Contacts of the helix formed by residues 284 - 295 (chain A) in PDB entry 3ENM
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 SER 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU* 2.5 35.3 + - - -
283A PHE* 1.3 73.6 - - - +
285A ALA* 1.3 59.4 + - - +
286A GLU* 3.7 16.2 + - - +
287A PHE* 3.0 15.1 + - - -
288A VAL* 2.9 31.5 + - - +
313A PHE* 4.6 0.2 - - - -
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Residues in contact with ALA 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 ALA* 5.4 1.1 + - - -
283A PHE 3.8 0.8 + - - -
284A SER* 1.3 71.9 - - - +
286A GLU* 1.3 66.4 + - - +
288A VAL* 3.7 7.3 - - - +
289A ASP* 2.8 32.3 + - - +
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Residues in contact with GLU 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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284A SER* 3.7 17.6 - - - +
285A ALA* 1.3 83.2 + - - +
287A PHE* 1.3 59.9 + - - +
289A ASP* 4.5 1.6 - - - -
290A PHE* 2.9 25.6 + - - +
311A HIS* 3.3 14.1 - - - -
312A PRO* 3.6 29.5 - - + +
313A PHE* 4.0 20.6 - - + +
316A LEU* 5.8 9.8 - - + +
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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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152A GLU* 3.4 23.1 - - + +
155A LEU* 3.8 35.2 - - + -
159A ALA* 5.8 0.2 - - + -
247A MSE 4.2 24.5 - - + -
251A ALA* 3.8 15.3 - - + -
278A LEU* 3.7 26.0 - - + -
283A PHE* 3.8 8.1 - + + -
284A SER* 3.0 19.6 + - - +
286A GLU* 1.3 77.1 - - - +
288A VAL* 1.3 58.7 + - - +
290A PHE* 3.3 5.9 + + - -
291A THR* 3.0 33.4 + - - -
313A PHE* 3.3 42.4 - + + -
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Residues in contact with VAL 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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277A GLN* 5.6 5.2 - - + +
278A LEU* 4.0 23.8 - - + +
280A ALA* 3.8 26.9 - - + -
283A PHE* 3.8 22.4 - - + +
284A SER 2.9 26.8 + - - +
285A ALA* 3.7 7.4 - - - +
287A PHE* 1.3 75.3 - - - +
289A ASP* 1.3 60.3 + - - +
291A THR* 3.2 10.2 - - + +
292A SER* 2.9 31.2 + - - -
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Residues in contact with ASP 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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285A ALA 2.8 22.3 + - - +
286A GLU* 3.9 3.1 - - - +
288A VAL* 1.3 74.6 - - - +
290A PHE* 1.3 59.5 + - - +
292A SER* 3.2 5.9 + - - -
293A GLN* 2.9 57.6 + - - +
311A HIS* 2.6 31.1 + - + +
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Residues in contact with PHE 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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159A ALA* 4.5 19.3 - - + -
163A VAL* 4.1 23.8 - - + -
243A LEU* 4.2 12.1 - - + -
244A GLY* 6.1 0.4 - - - -
247A MSE 4.6 10.1 - - + -
286A GLU 2.9 19.0 + - - +
287A PHE* 3.7 9.2 - + - +
289A ASP* 1.3 76.3 - - - +
291A THR* 1.3 67.0 + - - +
293A GLN* 3.4 3.7 + - - +
294A CYS* 3.2 34.2 + - - -
308A LEU* 3.9 31.6 - - + +
311A HIS* 3.5 33.6 - + + +
313A PHE* 3.8 23.6 - + + -
314A PHE* 4.6 10.3 - + + -
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Residues in contact with THR 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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244A GLY* 4.3 6.8 + - - -
247A MSE 4.3 5.2 - - - +
248A ILE* 3.5 30.6 - - + +
277A GLN* 5.2 1.1 - - - -
278A LEU* 3.6 37.6 - - + +
287A PHE* 3.0 22.0 + - - -
288A VAL* 3.2 11.7 - - + +
290A PHE* 1.3 83.0 - - - +
292A SER* 1.3 66.8 + - - +
294A CYS* 3.4 5.7 + - - +
295A LEU* 3.3 29.5 + - + +
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Residues in contact with SER 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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276A PRO 5.8 1.3 - - - -
277A GLN* 5.5 11.9 - - - +
288A VAL* 2.9 22.4 + - - -
289A ASP* 3.2 7.0 + - - -
291A THR* 1.3 78.9 - - - +
293A GLN* 1.3 71.3 + - - +
295A LEU* 3.3 13.2 + - - +
296A LYS* 3.3 29.5 + - - +
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Residues in contact with GLN 293 (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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289A ASP* 2.9 53.2 + - - +
290A PHE* 3.6 5.8 - - - +
292A SER* 1.3 82.6 + - - +
294A CYS* 1.4 63.8 + - - +
295A LEU 3.1 1.4 + - - -
296A LYS* 3.3 34.4 + - - +
301A GLU 4.6 9.7 + - - -
302A ARG* 3.8 1.7 - - - +
303A PRO* 3.6 31.9 - - + +
308A LEU* 5.4 1.1 - - + -
311A HIS* 4.4 10.5 - - + +
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Residues in contact with CYS 294 (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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240A ILE* 3.4 36.1 - - - +
241A TRP* 3.4 11.8 + - - -
243A LEU* 3.9 22.9 - - - -
244A GLY* 3.9 13.0 - - - -
290A PHE* 3.2 29.9 + - - -
291A THR* 3.8 7.0 - - - +
292A SER 3.3 0.2 - - - -
293A GLN* 1.4 79.4 - - - +
295A LEU* 1.3 57.4 - - - +
296A LYS 3.4 0.2 - - - -
302A ARG* 3.1 22.7 - - - -
303A PRO* 4.3 0.9 - - - -
308A LEU* 4.1 11.7 - - - -
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Residues in contact with LEU 295 (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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241A TRP* 3.3 54.1 - - + +
244A GLY* 3.9 16.2 - - - -
245A ILE* 3.5 22.7 - - + +
248A ILE* 3.7 29.6 - - + -
275A SER* 2.7 34.2 + - - +
276A PRO* 3.7 12.3 - - + +
291A THR 3.5 17.5 - - - +
292A SER* 3.3 7.9 + - - +
293A GLN 3.0 1.2 - - - -
294A CYS* 1.3 79.3 - - - +
296A LYS* 1.3 64.2 + - - +
297A LYS 3.3 0.5 + - - -
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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