Contacts of the helix formed by residues 176 - 184 (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 ASN 176 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D HIS* 5.0 0.2 - - - -
175D LYS* 1.3 71.2 - - - +
177D TYR* 1.3 58.2 + - - +
178D ASP* 3.2 9.5 + - - +
179D TYR* 2.8 31.6 + - + +
180D ILE* 3.0 25.0 + - - +
187D PRO* 5.2 3.9 - - + +
280D VAL* 5.1 1.4 - - - +
281D PRO* 3.0 36.4 + - - +
282D CYS* 2.9 14.4 + - - +
284D PHE* 2.9 40.3 - - + -
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Residues in contact with TYR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D ASN* 3.1 24.1 + - - -
141D ALA* 3.8 12.8 - - + -
174D HIS* 5.1 0.9 - - + -
175D LYS* 3.0 24.5 + - + +
176D ASN* 1.3 71.8 - - - +
178D ASP* 1.3 59.7 + - - +
180D ILE* 3.3 34.5 - - + -
181D LEU* 2.9 34.3 + - + +
216D VAL* 4.4 15.9 - - + -
218D LEU* 6.0 2.0 - - + -
242D TYR* 2.9 34.3 - + + +
243D TYR 3.4 13.2 - - - -
244D PRO* 3.3 25.6 - - + -
245D HIS* 3.1 33.8 + - + +
246D CYS* 4.9 0.4 - - - -
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D HIS* 5.4 0.2 - - - -
176D ASN* 3.1 9.5 - - - +
177D TYR* 1.3 80.7 + - - +
179D TYR* 1.3 58.3 + - - +
181D LEU* 3.8 2.0 - - - +
182D SER* 2.9 30.6 + - - -
245D HIS 3.9 2.3 - - - +
246D CYS* 3.1 24.5 - - - +
247D LEU* 2.8 42.2 + - - +
248D ALA 4.9 0.7 + - - -
284D PHE* 4.9 6.0 - - + -
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Residues in contact with TYR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ASN* 2.8 23.5 + - - +
178D ASP* 1.3 75.8 - - - +
180D ILE* 1.3 66.1 + - - +
182D SER* 2.9 8.9 + - - -
183D THR* 2.8 50.0 + - + +
185D CYS 3.5 14.2 + - - -
187D PRO* 3.3 49.1 - - + +
280D VAL* 4.5 27.6 - - + -
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Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LYS* 4.6 13.2 - - + +
176D ASN 3.0 18.4 - - - +
177D TYR* 3.3 39.0 - - + +
179D TYR* 1.3 80.6 - - - +
181D LEU* 1.3 55.0 + - + +
184D GLY* 2.5 41.5 + - - -
185D CYS 3.3 7.8 + - - +
186D ALA* 3.4 40.4 - - + +
187D PRO* 4.2 5.8 - - + -
204D THR* 4.9 7.9 - - + -
206D VAL* 5.1 0.7 - - + -
216D VAL* 4.6 17.3 - - + -
218D LEU* 6.2 3.1 - - + -
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Residues in contact with LEU 181 (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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211A ASN* 5.7 0.9 + - - -
177D TYR 2.9 14.6 + - - +
178D ASP* 3.9 3.1 - - - +
180D ILE* 1.3 80.6 - - + +
182D SER* 1.3 61.5 + - - +
184D GLY* 3.8 6.6 + - - +
206D VAL* 3.6 38.8 - - + -
213D ALA* 3.7 22.7 - - + -
216D VAL* 3.8 13.9 - - + -
244D PRO* 3.2 30.3 - - + +
246D CYS* 4.3 16.2 - - - -
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Residues in contact with SER 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ASN* 5.1 4.3 + - - +
178D ASP 2.9 20.3 + - - -
179D TYR* 2.9 12.2 + - - -
181D LEU* 1.3 80.8 - - - +
183D THR* 1.3 71.6 + - - +
184D GLY 3.9 0.2 + - - -
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Residues in contact with THR 183 (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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211A ASN* 3.6 22.2 - - - +
179D TYR* 2.8 42.1 + - + +
182D SER* 1.3 88.8 - - - +
184D GLY* 1.3 58.8 + - - +
185D CYS* 2.7 40.8 + - - +
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Residues in contact with GLY 184 (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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208A THR* 5.7 2.2 - - - -
210A ASN* 4.4 4.5 + - - -
211A ASN* 4.0 21.1 + - - +
180D ILE* 2.5 19.4 + - - -
181D LEU* 3.8 7.1 + - - -
182D SER 3.5 3.0 + - - -
183D THR* 1.3 70.3 - - - +
185D CYS* 1.3 63.4 + - - -
204D THR* 2.9 28.3 - - - +
206D VAL* 5.0 7.8 - - - +
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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