Contacts of the helix formed by residues 271 - 282 (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 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B LEU* 4.1 9.0 - - + -
234B LYS* 3.9 43.7 - - + +
237B LEU* 3.6 31.9 - - + -
238B LEU* 5.5 5.2 - - + -
264B PHE* 4.0 16.6 - - + +
265B LEU* 3.6 6.5 - - + -
268B ASP* 4.0 17.9 - - + +
269B SER 2.8 5.0 + - - -
270B THR* 1.3 83.6 - - + +
272B THR* 1.3 55.5 + - - -
274B PRO* 3.1 21.1 - - + +
275B VAL* 3.0 24.3 - - - +
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Residues in contact with THR 272 (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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265B LEU* 3.2 25.6 - - + +
269B SER* 2.6 30.5 + - - -
270B THR 2.8 4.0 + - - -
271B LEU* 1.3 70.3 - - - +
273B GLU* 1.3 66.9 + - - +
275B VAL* 3.2 1.1 + - - -
276B VAL* 2.9 34.3 + - + +
301B ILE* 5.2 0.4 - - + -
305B ILE* 4.0 29.1 - - + +
306B GLU 5.7 0.9 + - - -
309B GLU* 3.5 12.6 + - + +
313B ILE* 3.8 16.8 - - + -
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Residues in contact with GLU 273 (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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270B THR 4.9 0.9 - - - +
272B THR* 1.3 76.0 - - - +
274B PRO* 1.3 75.0 - - + +
276B VAL* 3.7 0.5 - - - +
277B MET* 2.8 45.2 + - + +
309B GLU* 3.8 5.1 + - - +
312B LYS* 4.0 40.9 + - + +
313B ILE* 3.4 20.8 - - + +
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Residues in contact with PRO 274 (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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238B LEU* 4.0 28.3 - - + -
242B LEU* 4.2 2.4 - - - +
270B THR 3.7 6.5 - - - +
271B LEU* 3.1 37.2 - - + +
272B THR 3.4 0.4 - - - -
273B GLU* 1.3 97.7 - - + +
275B VAL* 1.3 60.2 + - - +
277B MET* 3.7 6.1 - - + +
278B ALA* 3.0 25.3 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.9 26.2 - - + -
238B LEU* 4.5 1.1 - - + -
242B LEU* 3.5 25.2 - - + +
261B VAL* 3.8 25.6 - - + -
265B LEU* 4.2 15.9 - - + -
271B LEU 3.0 22.7 - - - +
272B THR 3.2 3.7 + - - +
274B PRO* 1.3 81.4 - - - +
276B VAL* 1.3 66.2 + - + +
278B ALA* 3.2 3.3 + - - +
279B LEU* 3.0 22.6 + - + +
301B ILE* 4.1 16.6 - - + -
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 2.9 30.9 + - + +
275B VAL* 1.3 74.0 - - + +
277B MET* 1.3 66.2 + - - +
279B LEU* 2.9 20.4 + - - +
280B LEU* 2.9 25.8 + - + +
298B LEU* 4.5 18.2 - - + -
301B ILE* 4.5 17.0 - - + -
305B ILE* 5.9 1.6 - - + -
313B ILE* 3.4 45.5 - - + -
317B LEU* 4.6 5.6 - - + -
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Residues in contact with MET 277 (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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273B GLU* 2.8 44.4 + - + +
274B PRO* 3.7 6.5 - - + +
276B VAL* 1.3 77.4 - - + +
278B ALA* 1.3 52.1 + - - +
280B LEU* 3.2 39.8 + - + +
281B LYS* 2.8 31.9 + - - +
312B LYS 5.5 0.9 - - - +
313B ILE* 4.9 7.6 - - + -
316B PRO* 3.6 28.5 - - + -
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Residues in contact with ALA 278 (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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242B LEU* 3.6 28.5 - - + -
274B PRO 3.0 13.9 + - - +
275B VAL 3.3 9.9 - - - +
277B MET* 1.3 73.6 - - - +
279B LEU* 1.3 67.7 + - - +
281B LYS* 2.8 23.7 + - + +
282B TYR* 2.9 25.0 + - + -
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Residues in contact with LEU 279 (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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242B LEU* 4.4 5.2 - - + -
245B HIS* 3.7 40.6 - - + +
275B VAL* 3.0 15.2 + - + +
276B VAL* 2.9 9.5 + - - +
278B ALA* 1.3 79.2 - - - +
280B LEU* 1.3 63.5 + - + +
282B TYR* 4.9 2.9 - - + -
283B TRP* 2.9 22.0 + - + +
294B PHE* 3.1 34.1 - - + +
297B GLU* 4.0 11.4 - - + +
298B LEU* 3.7 20.6 - - + +
301B ILE* 3.5 32.5 - - + -
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Residues in contact with LEU 280 (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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276B VAL* 2.9 20.6 + - + +
277B MET* 3.2 39.0 - - + +
279B LEU* 1.3 75.5 - - + +
281B LYS* 1.3 66.2 + - - +
283B TRP* 2.9 39.4 + - + +
285B LYS* 4.7 2.6 + - - -
298B LEU* 4.9 2.7 - - + -
316B PRO* 4.2 20.9 - - + +
317B LEU* 4.2 11.9 - - + +
320B GLN* 4.0 30.1 - - + +
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Residues in contact with LYS 281 (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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61A ASP* 4.6 28.0 + - + +
62A GLU* 6.0 3.6 - - - -
63A ASP* 4.3 18.7 + - - +
100A GLU* 5.3 5.5 + - - -
277B MET 2.8 13.2 + - - +
278B ALA* 2.8 17.8 + - + +
280B LEU* 1.3 78.9 - - - +
282B TYR* 1.3 88.9 + - + +
283B TRP 3.3 2.1 + - - -
285B LYS* 4.3 5.9 + - - -
307C TYR* 4.2 14.7 - - + +
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Residues in contact with TYR 282 (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* 4.4 1.9 + - - -
100A GLU* 4.8 8.3 + - - +
203B TYR* 4.8 1.7 + - - -
242B LEU* 4.4 12.1 - - + -
243B PRO* 3.8 28.8 - - + +
245B HIS* 5.4 1.3 - - + -
246B LYS* 3.7 41.9 + - + +
278B ALA* 2.9 31.5 + - + +
279B LEU* 3.4 6.5 - - + +
281B LYS* 1.3 109.3 + - + +
283B TRP* 1.3 66.5 + - - +
284B PRO* 2.9 9.4 - - - +
290B LYS* 5.0 0.9 + - - -
294B PHE* 3.5 15.9 - - + -
306C ASP* 4.5 2.4 - - - +
307C TYR* 3.6 42.6 - + + +
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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