Contacts of the strand formed by residues 206 - 215 (chain L) in PDB entry 1VPO
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 SER 206 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202L THR* 4.4 5.9 - - - +
203L HIS* 2.6 29.6 + - - +
204L LYS 2.8 6.1 + - - -
205L THR* 1.3 78.6 - - - +
207L THR* 1.3 62.6 + - - +
208L SER* 2.7 43.2 + - - +
210L ILE* 5.7 6.3 - - - -
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Residues in contact with THR 207 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202L THR* 5.2 5.3 - - - +
204L LYS 5.0 0.6 + - - +
206L SER* 1.3 71.9 + - - +
208L SER* 1.3 63.0 + - - +
209L PRO* 3.4 12.3 - - - +
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Residues in contact with SER 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L ALA 4.6 0.2 - - - +
202L THR* 5.7 0.2 - - - -
203L HIS 5.7 0.2 + - - -
206L SER* 2.7 30.1 + - - +
207L THR* 1.3 82.1 + - - +
209L PRO* 1.3 72.8 - - - +
210L ILE* 3.4 6.2 + - - +
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Residues in contact with PRO 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L GLU* 4.5 13.0 - - + +
201L ALA 3.2 16.2 - - - +
202L THR* 4.2 22.2 - - + +
207L THR 3.4 10.8 - - - +
208L SER* 1.3 87.4 - - - +
210L ILE* 1.3 63.5 + - - +
211L VAL* 3.5 20.1 + - + +
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Residues in contact with ILE 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L ALA* 4.1 20.2 - - + -
118L PRO* 3.7 31.2 - - + +
120L VAL* 4.0 26.9 - - + +
199L CYS 3.8 1.6 - - - +
200L GLU* 3.6 1.7 - - - -
201L ALA* 2.8 38.2 + - + +
203L HIS* 6.0 3.1 - - + -
206L SER* 5.7 5.6 - - - -
208L SER 3.4 6.0 + - - +
209L PRO* 1.3 71.7 - - - +
211L VAL* 1.3 65.7 + - - +
212L LYS* 4.3 8.5 + - - -
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Residues in contact with VAL 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L THR* 3.4 26.7 - - - +
199L CYS 3.8 3.8 - - - +
200L GLU* 4.2 20.9 - - + +
209L PRO* 3.5 17.9 + - + +
210L ILE* 1.3 81.1 - - - +
212L LYS* 1.3 80.9 + - - +
213L SER* 5.1 2.7 - - - +
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Residues in contact with LYS 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L VAL* 3.4 54.4 + - + +
121L SER* 4.5 2.0 - - - +
122L ILE* 3.8 19.9 - - + +
198L THR* 3.2 2.1 - - - -
199L CYS* 3.0 31.8 + - - -
210L ILE* 4.9 8.5 - - + -
211L VAL* 1.3 80.8 - - - +
213L SER* 1.3 63.8 + - - +
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Residues in contact with SER 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L ILE* 3.9 13.4 - - - +
196L SER* 4.5 5.7 + - - -
197L TYR 2.7 23.3 - - - -
198L THR* 3.1 18.2 - - - +
211L VAL* 5.1 3.2 - - - +
212L LYS* 1.3 77.6 - - - +
214L PHE* 1.3 66.2 + - - +
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Residues in contact with PHE 214 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132H GLY* 6.0 6.5 - - - -
122L ILE* 4.1 16.4 - - + -
124L PRO* 3.2 49.6 - - + -
125L PRO* 4.3 0.9 - - + -
137L VAL* 3.9 19.1 - - + -
191L TYR* 3.6 19.3 - + - -
195L ASN 3.7 0.5 - - - +
196L SER* 3.6 2.6 + - - -
197L TYR* 3.0 59.7 + + + +
213L SER* 1.3 81.9 + - - +
215L ASN* 1.3 74.4 + - - +
216L ARG* 4.1 8.3 - - - -
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Residues in contact with ASN 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L ASN* 3.0 8.2 - - - +
196L SER* 3.9 21.3 + - - -
214L PHE* 1.3 82.3 - - - +
216L ARG* 1.3 58.5 + - - +
217L ASP* 2.8 27.8 + - - +
218L GLU* 2.9 49.1 + - - +
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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