Contacts of the strand formed by residues 201 - 206 (chain A) in PDB entry 2V9R
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 THR 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU 3.2 7.8 + - - +
200A PRO* 1.3 76.6 - - - +
202A ILE* 1.3 63.0 + - - +
241A VAL 3.7 3.5 - - - +
242A GLY* 3.7 1.9 - - - -
243A THR* 3.0 44.5 + - - +
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Residues in contact with ILE 202 (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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191A CYS* 4.4 3.4 - - + +
192A GLN* 4.6 4.3 - - - +
193A PRO* 3.9 35.2 - - + -
200A PRO 4.3 1.8 - - - +
201A THR* 1.3 82.0 - - - +
203A SER* 1.3 66.4 + - - +
204A TRP* 3.8 16.7 - - + +
220A ILE* 5.5 5.7 - - + +
222A GLY 3.6 25.6 - - - +
223A GLY* 4.0 13.0 - - - +
240A CYS* 3.5 27.1 - - - -
241A VAL 3.5 3.1 - - - +
243A THR* 6.3 0.2 - - - -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 1.3 76.6 - - - +
204A TRP* 1.3 75.8 + - - +
211A LEU 5.6 2.7 - - - -
220A ILE* 5.9 0.7 - - - -
240A CYS* 3.6 1.2 - - - -
241A VAL* 2.7 49.2 + - - +
243A THR* 4.7 4.4 + - - -
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Residues in contact with TRP 204 (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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176A PRO* 3.9 14.4 - - + -
189A MET* 3.6 34.5 - - + -
190A GLU 4.2 1.3 - - - -
191A CYS* 3.6 23.3 - - + -
202A ILE* 3.8 10.6 - - + +
203A SER* 1.3 86.5 - - - +
205A LYS* 1.3 64.9 + - - +
210A PRO* 3.6 5.7 - - - +
211A LEU* 2.9 46.7 + - + +
220A ILE* 3.8 36.9 - - + +
222A GLY 5.4 0.4 + - - -
223A GLY 3.4 23.8 + - - -
224A LYS 4.8 0.6 + - - -
225A LEU* 3.5 31.9 - - + +
238A TYR* 4.9 4.5 - + + -
239A VAL 3.5 21.3 - - - -
240A CYS* 3.9 14.4 - - + -
241A VAL* 4.6 2.7 - - - +
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Residues in contact with LYS 205 (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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204A TRP* 1.3 79.6 - - - +
206A LYS* 1.3 59.0 + - - +
207A ASP 4.2 0.2 - - - -
208A GLY* 4.0 24.7 + - - +
209A SER 3.5 20.2 - - - +
210A PRO* 3.9 13.2 - - + -
211A LEU* 3.6 5.1 - - - +
237A LYS 3.4 1.4 - - - +
238A TYR* 3.3 6.2 - - - +
239A VAL* 2.9 48.5 + - + +
241A VAL* 4.5 11.7 - - + -
248A GLU* 4.3 17.7 + - - -
250A GLU* 4.0 21.6 + - - +
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Residues in contact with LYS 206 (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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205A LYS* 1.3 71.5 - - - +
207A ASP* 1.3 95.8 + - - +
208A GLY 3.1 2.3 + - - -
209A SER* 3.0 22.8 + - - +
211A LEU* 3.3 20.9 - - + +
233A SER 3.6 19.1 + - - -
234A ASP* 3.7 7.9 - - - +
235A ALA 3.1 25.9 + - - -
237A LYS 3.2 4.9 - - - +
238A TYR* 3.6 28.7 - - + +
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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