Contacts of the helix formed by residues 266 - 275 (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 LYS 266 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D VAL* 5.6 3.8 - - + -
226D GLU* 3.5 29.1 - - - +
229D VAL* 4.6 9.4 - - + -
262D MET* 2.8 37.3 + - + +
263D VAL 3.6 3.6 - - - +
265D ASP* 1.3 95.8 + - + +
267D PHE* 1.3 62.5 + - - +
269D GLU* 3.0 34.8 + - + +
270D LEU* 2.9 26.0 + - + +
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Residues in contact with PHE 267 (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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263D VAL* 3.1 26.0 + - + -
264D ALA* 3.1 17.3 + - - +
265D ASP 3.4 1.2 - - - -
266D LYS* 1.3 77.0 - - - +
268D THR* 1.3 52.2 + - - +
269D GLU* 3.5 0.4 + - - -
270D LEU* 2.6 30.2 + - + +
271D GLN* 2.7 16.0 + - - +
283D LEU* 3.6 37.6 - - + +
286D ALA* 4.5 3.8 - - + -
287D PHE* 3.0 59.0 - + + -
290D LEU* 4.2 14.8 - - + -
305D LYS* 3.5 9.3 - - + +
309D PHE* 3.5 30.3 - + + -
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Residues in contact with THR 268 (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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267D PHE* 1.3 75.0 - - - +
269D GLU* 1.3 78.3 + - - +
271D GLN* 3.1 28.8 + - - +
272D LYS* 3.2 15.6 + - - +
305D LYS* 3.2 34.0 + - + +
308D GLU* 3.1 48.8 + - + +
309D PHE* 4.2 9.4 - - + +
312D ASN* 5.4 0.2 - - - -
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Residues in contact with GLU 269 (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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229D VAL* 4.1 18.4 - - + +
233D GLN* 5.1 2.1 + - - -
265D ASP 3.9 4.2 - - - +
266D LYS* 3.0 42.9 + - + +
268D THR* 1.3 82.1 + - - +
270D LEU* 1.3 59.7 + - - +
272D LYS* 3.7 4.7 + - - +
273D ALA* 3.3 21.5 + - - +
305D LYS* 2.7 29.2 + - - -
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Residues in contact with LEU 270 (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* 5.0 4.5 - - + +
228D CYS* 4.2 17.3 - - + -
229D VAL* 3.3 36.6 - - + +
232D ALA* 5.7 1.1 - - + -
248D LEU* 3.4 32.1 - - + -
263D VAL* 4.1 24.9 - - + +
266D LYS* 2.9 19.5 + - + +
267D PHE* 2.6 14.2 + - + +
269D GLU* 1.3 69.2 - - - +
271D GLN* 1.3 69.3 + - - +
272D LYS 3.0 1.6 - - - -
273D ALA* 4.4 2.2 - - + +
274D VAL* 2.8 40.5 + - + +
283D LEU* 4.3 6.5 - - + -
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Residues in contact with GLN 271 (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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267D PHE 2.7 11.7 + - - +
268D THR* 3.1 20.8 + - - +
270D LEU* 1.3 76.8 - - - +
272D LYS* 1.3 61.3 + - + +
274D VAL* 4.1 0.2 - - - +
275D GLY 3.3 25.3 + - - +
279D THR* 3.4 16.0 + - + +
283D LEU* 3.6 12.9 - - + +
308D GLU 3.8 0.2 + - - -
309D PHE* 2.5 64.8 - - + +
312D ASN* 3.4 41.9 - - + +
313D LEU* 4.2 0.7 + - - +
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Residues in contact with LYS 272 (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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233D GLN* 6.0 2.0 - - - +
268D THR 3.2 13.9 + - - +
269D GLU* 4.1 4.7 - - - +
270D LEU 3.0 0.2 - - - -
271D GLN* 1.3 78.8 - - + +
273D ALA* 1.3 66.8 + - - +
274D VAL 2.9 3.3 + - - -
275D GLY* 3.3 12.8 + - - -
308D GLU* 6.1 0.2 - - - -
312D ASN* 3.7 38.3 + - + +
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Residues in contact with ALA 273 (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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229D VAL* 3.9 10.1 - - + +
232D ALA* 3.8 30.7 - - + +
233D GLN* 3.4 37.2 + - + +
240D LEU* 4.2 2.3 - - - +
269D GLU 3.3 15.5 + - - +
270D LEU* 3.1 5.9 + - - +
272D LYS* 1.3 78.0 - - - +
274D VAL* 1.3 63.1 + - + +
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Residues in contact with VAL 274 (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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232D ALA* 4.9 8.3 - - + -
237D GLN* 4.8 4.0 - - - +
240D LEU* 3.3 28.5 - - + +
244D VAL* 6.0 1.8 - - + -
245D MET* 4.6 5.8 - - - -
248D LEU* 4.5 21.1 - - + -
270D LEU* 2.8 30.2 + - + +
271D GLN 4.1 2.7 - - - +
272D LYS 2.9 0.6 + - - -
273D ALA* 1.3 80.8 - - + +
275D GLY* 1.3 60.3 + - - +
278D ILE* 3.1 48.7 - - + +
279D THR* 4.4 2.7 - - - +
283D LEU* 4.5 8.1 - - + -
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Residues in contact with GLY 275 (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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237D GLN* 5.8 1.8 - - - -
271D GLN 3.3 6.0 + - - +
272D LYS 3.3 11.2 + - - -
274D VAL* 1.3 79.6 - - - +
276D PRO* 1.3 66.8 - - - +
277D GLU 3.3 2.6 + - - -
278D ILE* 4.2 5.8 - - - -
279D THR* 2.4 34.3 + - - -
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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