Contacts of the helix formed by residues 282 - 292 (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 ASP 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLU* 3.8 10.0 - - - +
245A MSE 4.1 18.1 - - + +
249A ARG* 2.9 37.3 + - + +
278A ILE* 2.9 33.1 + - - +
281A THR* 1.3 88.7 - - - +
283A LEU* 1.3 61.2 + - + +
284A VAL 3.4 1.8 - - - -
285A PRO* 3.0 8.6 - - - +
286A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 283 (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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245A MSE 4.9 7.9 - - + -
248A LEU* 4.4 24.7 - - + -
263A VAL* 6.0 0.4 - - + -
267A PHE* 3.3 32.2 - - + +
270A LEU* 4.3 4.3 - - + -
271A GLN* 3.7 36.1 - - + +
274A VAL* 4.1 14.6 - - + -
278A ILE 4.5 2.5 - - - +
279A THR* 3.0 34.4 + - + +
282A ASP* 1.3 70.9 - - + +
284A VAL* 1.3 56.0 + - - +
286A ALA* 3.2 7.4 - - + +
287A PHE* 2.3 40.9 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR 3.0 16.5 + - - +
280A LYS* 3.9 20.9 - - + +
283A LEU* 1.3 76.9 - - - +
285A PRO* 1.3 78.3 - - + +
287A PHE* 3.2 7.6 + - - +
288A GLN* 3.2 14.9 + - - +
309A PHE* 4.1 22.2 - - + -
313A LEU* 4.2 16.6 - - + -
321A VAL* 5.1 4.3 - - + -
325A GLN* 4.0 37.5 - - + +
326A ILE* 4.4 9.0 - - + +
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Residues in contact with PRO 285 (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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280A LYS 4.2 5.4 - - - +
281A THR 4.1 13.2 - - - +
282A ASP* 3.0 19.3 - - - +
284A VAL* 1.3 97.4 - - + +
286A ALA* 1.3 64.1 + - - +
288A GLN* 2.8 32.2 + - - +
289A ASN* 3.2 17.2 - - - +
325A GLN* 5.9 1.3 - - - +
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Residues in contact with ALA 286 (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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249A ARG* 6.6 0.2 - - - -
252A ALA* 4.9 16.4 - - + +
267A PHE* 4.4 8.1 - - + -
282A ASP 3.0 18.2 + - - +
283A LEU* 3.2 13.0 - - + +
285A PRO* 1.3 78.1 - - - +
287A PHE* 1.3 61.5 + - - +
289A ASN* 3.1 29.9 - - - +
290A LEU* 3.3 14.1 + - + +
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Residues in contact with PHE 287 (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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264A ALA 5.8 0.2 - - - -
267A PHE* 3.4 37.4 - + + -
283A LEU 2.3 31.1 + - - +
284A VAL 3.5 5.4 - - - +
285A PRO 3.0 0.2 + - - -
286A ALA* 1.3 66.5 - - - +
288A GLN* 1.3 68.3 + - - +
290A LEU* 3.2 8.0 + - + +
291A MSE 3.1 51.5 + - + +
302A ALA* 3.7 42.2 - - + -
305A LYS* 4.3 7.2 - - + -
306A VAL* 4.0 25.1 - - + -
309A PHE* 3.4 33.9 - + + -
326A ILE* 4.5 7.6 - - + -
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Residues in contact with GLN 288 (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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284A VAL* 3.2 7.2 + - + +
285A PRO* 2.8 33.5 + - - +
287A PHE* 1.3 71.6 - - - +
289A ASN* 1.3 57.9 + - - +
291A MSE 2.5 44.8 + - + +
292A LYS* 3.0 18.6 + - + +
324A SER 5.5 0.4 + - - -
325A GLN* 3.2 41.9 + - - +
326A ILE* 5.4 0.9 - - + -
328A PRO* 5.7 1.0 - - - +
329A CYS* 3.7 23.6 - - - -
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Residues in contact with ASN 289 (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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252A ALA* 5.7 4.7 - - + +
253A GLU* 5.3 12.9 + - - +
285A PRO* 3.2 15.2 - - - +
286A ALA* 3.1 16.6 - - - +
288A GLN* 1.3 77.0 - - - +
290A LEU* 1.3 63.7 + - + +
292A LYS* 3.3 10.3 - - - +
293A ASP* 3.2 22.2 + - - +
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Residues in contact with LEU 290 (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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252A ALA* 4.3 20.6 - - + +
260A ARG* 4.4 18.6 - - + +
263A VAL* 4.5 14.4 - - + +
264A ALA* 4.5 6.1 - - + +
267A PHE* 4.0 30.7 - - + -
286A ALA* 3.5 17.5 - - + +
287A PHE* 3.2 11.9 + - + +
288A GLN 2.8 1.8 + - - -
289A ASN* 1.3 73.7 - - + +
291A MSE 1.3 59.8 + - - +
292A LYS 3.0 4.5 - - - -
293A ASP* 2.8 27.3 + - - +
298A VAL* 3.5 24.9 - - + +
299A ARG* 3.6 10.7 - - - -
302A ALA* 4.1 14.8 - - + -
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Residues in contact with MSE 291 (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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287A PHE* 3.1 46.4 + - + +
288A GLN* 2.5 45.5 + - + +
290A LEU* 1.3 71.7 - - - +
292A LYS* 1.3 56.3 + - + +
293A ASP 3.4 0.4 - - - -
299A ARG* 3.2 21.4 - - - +
302A ALA* 4.0 19.5 - - + -
306A VAL* 4.4 10.1 - - - -
326A ILE* 4.4 17.9 - - + +
329A CYS* 4.2 23.3 - - + -
330A ILE* 5.2 1.8 - - - -
333A LEU* 3.2 39.0 - - + +
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Residues in contact with LYS 292 (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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288A GLN* 3.0 18.7 + - + +
289A ASN* 3.3 10.8 - - - +
290A LEU 3.0 0.8 - - - -
291A MSE 1.3 82.1 - - + +
293A ASP* 1.3 65.1 + - - +
294A CYS* 3.9 2.4 + - - -
299A ARG* 4.2 4.0 - - - +
328A PRO* 5.3 0.6 - - - +
329A CYS* 3.3 43.1 - - + +
332A GLU* 4.4 17.8 - - - +
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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