Contacts of the strand formed by residues 204 - 211 (chain C) 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 LEU 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TRP* 4.7 9.6 - - + -
18A ILE* 5.6 4.7 - - - +
21A TYR* 4.4 23.0 - - + -
22A THR* 4.6 13.9 - - + -
143C PRO* 3.7 32.3 - - + -
171C LYS* 3.5 8.4 - - - +
172C PHE* 3.0 50.8 + - + +
203C GLY* 1.3 68.7 - - - -
205C LEU* 1.3 62.5 + - - +
206C THR* 3.9 15.9 + - + +
219C ASN* 3.9 20.9 - - + +
220C TYR 3.5 2.9 - - - +
221C LEU* 3.9 7.0 - - + +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LEU* 5.1 0.7 - - + -
156C ILE* 4.0 23.6 - - + -
169C LEU* 3.8 24.7 - - + -
170C LYS 3.5 11.7 - - - +
171C LYS* 3.5 25.4 - - + -
177C LEU* 4.6 4.9 - - + -
194C ILE* 4.8 1.8 - - + -
201C GLU* 3.3 36.6 - - + +
203C GLY 3.4 14.6 - - - +
204C LEU* 1.3 72.0 - - - +
206C THR* 1.3 61.8 + - - +
219C ASN* 3.7 0.7 - - - -
220C TYR* 2.8 44.5 + - + +
222C THR* 3.8 14.6 - - + +
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C THR 3.6 2.8 - - - +
169C LEU* 3.6 1.4 - - - -
170C LYS* 2.8 56.3 + - - +
171C LYS 4.6 0.5 + - - -
172C PHE* 5.5 2.5 + - + +
204C LEU* 3.9 23.5 + - + +
205C LEU* 1.3 76.8 - - - +
207C CYS* 1.3 63.5 + - - +
208C GLU* 4.1 7.7 - - - +
217C LYS* 5.4 7.0 - - + -
218C THR 3.6 4.3 - - - -
219C ASN* 3.4 24.7 - - - +
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Residues in contact with CYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.3 8.4 - - + -
156C ILE* 3.6 21.1 - - - -
158C CYS* 2.0 55.2 - - + -
167C VAL* 4.1 2.9 - - + -
168C THR 4.0 3.6 - - - -
169C LEU* 4.1 2.9 - - - -
192C PHE* 3.6 10.8 - - - -
205C LEU 4.1 0.4 + - - -
206C THR* 1.3 73.0 - - - +
208C GLU* 1.3 62.0 + - - +
217C LYS* 3.2 5.5 - - - +
218C THR* 2.8 45.3 + - + +
220C TYR* 4.1 1.8 - - - -
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.6 2.0 - - - -
166C THR 3.7 0.7 - - - +
167C VAL* 3.3 5.9 - - - +
168C THR* 3.2 43.3 + - - +
170C LYS* 2.9 38.8 + - + -
206C THR* 5.0 8.7 - - - +
207C CYS* 1.3 77.6 - - - +
209C ALA* 1.3 64.9 + - - +
215C LEU* 3.4 29.4 - - + +
216C TYR 3.4 1.8 - - - -
217C LYS* 2.6 36.6 + - + +
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PRO* 3.6 22.9 - - + -
135C PHE* 3.6 18.4 - - + -
165C ILE* 4.1 9.4 - - + -
166C THR 3.8 13.9 - - - +
167C VAL* 4.5 2.2 - - + -
208C GLU* 1.3 76.8 - - - +
210C THR* 1.3 59.1 + - - +
211C VAL* 4.8 0.2 - - + -
215C LEU* 4.4 1.7 - - - +
216C TYR* 2.8 47.6 + - - +
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Residues in contact with THR 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 5.7 1.9 - - - +
166C THR 4.6 3.1 + - - +
209C ALA* 1.3 70.0 - - - +
211C VAL* 1.3 64.8 + - - +
212C ASN 4.3 0.6 + - - +
213C GLY* 3.8 34.3 - - - +
214C HIS 3.3 5.4 - - - +
215C LEU* 3.4 23.5 - - - +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C GLY* 3.4 20.9 - - - +
134C PRO* 3.8 35.7 - - + -
165C ILE* 4.6 12.3 - - + -
209C ALA 3.7 2.0 + - - +
210C THR* 1.3 77.7 - - - +
212C ASN* 1.3 83.3 + - - +
213C GLY 3.3 0.2 - - - -
214C HIS* 3.0 24.1 + - - +
216C TYR* 3.6 13.5 + - + +
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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