Contacts of the strand formed by residues 203 - 211 (chain X) in PDB entry 2XAC
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 GLY 203 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B TYR* 4.5 5.4 - - - -
62B PRO* 3.8 14.8 - - - -
171X LYS* 5.8 1.6 - - - -
202X ILE* 1.3 75.3 - - - +
204X LEU* 1.3 60.3 + - - -
205X LEU* 3.4 7.1 - - - +
221X LEU* 4.6 6.1 - - - -
222X THR* 2.8 43.2 + - - -
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Residues in contact with LEU 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TRP* 4.0 29.8 - - + -
18B ILE* 6.2 2.2 - - + -
21B TYR* 3.3 44.6 + - + +
143X PRO* 5.3 1.6 - - + -
171X LYS* 3.5 25.1 - - - +
172X PHE* 4.4 18.9 + - + +
203X GLY* 1.3 70.5 - - - -
205X LEU* 1.3 63.4 + - - +
206X THR* 3.2 23.3 - - - +
219X ASN* 4.0 21.5 - - + -
220X TYR 3.3 9.6 - - - +
221X LEU* 4.4 5.8 - - + +
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Residues in contact with LEU 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X LEU* 4.8 3.1 - - + -
156X ILE* 4.1 18.6 - - + -
169X LEU* 3.8 35.2 - - + -
170X LYS 3.6 4.0 - - - +
171X LYS* 4.1 11.9 - - + -
177X LEU* 4.4 10.3 - - + -
194X ILE* 5.8 1.1 - - + -
201X GLU* 3.3 39.3 - - + +
203X GLY 3.4 15.5 - - - +
204X LEU* 1.3 76.7 - - - +
206X THR* 1.3 60.5 + - - +
207X CYS 4.1 0.4 - - - -
219X ASN 3.5 0.2 - - - -
220X TYR* 2.6 47.1 + - - +
222X THR* 3.5 15.3 - - + -
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Residues in contact with THR 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X THR 3.4 1.0 - - - +
169X LEU* 4.0 2.7 - - - +
170X LYS* 2.7 53.9 + - - +
172X PHE 5.6 0.2 + - - -
204X LEU* 3.2 27.2 - - - +
205X LEU* 1.3 73.5 + - - +
207X CYS* 1.3 61.5 + - - +
208X GLU* 3.5 6.9 + - + +
217X LYS* 3.5 37.7 - - + -
218X THR 3.4 14.6 - - - +
219X ASN* 4.1 7.8 - - + +
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Residues in contact with CYS 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X PHE* 3.6 13.1 - - + -
156X ILE* 3.5 22.7 - - - -
158X CYS* 2.0 54.3 - - + -
167X VAL* 4.0 2.5 - - + -
168X THR 3.5 5.4 - - - -
169X LEU* 4.0 2.4 - - - +
192X PHE* 3.6 12.3 - - - -
205X LEU 4.1 0.4 + - - -
206X THR* 1.3 70.5 - - - +
208X GLU* 1.3 59.2 + - - +
217X LYS* 3.1 4.9 - - - -
218X THR 2.8 39.2 + - - +
220X TYR* 4.0 1.3 - - - -
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Residues in contact with GLU 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X PHE* 3.9 1.1 - - - -
166X THR 4.0 0.7 - - - +
167X VAL* 3.3 8.0 - - - +
168X THR* 2.6 50.0 + - - +
170X LYS* 3.9 29.2 + - + +
206X THR* 4.2 10.2 - - + +
207X CYS* 1.3 77.5 - - - +
209X ALA* 1.3 62.0 + - - +
215X LEU* 4.1 27.9 - - + +
216X TYR 3.4 2.9 - - - +
217X LYS* 3.9 25.2 + - + +
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Residues in contact with ALA 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X PRO* 3.8 14.8 - - + -
135X PHE* 3.6 22.9 - - + -
165X ILE* 4.0 21.5 - - + -
166X THR 4.3 4.5 - - - -
167X VAL* 4.2 3.4 - - + -
208X GLU* 1.3 76.3 - - - +
210X THR* 1.3 62.4 + - - +
214X HIS 3.6 1.0 - - - +
215X LEU* 3.4 3.3 - - - +
216X TYR* 2.6 44.8 + - - +
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Residues in contact with THR 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165X ILE* 5.4 3.9 - - - +
166X THR 4.9 3.6 + - - -
209X ALA* 1.3 72.6 - - - +
211X VAL* 1.3 64.3 + - - +
212X ASN 4.2 0.5 + - - -
213X GLY* 3.4 38.4 - - - +
214X HIS 3.4 3.4 - - - +
215X LEU* 3.4 21.7 - - + +
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Residues in contact with VAL 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X GLY* 3.4 26.2 - - - +
134X PRO* 4.1 26.2 - - + -
165X ILE* 4.4 20.0 - - + -
209X ALA 4.0 0.4 + - - -
210X THR* 1.3 78.1 - - - +
212X ASN* 1.3 87.6 + - - +
213X GLY 3.3 0.2 - - - -
214X HIS* 2.8 28.1 + - - +
216X TYR* 3.8 13.4 + - + +
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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