Contacts of the helix formed by residues 275 - 288 (chain A) in PDB entry 5A91
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 ARG 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER 5.6 0.2 + - - -
40A SER* 3.3 25.3 + - - +
244A THR* 2.9 17.4 + - - +
265A PHE* 3.8 14.5 - - + -
267A GLN* 3.6 23.2 + - - +
273A GLU* 3.6 26.6 + - - +
274A ASN* 1.3 82.5 - - - +
276A ASN* 1.3 65.0 + - - +
277A ASP* 2.8 41.9 + - - +
278A ILE* 3.1 39.8 + - + +
279A LEU* 3.7 5.0 + - - +
1293A SO4 3.8 2.0 + - - -
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Residues in contact with ASN 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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219A ALA* 3.4 21.9 - - + +
220A SER* 2.4 30.1 + - - +
235A THR* 5.1 2.4 - - - +
244A THR* 3.3 22.5 - - - +
245A ASN 4.8 2.3 - - - +
274A ASN* 4.6 6.1 - - - +
275A ARG* 1.3 75.6 - - - +
277A ASP* 1.3 61.3 + - - +
279A LEU* 3.0 20.0 + - - +
280A ALA 3.0 10.0 + - - -
1293A SO4 2.8 33.2 + - - +
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Residues in contact with ASP 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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219A ALA 4.7 1.6 - - - -
275A ARG* 2.8 47.8 + - - -
276A ASN* 1.3 77.6 - - - +
278A ILE* 1.3 62.7 + - - +
280A ALA* 3.4 8.1 + - - +
281A ALA* 2.9 28.8 + - - +
1293A SO4 3.0 22.3 + - - +
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Residues in contact with ILE 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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36A LEU* 3.8 26.3 - - + +
37A GLU* 6.4 0.2 - - - -
40A SER* 3.9 24.9 - - - -
44A LEU* 4.1 15.9 - - + -
265A PHE* 4.0 29.8 - - + -
275A ARG* 3.1 50.8 + - + +
277A ASP* 1.3 80.3 - - - +
279A LEU* 1.3 57.0 + - + +
281A ALA* 3.3 4.9 + - + +
282A ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 5.0 2.0 - - + -
220A SER* 4.3 2.9 - - - -
221A ILE* 4.5 9.3 - - - +
244A THR* 3.4 23.1 - - + +
245A ASN 3.5 35.0 - - - +
246A ASP* 3.8 9.2 - - + +
263A THR* 3.6 34.1 - - - +
264A TYR 4.4 0.9 - - - +
265A PHE* 3.9 16.4 - - + -
275A ARG 4.1 7.9 - - - +
276A ASN* 3.0 24.1 + - - +
278A ILE* 1.3 77.2 - - + +
280A ALA* 1.3 60.6 + - - +
282A ALA* 3.3 3.4 + - - +
283A ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 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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219A ALA 4.0 3.1 - - - +
220A SER 3.3 24.0 + - - +
223A ALA* 3.9 12.8 - - + +
224A GLY* 3.4 23.2 - - - +
276A ASN 3.0 11.3 + - - +
277A ASP* 3.6 10.1 - - - +
279A LEU* 1.3 76.8 - - - +
281A ALA* 1.3 55.9 + - - +
283A ALA* 3.3 1.9 + - - -
284A LYS* 3.0 25.8 + - - +
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Residues in contact with ALA 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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36A LEU* 3.9 24.2 - - + -
277A ASP 2.9 17.4 + - - +
278A ILE* 3.6 5.8 - - + +
280A ALA* 1.3 75.4 - - - +
282A ALA* 1.3 64.0 + - - +
284A LYS* 3.3 8.4 + - - +
285A ILE* 3.0 28.1 + - + +
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Residues in contact with ALA 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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33A LEU* 4.3 7.9 - - + -
36A LEU* 3.7 15.8 - - + +
44A LEU* 4.4 6.3 - - + -
46A VAL* 4.2 18.2 - - + -
263A THR* 4.1 16.8 - - + -
278A ILE 2.9 17.6 + - - +
279A LEU* 3.3 5.1 + - - +
281A ALA* 1.3 76.1 - - - +
283A ALA* 1.3 63.4 + - - +
285A ILE* 3.2 3.9 + - - +
286A VAL* 3.0 28.9 + - - +
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Residues in contact with ALA 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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221A ILE* 3.7 27.4 - - + +
224A GLY* 4.1 1.6 - - - -
225A LEU* 4.3 5.8 - - + -
261A LEU* 3.8 28.7 - - + -
263A THR* 4.6 0.6 - - - +
279A LEU 2.9 17.9 + - - +
280A ALA 3.5 4.5 - - - +
282A ALA* 1.3 76.9 - - - +
284A LYS* 1.3 60.3 + - - +
286A VAL* 4.1 0.4 - - - -
287A THR* 2.8 34.1 + - - +
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Residues in contact with LYS 284 (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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224A GLY* 3.3 23.5 + - - +
280A ALA 3.0 12.7 + - - +
281A ALA* 3.6 11.2 - - - +
283A ALA* 1.3 77.4 - - - +
285A ILE* 1.3 63.7 + - + +
287A THR* 3.8 2.3 + - - -
288A HIS* 3.3 31.0 + - + +
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Residues in contact with ILE 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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29A VAL* 4.0 20.3 - - + +
32A GLN* 3.8 60.3 - - + +
33A LEU* 3.8 21.5 - - + -
36A LEU* 4.1 21.8 - - + -
281A ALA* 3.0 19.7 + - + +
282A ALA 3.2 6.9 + - - +
284A LYS* 1.3 79.9 - - + +
286A VAL* 1.3 62.3 + - - +
287A THR 3.5 0.3 + - - -
288A HIS* 3.7 13.2 + - - +
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Residues in contact with VAL 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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29A VAL* 4.1 4.5 - - + -
33A LEU* 3.9 22.7 - - + -
46A VAL* 4.1 9.0 - - + -
48A LEU* 3.7 27.1 - - + +
57A ILE* 3.6 49.2 - - + +
261A LEU* 3.9 18.6 - - + -
282A ALA 3.0 20.1 + - - +
283A ALA* 3.7 7.9 - - - +
284A LYS 3.3 0.2 - - - -
285A ILE* 1.3 76.5 - - - +
287A THR* 1.3 62.5 + - + +
288A HIS 3.4 3.0 - - - +
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Residues in contact with THR 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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48A LEU* 4.0 11.0 - - + -
224A GLY 4.2 1.7 + - - -
225A LEU* 3.5 25.8 - - + +
226A PRO* 5.0 1.9 - - - +
229A TRP* 4.0 17.3 - - + -
250A ILE* 4.5 6.5 - - + -
259A LEU* 4.0 24.7 - - + -
261A LEU* 4.7 2.2 - - + -
283A ALA 2.8 22.7 + - - +
284A LYS* 3.8 4.5 + - - -
286A VAL* 1.3 81.6 - - + +
288A HIS* 1.3 66.9 + - - +
290A PHE* 3.1 24.5 - - - +
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Residues in contact with HIS 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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29A VAL* 6.4 0.2 - - + -
284A LYS* 3.3 24.0 + - + +
285A ILE* 3.7 10.7 - - - +
286A VAL 3.4 4.3 - - - +
287A THR* 1.3 80.1 - - - +
289A GLY* 1.3 84.8 + - - +
290A PHE* 3.7 1.6 - - - +
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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