Contacts of the strand formed by residues 204 - 209 (chain D) in PDB entry 1NBI
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 204 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.5 8.3 - - - +
210A ASN* 3.0 36.1 + - - +
180D ILE* 4.9 7.0 - - + -
184D GLY 2.9 30.9 + - - +
185D CYS* 4.4 2.9 - - - +
186D ALA* 4.2 15.6 + - - +
202D ILE* 4.3 2.3 + - - +
203D THR* 1.3 72.5 - - - +
205D SER* 1.3 69.2 + - - +
206D VAL* 4.3 16.8 - - + +
216D VAL* 5.2 0.7 - - + -
217D THR 3.6 3.1 - - - -
218D LEU* 4.0 16.0 - - + +
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Residues in contact with SER 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 4.2 19.2 - - - +
208A THR 3.8 5.4 - - - -
209A VAL* 4.3 10.0 - - - +
203D THR* 4.0 7.3 + - - +
204D THR* 1.3 78.1 + - - +
206D VAL* 1.3 63.8 + - - +
207D LEU* 3.9 1.9 + - - +
215D MET 4.0 0.2 - - - +
216D VAL* 3.6 0.5 - - - -
217D THR* 2.8 53.3 + - - +
219D ASP* 4.5 4.9 + - - -
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL 3.8 1.2 - - - +
207A LEU* 3.5 3.7 - - - +
208A THR* 3.0 45.6 + - + +
180D ILE* 5.1 2.2 - - + -
181D LEU* 3.6 27.4 - - + -
184D GLY* 5.0 8.7 - - - +
204D THR* 4.2 14.5 - - + +
205D SER* 1.3 74.2 - - - +
207D LEU* 1.3 63.4 + - - +
208D THR* 3.6 24.5 - - + -
213D ALA* 4.7 1.6 - - + -
215D MET 3.6 6.3 - - - +
216D VAL* 3.3 25.4 - - + -
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER* 4.1 22.0 - - - +
206A VAL 3.6 4.0 - - - +
207A LEU* 4.2 25.8 - - + +
205D SER 3.9 1.5 + - - +
206D VAL* 1.3 72.8 - - - +
208D THR* 1.3 63.2 + - - +
209D VAL* 4.3 7.9 - - + -
213D ALA* 3.8 0.5 - - - -
214D HIS* 2.8 46.2 + - + -
215D MET* 2.8 37.3 + - + +
217D THR* 6.1 0.2 - - - +
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Residues in contact with THR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A SER* 4.6 0.2 - - - -
206A VAL* 2.8 46.5 + - - +
208A THR* 5.5 5.2 - - + -
181D LEU* 6.0 0.2 - - + -
206D VAL* 3.6 19.5 - - + +
207D LEU* 1.3 78.1 - - - +
209D VAL* 1.3 61.7 + - - +
210D ASN 4.2 0.2 + - - -
211D ASN* 4.7 8.2 + - - -
212D LYS 3.0 24.5 + - - -
213D ALA* 3.5 15.9 - - + +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 4.6 7.4 - - + -
204A THR 3.3 7.2 - - - +
205A SER* 3.4 22.7 - - - +
207D LEU* 4.3 7.4 - - + -
208D THR* 1.3 73.7 - - - +
210D ASN* 1.3 85.0 + - - +
211D ASN 3.2 2.0 - - - -
212D LYS* 2.8 38.5 + - - +
214D HIS* 3.3 34.1 - - + +
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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