Contacts of the helix formed by residues 246 - 258 (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 CYS 246 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D HIS* 4.9 0.4 - - - -
178D ASP* 3.1 28.0 - - - +
181D LEU* 4.3 24.2 - - - -
244D PRO 3.6 3.4 + - - -
245D HIS* 1.3 76.5 - - - +
247D LEU* 1.3 68.3 + - - +
248D ALA* 4.6 4.7 - - + +
249D SER* 3.4 12.5 + - - +
250D PHE* 2.9 22.9 + - - +
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Residues in contact with LEU 247 (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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174D HIS* 4.3 9.1 - - + +
178D ASP* 2.8 22.5 + - - +
245D HIS 3.9 0.4 + - - -
246D CYS* 1.3 69.9 - - - +
248D ALA* 1.3 53.5 + - - +
250D PHE* 3.0 2.8 + - - -
251D THR* 2.7 46.5 + - - +
266D VAL* 4.0 14.4 - - + -
273D TYR* 4.3 15.7 - - + +
284D PHE* 3.1 45.3 - - + -
286D HIS* 3.5 27.6 - - + +
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Residues in contact with ALA 248 (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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178D ASP* 4.9 1.0 + - - -
246D CYS* 3.4 3.9 - - + +
247D LEU* 1.3 76.5 - - - +
249D SER* 1.3 64.6 + - - +
251D THR* 3.0 9.6 + - - -
252D GLU* 2.8 26.3 + - - +
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Residues in contact with SER 249 (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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150D GLN* 4.4 8.8 + - - -
245D HIS* 4.6 4.2 - - - -
246D CYS* 3.4 16.6 + - - +
247D LEU 3.4 0.4 - - - -
248D ALA* 1.3 78.2 - - - +
250D PHE* 1.3 54.2 + - - +
252D GLU* 3.7 9.1 - - - +
253D LEU* 2.6 57.0 + - - +
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Residues in contact with PHE 250 (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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140D PHE* 3.4 33.4 - + + -
157D LEU* 4.4 6.5 - - + -
172D ILE* 3.6 49.4 - - + -
173D ASP 4.8 1.6 - - - -
174D HIS* 3.3 39.3 - + + +
245D HIS* 3.6 25.1 - + + -
246D CYS 2.9 18.6 + - - +
247D LEU 3.6 2.0 - - - +
249D SER* 1.3 75.9 + - - +
251D THR* 1.3 56.1 + - - +
253D LEU* 3.9 4.3 - - + -
254D VAL* 2.6 48.8 + - + +
286D HIS* 3.8 14.8 - + + -
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Residues in contact with THR 251 (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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247D LEU* 2.7 40.2 + - - +
248D ALA* 3.3 10.1 - - - -
250D PHE* 1.3 74.7 - - - +
252D GLU* 1.3 64.8 + - - +
254D VAL* 3.2 4.0 - - - +
255D GLN* 3.0 36.3 + - - +
264D HIS* 3.7 30.4 - - + +
266D VAL* 5.4 3.0 - - + +
286D HIS* 3.7 4.1 - - - -
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Residues in contact with GLU 252 (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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154D ARG* 5.0 9.7 + - - -
248D ALA 2.8 15.4 + - - +
249D SER* 3.7 8.1 - - - +
251D THR* 1.3 81.1 - - - +
253D LEU* 1.3 66.4 + - - +
255D GLN* 3.8 4.8 - - - +
256D GLU* 3.1 26.2 + - + +
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Residues in contact with LEU 253 (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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150D GLN* 4.6 15.5 - - + +
153D HIS* 4.7 4.3 - - + -
154D ARG* 3.2 53.4 - - + +
157D LEU* 4.0 22.9 - - + +
245D HIS* 3.9 25.4 - - + +
249D SER* 2.6 37.7 + - - +
250D PHE* 3.4 5.4 - - + +
252D GLU* 1.3 76.7 - - - +
254D VAL* 1.3 60.7 + - - +
256D GLU* 3.7 8.3 + - - +
257D ALA* 3.5 16.5 + - - +
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Residues in contact with VAL 254 (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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157D LEU* 4.3 16.5 - - + +
170D LEU* 4.3 11.9 - - + -
172D ILE* 4.0 26.9 - - + -
250D PHE* 2.6 26.1 + - + +
251D THR 3.2 4.9 - - - +
253D LEU* 1.3 71.0 - - - +
255D GLN* 1.3 69.3 + - - +
257D ALA* 3.1 19.4 - - + +
258D PHE* 3.6 8.7 - - - -
264D HIS* 3.2 37.9 - - + +
286D HIS* 4.4 2.5 - - - +
288D LEU* 4.2 15.3 - - + -
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Residues in contact with GLN 255 (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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251D THR* 3.0 28.1 + - - +
252D GLU* 3.9 4.8 - - - +
254D VAL* 1.3 77.2 - - - +
256D GLU* 1.3 63.0 + - - +
257D ALA 3.0 4.9 - - - -
258D PHE* 3.0 15.2 + - - +
260D GLY* 3.2 21.9 + - - -
262D CYS* 3.3 30.2 + - - -
264D HIS* 3.0 43.0 - - + +
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Residues in contact with GLU 256 (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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154D ARG* 3.4 34.2 + - + +
252D GLU* 3.1 18.8 + - + +
253D LEU* 3.9 7.1 - - - +
255D GLN* 1.3 77.1 - - - +
257D ALA* 1.3 57.8 + - - +
259D GLY* 2.8 24.3 + - - +
260D GLY* 4.3 5.2 - - - +
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Residues in contact with ALA 257 (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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154D ARG 5.5 1.8 - - - +
157D LEU* 3.7 34.5 - - + +
158D LYS* 4.1 21.2 - - - +
161D ALA* 3.8 16.5 - - + +
170D LEU* 6.0 0.2 - - + -
253D LEU 3.5 7.7 + - - +
254D VAL* 3.1 20.6 + - + +
256D GLU* 1.3 81.9 - - - +
258D PHE* 1.3 58.7 + - + +
259D GLY 3.4 2.1 + - - -
290D LYS* 5.7 0.2 + - - -
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Residues in contact with PHE 258 (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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161D ALA* 3.5 30.3 - - + -
164D VAL* 4.0 13.9 - - + -
170D LEU* 3.2 47.1 - - + -
254D VAL 3.6 14.4 - - - -
255D GLN 3.0 8.4 + - - +
257D ALA* 1.3 76.5 - - + +
259D GLY* 1.3 62.2 + - - +
260D GLY 3.3 0.7 - - - -
261D ARG* 3.2 33.9 + - - +
262D CYS* 3.8 16.4 - - + -
288D LEU* 3.7 21.1 - - + -
290D LYS* 3.6 34.2 - - + +
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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