Contacts of the strand formed by residues 206 - 213 (chain A) in PDB entry 2UUY
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 LYS 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 4.3 0.7 - - - -
124A SER* 3.4 14.4 - - - -
125A LEU 3.4 21.5 - - - +
126A PRO* 4.1 16.2 - - + -
127A THR* 4.7 12.3 - - - +
202A VAL* 3.3 6.3 - - - +
203A CYS 2.9 31.3 + - - +
204A SER* 3.7 18.3 - - - -
205A GLY* 1.3 87.5 + - - +
207A LEU* 1.3 59.3 + - - +
208A GLN* 3.1 19.3 - - - +
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Residues in contact with LEU 207 (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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48A SER* 3.5 36.3 - - - +
50A ILE* 4.1 18.4 - - + -
56A VAL* 4.2 19.3 - - + -
123A ILE* 3.9 11.9 - - + +
124A SER 2.9 18.1 - - - -
125A LEU* 4.4 11.0 - - + -
126A PRO* 3.2 21.4 - - - +
200A PRO* 3.7 16.2 - - + -
201A VAL 3.8 4.7 - - - +
202A VAL* 4.2 5.6 - - + -
206A LYS* 1.3 68.2 + - - +
208A GLN* 1.3 58.0 - - - +
209A GLY 3.5 22.9 - - - +
210A ILE* 5.3 0.4 - - + -
229A VAL* 3.4 14.9 - - + +
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PRO* 3.5 24.7 - - - +
128A SER 3.0 24.3 - - - -
129A CYS* 3.9 0.6 - - - -
130A ALA* 3.6 33.1 + - + +
162A ILE* 5.2 0.2 - - + -
181A PHE* 3.3 17.5 - - + -
201A VAL 2.9 5.3 + - - -
203A CYS* 3.8 26.7 + - + -
206A LYS* 3.1 21.5 - - + +
207A LEU* 1.3 74.6 - - - +
209A GLY* 1.3 58.4 + - - +
228A LYS* 3.9 1.6 - - - +
229A VAL* 3.0 24.0 + - - -
230A CYS* 3.8 12.5 + - - +
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Residues in contact with GLY 209 (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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181A PHE* 3.8 9.0 - - - -
199A GLY 3.8 0.7 - - - +
201A VAL* 3.0 40.5 + - - +
207A LEU* 3.5 14.5 - - - +
208A GLN* 1.3 81.2 - - - +
210A ILE* 1.3 66.3 + - - +
226A TYR* 4.5 0.2 - - - -
227A THR 3.2 9.2 - - - -
229A VAL* 3.8 2.2 - - - +
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Residues in contact with ILE 210 (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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56A VAL* 3.4 30.7 - - + -
57A SER 3.6 4.0 - - - +
58A ALA* 3.9 14.6 - - + +
104A ASP 4.0 5.2 - - - +
105A ILE* 3.6 31.6 - - + -
198A GLY* 3.5 32.5 - - - +
199A GLY 3.3 3.8 - - - +
207A LEU* 5.3 1.6 - - + -
209A GLY* 1.3 78.6 - - - +
211A VAL* 1.3 72.6 + - - +
212A SER* 3.1 1.7 + - - -
226A TYR* 3.3 6.4 - - - -
227A THR* 3.0 38.1 + - - +
229A VAL* 3.6 13.9 - - + -
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Residues in contact with VAL 211 (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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58A ALA* 4.0 2.9 - - - +
138A ILE* 4.1 18.2 - - + -
139A SER 4.9 2.0 - - - +
192A SER* 3.6 24.0 - - - +
196A ASP* 3.3 26.9 - - + +
197A SER* 3.4 21.7 + - - +
198A GLY 2.9 24.5 + - - +
199A GLY* 3.0 19.3 + - - +
200A PRO 4.5 0.9 - - - +
201A VAL* 4.6 0.4 - - + +
209A GLY 4.3 0.2 - - - -
210A ILE* 1.3 73.8 - - - +
212A SER* 1.3 59.8 + - - +
225A VAL 5.5 0.2 - - - +
226A TYR* 3.6 20.8 - - + -
39B LYS* 3.9 13.2 - - + -
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Residues in contact with SER 212 (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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60A HIS* 3.2 12.2 - - - -
101A LEU* 4.4 2.4 + - - +
104A ASP* 2.7 31.0 + - - +
180A MET* 6.1 0.6 - - - +
197A SER* 3.5 0.2 + - - -
210A ILE 3.1 8.8 + - - -
211A VAL* 1.3 75.4 - - - +
213A TRP* 1.3 80.7 + - - +
225A VAL 3.3 14.7 + - - -
226A TYR* 4.2 1.1 - - - -
227A THR* 3.8 15.0 + - - -
38B CYS* 3.4 0.7 - - - -
39B LYS* 3.1 24.7 + - - -
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Residues in contact with TRP 213 (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 THR 5.0 4.0 - - - -
101A LEU* 3.5 29.3 - - + +
172A TYR* 3.7 39.7 - + - -
175A GLN* 3.7 41.7 - - + -
176A ILE* 3.9 6.7 - - + -
180A MET* 3.7 16.8 - - + +
212A SER* 1.3 104.2 - - - +
214A GLY* 1.3 70.2 - - - +
225A VAL* 2.8 59.3 + - + +
37B LEU* 3.3 39.7 - - + +
39B LYS* 3.8 14.8 + - - +
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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