Contacts of the helix formed by residues 241 - 247 (chain B) 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 LEU 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PHE* 5.5 2.5 - - + -
215B LEU* 4.1 15.7 - - + -
222B ILE* 4.2 0.2 - - + -
236B PHE* 2.7 51.5 + - + -
237B LEU* 3.0 25.5 + - + +
240B VAL* 1.3 72.0 - - - +
242B LEU* 1.3 66.2 + - - +
244B LEU* 3.3 16.8 + - + +
245B HIS* 3.4 11.9 + - + -
257B LEU* 3.3 33.4 - - + +
260B CYS* 4.2 17.5 - - + +
261B VAL* 5.0 1.8 - - + +
264B PHE* 3.7 25.6 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LEU* 2.8 19.2 + - + +
238B LEU* 3.5 30.5 - - + +
241B LEU* 1.3 67.2 - - - +
243B PRO* 1.3 59.4 - - + +
244B LEU 2.6 16.6 + - - -
245B HIS* 2.7 45.7 + - + +
246B LYS 4.2 0.5 + - - -
261B VAL* 4.5 5.6 - - + -
274B PRO 4.2 0.4 - - - +
275B VAL* 3.5 53.4 - - + +
278B ALA* 3.6 21.5 - - + -
279B LEU* 4.4 8.2 - - + +
282B TYR* 4.4 7.4 - - + -
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Residues in contact with PRO 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU* 5.1 2.7 - - - +
202B ILE* 3.7 11.9 - - + +
203B TYR* 3.5 21.5 - - - +
238B LEU 3.0 20.9 - - - +
239B LYS* 3.0 28.5 - - - +
240B VAL* 3.3 10.3 - - - +
241B LEU 3.5 0.9 - - - -
242B LEU* 1.3 92.3 - - + +
244B LEU* 1.3 55.4 + - - -
245B HIS 3.3 0.7 - - - -
246B LYS* 2.8 28.8 - - + +
282B TYR* 3.8 26.9 - - + +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 3.8 46.4 - - + -
201B PHE* 4.5 8.1 - - + -
202B ILE* 4.0 19.3 - - + -
211B ILE* 4.6 2.7 - - + -
215B LEU* 5.1 4.9 - - + -
240B VAL 3.4 10.8 - - - +
241B LEU* 3.3 17.0 + - + +
242B LEU 2.6 7.7 + - - -
243B PRO* 1.3 73.3 - - - +
245B HIS* 1.3 58.9 + - - -
246B LYS 2.9 6.1 + - - -
247B VAL* 3.5 6.9 + - - +
253B TYR* 2.9 50.9 + - + +
257B LEU* 4.0 8.5 - - + -
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Residues in contact with HIS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU 3.4 10.4 + - - -
242B LEU* 2.7 47.9 + - + +
244B LEU* 1.3 77.0 - - - +
246B LYS* 1.3 51.5 + - - +
247B VAL 3.4 2.3 + - - +
250B LEU* 3.8 17.9 - - + +
254B HIS* 4.9 0.9 - + - -
257B LEU* 3.5 26.6 - - + +
261B VAL* 3.8 7.7 - - + +
279B LEU* 3.7 12.1 - - + +
282B TYR* 5.4 3.6 - - + -
290B LYS* 2.8 34.8 + - - -
294B PHE* 4.0 23.7 - + + -
297B GLU* 2.7 43.7 + - - -
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 4.6 0.6 + - - -
100A GLU* 5.4 0.4 - - - +
101A GLU* 3.4 38.7 - - - +
202B ILE* 4.6 8.1 - - + -
203B TYR* 3.4 24.4 + - + -
206B GLU* 5.9 2.2 - - - +
242B LEU 4.2 0.4 + - - -
243B PRO* 2.8 22.9 - - + +
244B LEU 2.9 1.0 - - - -
245B HIS* 1.3 78.7 - - - +
247B VAL* 1.3 58.3 + - + +
248B LYS* 4.1 4.9 + - - +
282B TYR* 3.7 36.2 + - + +
290B LYS* 2.8 18.8 + - - +
302C ARG* 5.0 3.8 - - - +
305C PRO* 5.3 2.2 - - + -
306C ASP* 3.0 12.5 - - - +
307C TYR* 3.2 39.4 + - + -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 3.7 32.3 - - + +
202B ILE* 4.2 24.0 - - + -
206B GLU* 4.3 31.9 - - + +
244B LEU 4.0 5.2 - - - +
245B HIS 3.4 3.1 - - - +
246B LYS* 1.3 80.7 - - + +
248B LYS* 1.3 76.6 + - + +
249B SER* 3.3 25.0 + - - +
250B LEU* 3.9 5.7 + - - +
253B TYR* 3.5 13.7 - - - +
290B LYS* 3.4 15.4 + - - +
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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