Contacts of the helix formed by residues 244 - 254 (chain D) in PDB entry 2NPP
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 VAL 244 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D ILE* 4.7 0.9 - - + -
209D PHE* 4.6 7.2 - - + -
228D CYS* 3.8 28.9 - - - -
231D ILE* 4.3 13.7 - - + -
232D ALA* 4.5 12.3 - - + -
235D LEU* 3.6 30.1 - - + -
240D LEU* 3.0 24.9 + - + +
242D ALA 3.9 0.6 - - - -
243D LEU* 1.3 79.3 - - - +
245D MET* 1.3 66.4 + - - +
246D PRO* 3.2 2.5 - - - -
247D THR* 2.7 34.5 + - - -
248D LEU* 3.4 7.2 + - + -
274D VAL* 6.0 1.8 - - + -
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Residues in contact with MET 245 (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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240D LEU* 2.9 25.1 + - + +
241D GLU* 3.6 23.3 - - - +
244D VAL* 1.3 80.6 - - - +
246D PRO* 1.3 70.0 - - + +
248D LEU* 3.8 32.5 - - + -
249D ARG* 2.8 45.3 + - + +
274D VAL* 4.6 9.4 - - - -
278D ILE* 3.7 20.4 - - + -
282D ASP* 3.4 33.7 - - + -
283D LEU* 4.7 4.9 - - + -
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Residues in contact with PRO 246 (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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241D GLU* 3.5 20.2 - - - +
242D ALA 4.4 8.3 - - - +
243D LEU 4.4 2.0 - - - -
244D VAL 3.2 11.0 - - - +
245D MET* 1.3 95.4 - - + +
247D THR* 1.3 61.1 + - - +
249D ARG* 3.5 23.6 + - - +
250D GLN* 3.4 18.2 + - - +
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Residues in contact with THR 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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209D PHE* 3.9 25.4 - - + -
210D SER* 3.9 20.3 - - - -
213D ALA* 3.4 32.8 - - + -
243D LEU 4.6 4.3 + - - -
244D VAL 2.7 17.3 + - - -
246D PRO* 1.3 71.4 - - - +
248D LEU* 1.3 59.4 + - - +
249D ARG 3.1 1.3 - - - -
250D GLN* 2.8 11.7 + - + +
251D ALA* 2.8 28.2 + - + +
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Residues in contact with LEU 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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225D VAL* 5.4 2.9 - - + -
228D CYS* 4.2 19.8 - - - -
244D VAL* 3.4 3.7 + - + +
245D MET* 3.2 39.0 + - + +
247D THR* 1.3 79.2 - - - +
249D ARG* 1.3 63.4 + - - +
251D ALA* 3.2 8.2 + - + +
252D ALA* 3.1 21.6 + - + +
263D VAL* 4.0 19.3 - - + -
270D LEU* 3.4 41.1 - - + -
274D VAL* 4.5 8.3 - - + -
283D LEU* 3.9 20.9 - - + -
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Residues in contact with ARG 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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241D GLU* 2.7 34.4 + - - -
245D MET* 2.8 46.0 + - + +
246D PRO* 3.5 26.4 + - - +
248D LEU* 1.3 73.5 - - - +
250D GLN* 1.3 63.1 + - - +
252D ALA* 3.4 13.2 + - - +
253D GLU* 3.4 27.3 + - - +
282D ASP* 3.1 27.7 + - + -
286D ALA* 6.6 0.2 - - - -
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Residues in contact with GLN 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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213D ALA 6.0 2.2 - - - +
214D SER* 6.3 3.6 - - - -
246D PRO 3.4 11.5 + - - +
247D THR* 2.8 12.4 + - + +
249D ARG* 1.3 75.3 - - - +
251D ALA* 1.3 55.3 + - - +
253D GLU* 2.9 15.2 + - - +
254D ASP* 2.7 51.3 + - - +
255D LYS* 4.5 12.7 - - - +
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Residues in contact with ALA 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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225D VAL* 3.9 19.5 - - + -
247D THR* 2.8 15.2 + - + +
248D LEU* 3.3 15.9 - - + +
250D GLN* 1.3 76.2 - - - +
252D ALA* 1.3 62.4 + - - +
253D GLU 3.2 1.0 + - - -
254D ASP* 3.2 19.4 + - - +
259D VAL* 3.7 13.3 - - + +
260D ARG* 4.0 4.9 - - - +
263D VAL* 3.5 22.3 - - + +
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Residues in contact with ALA 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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248D LEU* 3.1 9.8 + - + +
249D ARG* 3.6 12.1 - - - +
251D ALA* 1.3 80.0 - - - +
253D GLU* 1.3 61.5 + - + +
254D ASP 3.5 0.2 - - - -
260D ARG* 3.1 22.5 - - - +
263D VAL* 3.8 22.6 - - + +
286D ALA* 4.8 18.8 - - + -
290D LEU* 4.3 16.0 - - + +
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Residues in contact with GLU 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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249D ARG* 3.4 21.8 + - - +
250D GLN* 2.9 19.7 + - - +
252D ALA* 1.3 80.8 - - + +
254D ASP* 1.3 71.3 + - - +
255D LYS* 3.4 14.5 + - - +
260D ARG* 4.1 2.9 - - - +
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Residues in contact with ASP 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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213D ALA 4.7 2.9 - - - +
221D ARG* 2.5 48.4 + - - +
250D GLN* 2.7 22.9 + - - +
251D ALA* 3.2 18.9 + - - +
252D ALA 3.5 0.2 - - - -
253D GLU* 1.3 84.9 - - - +
255D LYS* 1.3 65.2 + - - +
256D SER* 2.7 22.8 + - - +
259D VAL* 3.6 24.3 - - + +
260D ARG* 3.1 19.5 + - + -
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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