Contacts of the helix formed by residues 282 - 292 (chain F) in PDB entry 4DEM
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 282 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207F TYR* 3.8 1.3 - - - -
258F ASP* 3.3 26.2 + - - +
275F ASP* 4.2 19.4 + - - +
280F LYS* 2.9 15.3 + - - +
281F CYS* 1.3 73.8 - - - +
283F TRP* 1.3 68.3 + - - +
284F LEU* 3.1 20.4 + - - +
285F VAL* 3.1 11.9 + - - +
286F VAL* 3.1 20.6 + - - +
304F TYR* 4.2 7.2 - - - -
319F TYR* 5.6 0.4 - - - -
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Residues in contact with TRP 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLU* 6.4 0.2 - - + -
207F TYR* 3.3 31.8 - + - +
255F ILE* 3.5 47.4 - - + +
258F ASP* 3.0 16.5 + - + +
259F TYR* 5.4 0.9 - - + -
282F SER* 1.3 73.3 + - - +
284F LEU* 1.3 82.5 + - + +
286F VAL* 3.3 7.4 + - + +
287F GLN* 3.0 66.4 + - + +
324F LEU* 4.7 3.6 - - + -
327F VAL* 3.9 13.5 - - + -
328F PHE* 3.8 42.0 - + + -
331F TYR* 4.0 26.7 - + + -
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Residues in contact with LEU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F ASP 3.6 22.7 - - - +
259F TYR* 4.0 19.3 - - + +
262F LEU* 3.9 34.1 - - + -
263F PHE* 4.1 18.2 - - + -
282F SER* 3.1 10.7 + - - +
283F TRP* 1.3 99.9 - - + +
285F VAL* 1.3 57.8 + - - +
287F GLN* 3.2 1.8 + - - -
288F CYS* 2.8 28.9 + - - +
319F TYR* 3.4 17.5 - - + +
324F LEU* 3.6 23.1 - - + +
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Residues in contact with VAL 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F LEU* 4.4 0.9 - - + -
202F PHE* 3.6 29.8 - - + -
280F LYS 3.6 20.6 - - - +
281F CYS* 4.3 0.7 - - - -
282F SER* 3.1 16.5 + - - +
284F LEU* 1.3 76.6 - - - +
286F VAL* 1.3 61.2 + - - +
288F CYS* 3.3 1.8 + - - +
289F LEU* 2.9 36.4 + - + +
300F LEU* 3.9 24.2 - - + -
304F TYR* 3.7 22.2 - - + +
319F TYR* 3.3 21.3 + - - +
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Residues in contact with VAL 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F PHE* 3.8 26.2 - - + +
203F THR 4.0 5.4 - - - +
204F GLU* 3.8 40.2 - - + +
207F TYR* 4.2 9.9 - - + -
281F CYS* 3.9 23.1 - - - -
282F SER 3.1 13.7 + - - +
283F TRP* 3.5 10.8 - - + +
285F VAL* 1.3 78.5 - - - +
287F GLN* 1.3 66.8 + - - +
289F LEU* 3.3 4.2 + - - +
290F GLN* 3.2 27.3 + - + +
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Residues in contact with GLN 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLU* 4.0 14.3 + - - +
283F TRP* 3.0 69.0 + - + +
284F LEU 3.7 3.8 - - - +
286F VAL* 1.3 77.5 - - - +
288F CYS* 1.3 67.2 + - - +
290F GLN* 3.3 26.4 + - - +
291F ARG* 2.6 59.0 + - - +
324F LEU* 4.1 15.3 - - + -
327F VAL* 4.2 2.6 - - + +
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Residues in contact with CYS 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F LEU 2.8 17.0 + - - +
285F VAL* 3.5 6.1 - - - +
287F GLN* 1.3 77.0 - - - +
289F LEU* 1.3 61.8 + - - +
291F ARG* 3.0 4.2 + - - +
292F ALA* 3.0 29.4 + - - +
300F LEU* 3.8 16.2 - - + -
318F LEU* 3.7 29.6 - - - -
319F TYR* 3.6 26.9 - - + -
322F LEU* 3.8 17.8 - - - +
324F LEU* 4.0 7.3 - - + +
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Residues in contact with LEU 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F LEU* 3.6 21.8 - - + +
202F PHE* 3.6 43.3 - - + +
285F VAL* 2.9 21.2 + - + +
286F VAL* 3.7 5.4 - - - +
287F GLN 3.3 0.4 - - - -
288F CYS* 1.3 76.5 - - - +
290F GLN* 1.3 62.6 + - + +
291F ARG 3.3 0.5 + - - -
292F ALA* 3.7 13.4 + - + +
297F TYR* 3.6 38.4 - - + -
300F LEU* 3.6 21.8 - - + -
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Residues in contact with GLN 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLU* 2.4 49.5 + - - +
286F VAL* 3.2 18.1 + - + +
287F GLN* 3.5 24.3 - - - +
288F CYS 3.2 0.4 - - - -
289F LEU* 1.3 76.9 - - + +
291F ARG* 1.3 67.9 + - + +
292F ALA 5.5 0.2 - - - -
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Residues in contact with ARG 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F GLN* 2.6 47.4 + - - +
288F CYS 3.0 4.2 + - - +
290F GLN* 1.3 89.3 + - + +
292F ALA* 1.3 62.3 + - - +
293F THR* 3.6 3.6 + - - +
296F GLN* 4.1 0.3 - - - +
322F LEU* 3.8 32.8 - - + +
324F LEU* 4.0 16.4 - - - -
327F VAL* 3.4 38.3 - - - +
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Residues in contact with ALA 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F CYS* 3.0 21.7 + - - +
289F LEU* 3.7 12.0 + - + +
290F GLN 3.7 1.8 - - - -
291F ARG* 1.3 78.0 - - - +
293F THR* 1.3 71.2 + - - +
294F PRO* 4.5 0.7 - - - +
296F GLN* 3.5 19.5 - - + -
297F TYR* 3.9 17.2 - - + +
322F LEU* 4.5 5.2 - - + -
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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