Contacts of the helix formed by residues 266 - 275 (chain A) in PDB entry 2NYM
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A VAL* 5.2 3.8 - - + +
226A GLU* 2.9 42.5 + - - +
229A VAL* 4.3 15.7 - - + -
262A MSE 2.7 33.8 + - + +
263A VAL* 3.9 3.6 - - - -
265A ASP* 1.3 95.1 + - + +
267A PHE* 1.3 56.6 + - - +
268A THR 3.8 0.9 - - - -
269A GLU* 3.7 31.6 + - + +
270A LEU* 3.0 33.2 + - + +
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Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 3.0 34.4 + - + +
264A ALA 3.5 12.1 - - - +
265A ASP 3.2 4.6 - - - -
266A LYS* 1.3 73.2 - - - +
268A THR* 1.3 55.3 + - - +
269A GLU 2.9 1.3 - - - -
270A LEU* 2.8 8.7 + - + +
271A GLN* 2.7 33.6 + - - +
283A LEU* 3.3 47.5 - - + +
286A ALA* 4.7 3.6 - - + -
287A PHE* 3.4 36.6 - + + -
290A LEU* 4.0 16.4 - - + -
305A LYS* 4.4 8.3 - - + +
309A PHE* 3.4 38.8 - + + -
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 1.3 79.1 - - - +
269A GLU* 1.3 74.2 + - - +
271A GLN* 3.2 30.2 + - - +
272A LYS* 3.2 14.2 + - - +
305A LYS* 4.0 25.5 + - + +
308A GLU* 3.5 45.7 + - + +
309A PHE* 3.8 20.9 - - + +
312A ASN* 5.1 1.6 + - - -
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A VAL* 3.6 27.3 - - + +
233A GLN* 5.4 1.0 + - - -
265A ASP 3.5 20.4 - - - +
266A LYS* 3.7 33.2 + - + +
267A PHE 2.9 0.4 - - - -
268A THR* 1.3 88.9 + - - +
270A LEU* 1.3 63.9 + - - +
271A GLN 3.5 0.2 + - - -
272A LYS* 3.6 6.3 + - - +
273A ALA* 3.3 16.5 + - - +
305A LYS* 3.8 5.2 + - - -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 4.8 5.6 - - + +
228A CYS* 4.0 9.4 - - + +
229A VAL* 3.3 38.4 - - + +
232A ALA* 5.5 1.6 - - + -
248A LEU* 3.4 43.3 - - + -
263A VAL* 3.9 22.0 - - + +
266A LYS* 3.0 22.5 + - + +
267A PHE* 2.8 12.6 + - + +
269A GLU* 1.3 73.4 - - - +
271A GLN* 1.3 70.4 + - - +
273A ALA* 4.5 1.6 - - + -
274A VAL* 2.7 34.0 + - + +
283A LEU* 4.3 6.1 - - + -
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE 2.7 15.8 + - - +
268A THR* 3.2 23.1 + - - +
270A LEU* 1.3 78.0 - - - +
272A LYS* 1.3 64.6 + - - +
274A VAL* 3.5 0.9 - - - +
275A GLY 3.2 22.4 + - - +
276A PRO* 6.3 0.4 - - + -
279A THR* 3.7 25.1 - - + +
283A LEU* 3.7 12.3 - - + +
308A GLU 3.9 1.4 + - - -
309A PHE* 2.6 51.7 + - + +
312A ASN* 3.3 38.4 - - + +
313A LEU* 4.2 1.6 + - - +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN* 6.1 1.6 - - - +
268A THR 3.2 8.2 + - - +
269A GLU* 3.9 9.2 - - - +
271A GLN* 1.3 80.4 - - - +
273A ALA* 1.3 64.8 + - - +
275A GLY* 3.7 11.0 + - - -
308A GLU* 5.2 7.6 + - - -
312A ASN* 3.8 27.6 - - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A VAL* 3.6 27.8 - - + +
232A ALA* 3.7 25.6 - - + +
233A GLN* 3.7 21.9 - - + +
240A LEU* 4.2 0.7 - - - +
269A GLU 3.3 14.9 + - - +
270A LEU* 3.8 3.8 - - - +
272A LYS* 1.3 80.3 - - - +
274A VAL* 1.3 68.2 + - - +
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ALA* 4.5 2.9 - - + +
237A GLN* 4.5 3.5 - - - +
240A LEU* 2.8 34.1 - - + +
245A MSE 4.1 11.4 - - + -
248A LEU* 4.4 20.9 - - + -
270A LEU* 2.7 37.5 + - + +
271A GLN 3.5 2.9 - - - +
273A ALA* 1.3 77.4 - - + +
275A GLY* 1.3 61.3 + - - +
278A ILE* 3.2 47.2 - - + +
279A THR 4.5 0.2 - - - +
283A LEU* 4.1 14.4 - - + -
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 5.4 1.1 - - - -
271A GLN* 3.2 11.6 + - - +
272A LYS* 4.1 7.6 - - - -
273A ALA 3.6 0.6 - - - -
274A VAL* 1.3 80.7 - - - +
276A PRO* 1.3 66.3 - - - +
277A GLU 3.2 2.2 - - - -
278A ILE* 3.9 11.7 - - - -
279A THR* 2.4 30.4 + - - -
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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