
231D LEU* 2.7 52.9 + - + +
237D GLY* 4.5 4.1 - - - -
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Residues in contact with PHE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA* 3.4 33.2 - - + -
150D TRP* 3.5 35.2 - + + -
152D LEU* 4.0 25.1 - - + -
168D TYR 3.5 1.6 - - - +
169D VAL* 3.1 6.2 - - - -
170D VAL 2.9 44.9 + - - +
172D ALA* 4.3 4.7 - - + -
174D THR* 3.7 12.1 - - + -
188D SER* 3.9 24.9 - - - -
189D ALA* 1.3 78.1 - - - +
191D ALA* 1.3 59.5 + - - +
192D PHE* 4.0 10.6 - - + -
225D VAL* 4.2 12.8 - - + -
229D ALA* 3.3 7.2 - - + +
230D LEU* 3.8 22.4 - - + -
231D LEU* 4.8 0.2 - - - -
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Residues in contact with ALA 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ILE* 4.3 11.0 - - + -
108D GLN* 5.6 2.5 - - + +
112D PHE* 3.6 27.1 - - + -
168D TYR 3.3 7.0 - - - +
169D VAL* 4.3 14.6 - - + +
190D PHE* 1.3 72.3 - - - +
192D PHE* 1.3 63.9 + - - +
226D PRO* 5.9 0.3 - - - +
228D GLU 4.5 0.2 - - - +
229D ALA* 2.7 32.2 + - - +
231D LEU* 4.4 17.0 - - + +
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Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PHE* 3.8 14.8 - - - -
152D LEU* 4.3 7.4 - - + -
167D VAL* 3.5 2.4 - - - +
168D TYR* 2.8 55.3 + - + +
170D VAL* 4.1 23.3 - - + -
190D PHE* 4.0 12.8 - - + -
191D ALA* 1.3 79.0 - - - +
193D PHE* 1.3 79.8 + - - +
195D PRO* 3.8 23.8 - - + -
199D LEU* 4.1 6.7 - - + -
223D LEU* 3.5 25.1 - - + -
225D VAL* 3.5 30.7 - - + -
226D PRO* 5.3 7.0 - - + -
229D ALA* 4.8 2.5 - - + -
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Residues in contact with PHE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.6 23.1 - - + -
112D PHE* 3.3 31.4 - + - -
115D LYS* 4.1 31.6 - - + -
121D ALA* 5.5 0.4 - - + -
166D GLY 3.3 17.3 - - - +
167D VAL* 3.9 18.6 - - + +
168D TYR* 4.6 0.2 - - - -
192D PHE* 1.3 91.0 - - - +
194D ARG* 1.3 71.4 + - - +
195D PRO* 2.9 6.1 - - - +
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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