Contacts of the helix formed by residues 274 - 283 (chain A) in PDB entry 4R8A
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 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A CYS* 2.9 25.6 + - + +
272A GLN* 3.1 6.8 + - + +
273A ARG* 1.3 74.9 - - - +
275A PHE* 1.3 62.3 + - - +
276A ASP* 3.8 7.4 + - - +
277A LEU* 3.2 39.4 + - - +
278A ALA* 3.2 15.2 + - - +
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Residues in contact with PHE 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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270A GLU* 3.3 37.2 - - + -
273A ARG* 3.4 54.5 + - + -
274A ASP* 1.3 71.8 + - - +
276A ASP* 1.3 61.3 + - - +
277A LEU 3.3 0.2 - - - -
278A ALA* 3.7 6.2 - - - +
279A GLN* 2.9 30.5 + - - +
297A SER* 3.5 22.4 - - - +
300A ARG* 3.5 64.4 - - + -
301A GLY* 4.2 8.5 - - - +
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Residues in contact with ASP 276 (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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274A ASP* 3.3 7.7 + - - +
275A PHE* 1.3 80.8 - - - +
277A LEU* 1.3 58.6 + - - +
279A GLN* 3.2 20.1 - - - +
280A ARG* 3.5 9.2 + - - +
301A GLY* 4.7 8.8 - - - +
303A ARG* 3.3 42.7 + - - +
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Residues in contact with LEU 277 (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 LEU* 5.3 7.2 - - + -
241A LEU* 4.7 10.8 - - + -
269A CYS* 3.8 18.2 - - - -
274A ASP* 3.2 28.8 + - - +
275A PHE 3.3 0.2 - - - -
276A ASP* 1.3 76.7 - - - +
278A ALA* 1.3 67.2 + - - +
279A GLN 3.2 0.2 - - - -
280A ARG* 3.2 15.3 + - + +
281A LEU* 2.9 44.3 + - + +
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Residues in contact with ALA 278 (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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266A ALA* 3.4 27.7 - - - +
269A CYS* 3.9 8.2 - - - +
270A GLU* 3.7 20.2 - - + +
274A ASP 3.2 17.1 + - - +
275A PHE* 3.7 7.2 - - - +
277A LEU* 1.3 78.4 - - - +
279A GLN* 1.3 56.9 + - - +
281A LEU* 3.3 0.6 + - - -
282A TYR* 2.9 36.9 + - + -
297A SER* 4.1 5.8 - - - +
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Residues in contact with GLN 279 (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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275A PHE 2.9 18.8 + - - +
276A ASP* 3.2 11.5 - - - +
278A ALA* 1.3 76.5 - - - +
280A ARG* 1.3 82.5 + - - +
281A LEU 3.1 1.6 + - - -
282A TYR* 3.1 14.6 + - - +
283A ARG* 3.1 56.2 + - + +
294A ALA 4.1 5.4 - - - +
297A SER* 4.1 15.4 - - - -
298A LEU* 3.5 39.0 - - + +
303A ARG* 3.5 17.2 + - - +
306A GLU* 5.7 0.4 + - - -
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Residues in contact with ARG 280 (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 ASP 3.5 11.2 + - - +
277A LEU* 3.2 19.7 + - + +
279A GLN* 1.3 92.6 + - - +
281A LEU* 1.3 60.5 + - + +
283A ARG* 3.8 5.3 + - - +
284A GLN* 3.3 36.3 + - + +
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Residues in contact with LEU 281 (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 LEU* 4.2 5.2 - - + -
241A LEU* 3.7 23.3 - - + -
262A LEU* 3.9 31.0 - - + +
265A PHE* 3.9 24.9 - - + -
266A ALA* 3.6 17.3 - - + +
269A CYS* 3.9 17.9 - - - -
277A LEU* 2.9 34.1 + - + +
280A ARG* 1.3 76.3 - - + +
282A TYR* 1.3 64.2 + - - +
283A ARG 3.1 1.8 - - - -
284A GLN* 3.0 28.7 + - - +
285A SER* 3.4 11.1 + - - -
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Residues in contact with TYR 282 (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 PHE* 3.7 35.7 - + - -
266A ALA* 3.5 26.4 - - + +
267A GLN* 3.3 23.7 - - - +
270A GLU* 2.6 30.3 + - - -
278A ALA* 2.9 25.3 + - + +
279A GLN 3.1 4.9 + - - +
281A LEU* 1.3 75.7 - - - +
283A ARG* 1.3 57.6 + - - +
285A SER* 3.2 24.5 + - - +
290A ALA* 3.4 30.3 - - - +
291A ARG* 4.6 0.9 + - - -
293A ARG* 3.4 36.0 + - + +
294A ALA* 3.7 8.3 - - + -
297A SER* 3.5 10.8 - - - -
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Residues in contact with ARG 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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279A GLN* 3.1 43.5 + - - +
280A ARG* 4.1 5.8 - - - +
281A LEU 3.1 0.8 - - - -
282A TYR* 1.3 74.2 - - - +
284A GLN* 1.3 59.8 - - + +
285A SER 3.1 9.2 + - - +
291A ARG* 6.0 2.2 - - - +
294A ALA* 3.7 11.9 - - + -
298A LEU* 4.9 6.1 - - - +
306A GLU* 5.8 3.2 + - - +
310A LEU* 3.7 46.4 - - - +
313A GLU* 5.6 0.2 + - - -
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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