Contacts of the strand formed by residues 208 - 215 (chain A) in PDB entry 2NRY
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A TYR* 3.3 7.2 - - - -
205A VAL* 2.9 35.5 + - - +
206A ASN* 2.9 16.8 + - - +
207A ASN* 1.3 78.1 + - - +
209A THR* 1.3 73.5 + - - +
210A VAL* 3.7 15.0 + - + -
249A LEU* 5.1 7.2 - - + -
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Residues in contact with THR 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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202A LYS* 3.5 29.8 - - + -
203A GLY 3.3 12.6 - - - +
204A TYR* 3.9 14.1 - - + -
207A ASN 4.4 0.2 + - - -
208A THR* 1.3 79.1 - - - +
210A VAL* 1.3 65.1 + - - +
264A TYR* 3.2 47.4 + - + +
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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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168A PHE* 6.1 0.2 - - + -
173A LEU* 5.7 0.4 - - + -
176A VAL* 5.4 1.8 - - + -
202A LYS* 3.5 8.7 - - - +
203A GLY* 2.8 40.0 + - - +
205A VAL* 3.8 33.4 - - + -
208A THR* 3.9 10.3 - - + -
209A THR* 1.3 78.9 - - - +
211A ALA* 1.3 58.7 + - - +
212A VAL* 3.8 22.4 - - + -
249A LEU* 3.8 26.0 - - + -
261A VAL* 3.7 12.1 - - + -
262A TYR 3.7 10.1 - - - +
264A TYR* 3.9 8.2 - - - -
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Residues in contact with ALA 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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192A MET* 3.7 14.1 - - + -
200A VAL* 4.0 4.0 - - + -
201A TYR 3.4 4.7 - - - -
210A VAL* 1.3 73.9 - - - +
212A VAL* 1.3 62.4 + - - +
213A LYS 4.0 0.2 - - - -
260A LEU 3.7 0.9 - - - +
261A VAL* 3.3 4.0 - - - +
262A TYR* 2.9 35.4 + - + +
263A VAL 4.6 0.2 - - - +
264A TYR* 4.4 1.6 - - - +
504A STU 3.4 47.1 - - + +
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Residues in contact with VAL 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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173A LEU* 4.0 36.8 - - + -
176A VAL* 5.1 0.9 - - + -
177A THR* 4.0 21.8 - - + -
180A PHE* 3.9 24.2 - - + -
199A VAL 3.5 1.7 - - - +
200A VAL* 3.4 2.7 - - - -
201A TYR* 2.7 44.8 + - + +
203A GLY* 4.5 2.5 - - - +
210A VAL* 3.8 22.7 - - + -
211A ALA* 1.3 77.2 - - - +
213A LYS* 1.3 60.0 - - - +
259A CYS* 4.1 7.0 - - + -
260A LEU 3.4 6.7 - - - +
261A VAL* 4.4 3.8 - - + -
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Residues in contact with LYS 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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195A GLY 3.6 9.4 - - - +
196A GLY* 3.0 26.0 + - - +
198A GLY* 4.2 4.7 - - - -
199A VAL 3.3 6.5 - - - +
200A VAL* 3.8 22.0 - - + +
211A ALA 4.0 1.0 + - - -
212A VAL* 1.3 70.7 - - - +
214A LYS* 1.3 61.0 + - - +
215A LEU* 3.4 28.0 + - + +
233A GLU* 2.8 31.5 + - - -
258A LEU 3.9 0.2 - - - +
259A CYS* 3.2 6.0 - - - -
260A LEU* 2.7 41.3 + - + +
262A TYR* 3.4 25.0 + - + +
329A ASP* 4.9 1.8 + - - -
330A PHE 5.4 1.0 + - - -
504A STU 3.4 27.0 - - - -
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Residues in contact with LYS 214 (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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170A PHE* 3.7 29.2 - - + -
180A PHE* 3.9 34.0 - - + +
198A GLY* 3.1 1.4 - - - -
199A VAL* 2.9 32.6 + - - +
201A TYR* 4.1 19.3 + - + +
212A VAL 3.7 1.4 + - - -
213A LYS* 1.3 72.5 - - - +
215A LEU* 1.3 72.0 + - - +
216A ALA* 3.5 1.7 + - - +
257A ASP* 4.1 11.3 + - - -
258A LEU 3.7 6.7 - - - +
259A CYS* 3.9 15.7 - - - -
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Residues in contact with LEU 215 (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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196A GLY 3.5 15.5 - - - +
197A PHE* 3.4 12.1 - - + +
213A LYS* 3.4 34.5 - - + +
214A LYS* 1.3 80.4 + - - +
216A ALA* 1.3 59.0 + - - +
217A ALA 4.5 0.2 + - - -
226A LEU* 4.2 28.2 - - + +
229A GLN* 5.3 1.6 - - + -
230A PHE* 3.6 43.5 - - + +
233A GLU* 5.6 0.7 - - - +
258A LEU* 2.9 31.7 + - + +
260A LEU* 5.1 6.1 - - + -
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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