Contacts of the strand formed by residues 206 - 212 (chain A) in PDB entry 1PQA
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 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 4.2 7.2 - - + -
44A SER* 3.8 24.5 - - - +
46A LEU* 4.8 0.2 - - + -
52A LEU* 4.3 14.4 - - + -
118A ALA* 4.0 12.6 - - + -
119A ARG 2.8 18.9 + - - +
120A LEU* 3.7 23.8 - - + -
121A ALA* 3.0 25.8 + - - +
198A PRO* 3.4 28.5 - - + -
199A ILE 3.6 6.5 - - - +
200A VAL* 4.1 3.8 - - + -
204A ASN 3.7 2.8 + - - -
205A THR* 1.3 67.9 - - - +
207A ILE* 1.3 59.5 + - - +
208A GLY 3.4 25.1 - - - +
228A VAL* 3.7 11.3 - - + +
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Residues in contact with ILE 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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121A ALA* 4.0 18.6 - - + -
127A PRO* 3.8 24.4 - - + +
133A ALA* 4.1 8.5 - - + -
159A ILE* 4.0 15.9 - - + -
179A PHE* 3.2 29.9 - - + -
199A ILE* 3.0 22.6 + - + +
200A VAL 3.9 15.5 - - - -
201A ASP* 4.0 22.2 - - + +
205A THR* 3.3 11.0 + - + +
206A LEU* 1.3 73.9 - - - +
208A GLY* 1.3 57.6 + - - +
227A SER* 3.9 1.0 + - - -
228A VAL* 3.0 21.7 + - - +
229A GLY 4.4 2.3 + - - -
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Residues in contact with GLY 208 (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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52A LEU* 6.2 0.4 - - - -
179A PHE* 3.9 2.9 - - - -
198A PRO* 3.7 1.0 - - - +
199A ILE* 3.1 38.1 + - - +
206A LEU* 3.4 13.8 - - - +
207A ILE* 1.3 81.0 - - - +
209A ALA* 1.3 58.7 + - - +
226A ALA 3.0 14.1 - - - -
228A VAL* 3.7 10.4 - - - +
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Residues in contact with ALA 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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52A LEU* 5.6 4.9 - - + -
53A THR* 4.8 3.8 - - - -
54A ALA* 4.8 1.8 - - - +
99A ASP 5.0 0.2 - - - +
100A LEU* 3.8 27.1 - - + -
196A GLY* 3.8 23.1 - - - +
197A GLY 3.2 5.6 - - - -
208A GLY* 1.3 73.7 - - - -
210A VAL* 1.4 69.3 + - - +
211A SER* 3.2 1.0 + - - -
225A TYR* 3.3 6.6 - - - -
226A ALA* 2.9 29.4 + - + -
228A VAL* 4.9 0.6 - - - +
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Residues in contact with VAL 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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54A ALA* 3.8 7.3 - - - +
135A VAL* 3.5 32.1 - - + -
136A ALA 5.1 0.9 - - - +
190A SER* 3.4 26.2 - - - +
191A CYS 5.1 0.4 - - - +
194A ASP* 3.2 26.2 - - + +
195A SEB 3.6 26.9 - - - +
196A GLY* 2.8 24.7 + - - +
197A GLY* 2.9 17.3 + - - +
198A PRO 4.8 0.2 - - - +
209A ALA* 1.4 71.4 - - - +
211A SER* 1.3 62.8 + - - +
212A TRP 5.2 0.7 - - - +
224A VAL 5.3 0.4 - - - +
225A TYR* 3.6 13.6 - - + -
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Residues in contact with SER 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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56A HIS* 2.8 29.3 + - - -
96A ASN 4.0 1.4 + - - -
99A ASP* 2.6 31.0 + - - +
178A MET* 6.1 0.6 - - - +
195A SEB 3.6 10.1 + - - +
209A ALA 3.8 0.2 - - - -
210A VAL* 1.3 77.3 - - - +
212A TRP* 1.3 79.4 + - - +
224A VAL 3.2 15.1 + - - -
225A TYR* 4.0 1.1 - - - -
226A ALA* 3.7 20.6 - - - -
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Residues in contact with TRP 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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56A HIS* 5.8 0.2 - - - +
96A ASN* 3.4 52.4 - - + +
169A TYR* 3.5 41.7 - + - -
173A ALA* 3.6 30.3 - - + -
174A ILE* 3.7 15.3 - - + -
178A MET* 3.6 9.0 - - + +
195A SEB 4.9 7.6 - - - -
210A VAL* 5.2 1.2 - - - +
211A SER* 1.3 101.4 - - - +
213A GLY* 1.3 77.5 + - - +
214A ASN* 5.6 0.2 - - - -
223A GLY* 4.2 1.6 - - - -
224A VAL* 2.8 54.4 + - + +
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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