Contacts of the helix formed by residues 276 - 289 (chain A) in PDB entry 1BSG
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 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ASP* 3.5 39.0 - - + +
220A ARG* 3.7 11.7 - - - +
244A ASN* 2.8 13.7 + - - +
274A ARG* 2.7 49.0 + - - -
275A ASP* 1.3 72.4 + - - +
277A GLY* 1.3 60.7 + - - +
279A VAL* 3.1 5.5 + - - +
280A ALA 2.9 23.7 + - - -
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Residues in contact with GLY 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 ASP 5.1 0.4 - - - -
275A ASP* 3.2 8.2 + - - -
276A ASP* 1.3 76.8 - - - +
278A LEU* 1.3 54.6 + - - +
280A ALA* 3.7 6.6 - - - +
281A ASP* 2.7 46.5 + - - -
284A ARG* 6.0 0.2 - - - -
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Residues in contact with LEU 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* 4.0 35.0 - - + +
37A GLU 4.7 0.2 - - - +
40A SER* 3.6 28.7 - - - +
42A ALA* 3.9 16.4 - - + -
44A LEU* 4.3 23.3 - - + -
265A THR* 3.6 28.5 - - + +
275A ASP* 3.1 27.6 + - + +
276A ASP 3.3 0.2 - - - -
277A GLY* 1.3 76.7 - - - +
279A VAL* 1.3 57.3 + - - +
281A ASP* 3.4 4.6 + - - +
282A ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 4.0 17.5 - - + -
221A PHE* 3.9 11.6 - - + -
244A ASN* 3.7 34.3 - - - +
246A ASP* 3.8 29.8 - - + +
263A VAL* 4.3 13.5 - - + -
265A THR* 4.1 11.7 - - + -
275A ASP 3.6 15.7 - - - +
276A ASP 3.1 6.0 + - - +
278A LEU* 1.3 75.4 - - - +
280A ALA* 1.3 63.7 + - - +
282A ALA* 3.4 3.1 + - - +
283A ALA* 3.2 21.1 + - - +
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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 ASP 3.7 9.2 - - - +
220A ARG 3.5 24.6 + - - +
223A ALA* 4.2 5.6 - - + -
224A GLY* 3.5 8.7 - - - +
276A ASP 2.9 16.3 + - - +
277A GLY* 3.8 6.3 - - - +
279A VAL* 1.3 75.8 - - - +
281A ASP* 1.3 63.0 + - - +
283A ALA* 3.2 5.6 + - - +
284A ARG* 3.0 39.2 + - - +
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.8 27.8 - - + +
277A GLY* 2.7 32.0 + - - +
278A LEU* 3.8 5.8 + - - +
280A ALA* 1.3 73.2 - - - +
282A ALA* 1.3 61.7 + - - +
284A ARG* 2.9 39.8 + - - +
285A VAL* 3.1 17.2 + - - +
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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* 4.2 16.5 - - + +
36A LEU* 3.7 11.6 - - + +
44A LEU* 4.6 8.3 - - + -
46A VAL* 4.6 0.9 - - + -
263A VAL* 4.0 26.2 - - + -
278A LEU 2.9 18.5 + - - +
279A VAL 3.7 4.9 - - - +
280A ALA 3.3 0.4 - - - -
281A ASP* 1.3 75.0 - - - +
283A ALA* 1.3 63.6 + - - +
285A VAL* 3.3 5.2 + - - +
286A LEU* 3.1 28.6 + - + +
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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 PHE* 3.9 23.6 - - + -
224A GLY* 4.1 15.0 - - - -
225A LEU* 3.9 16.5 - - + +
261A LEU* 5.3 1.3 - - + -
263A VAL* 5.1 0.6 - - - +
279A VAL 3.2 12.6 + - - +
280A ALA* 3.3 11.0 - - - +
282A ALA* 1.3 74.5 - - - +
284A ARG* 1.3 59.9 + - - +
286A LEU* 3.1 12.8 + - - +
287A ALA* 2.8 30.0 + - - +
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Residues in contact with ARG 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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32A ARG* 5.9 1.3 - - - +
223A ALA* 3.5 25.5 + - - +
224A GLY* 3.5 19.0 + - - +
280A ALA* 3.0 31.3 + - - +
281A ASP* 2.9 35.8 + - - +
283A ALA* 1.3 76.8 - - - +
285A VAL* 1.3 63.6 + - + +
287A ALA* 3.4 3.5 + - - +
288A GLU* 3.1 41.3 + - - +
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Residues in contact with VAL 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 ALA* 4.2 13.7 - - + +
32A ARG* 3.9 55.2 - - + +
33A LEU* 4.3 11.0 - - + -
36A LEU* 3.9 20.2 - - + -
281A ASP 3.1 13.8 + - - +
282A ALA 3.6 7.4 - - - +
283A ALA 3.2 0.2 - - - -
284A ARG* 1.3 75.8 - - + +
286A LEU* 1.3 58.9 + - + +
288A GLU* 3.4 2.8 + - - +
289A THR* 2.7 43.5 + - - +
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Residues in contact with LEU 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 ALA* 6.1 0.2 - - + -
33A LEU* 5.0 4.9 - - + -
46A VAL* 4.0 22.4 - - + -
48A ALA* 4.1 14.8 - - + -
57A VAL* 4.0 39.3 - - + -
225A LEU* 5.7 0.4 - - + -
229A TRP* 4.9 1.6 - - - -
259A ILE* 6.4 0.2 - - + -
261A LEU* 4.0 30.1 - - + -
263A VAL* 4.5 11.0 - - + -
282A ALA 3.1 16.1 + - - +
283A ALA* 3.1 8.8 + - - +
285A VAL* 1.3 77.7 - - + +
287A ALA* 1.3 56.3 + - - +
289A THR* 4.3 2.9 - - - -
290A LEU* 2.7 42.9 + - + +
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Residues in contact with ALA 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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224A GLY 4.5 4.3 - - - +
225A LEU* 4.1 7.7 - - + +
226A PRO* 3.8 30.7 - - + +
229A TRP* 3.8 19.8 - - + -
283A ALA 2.8 16.0 + - - +
284A ARG* 3.8 5.6 - - - +
286A LEU* 1.3 76.3 - - - +
288A GLU* 1.3 60.4 + - + +
290A LEU 3.1 7.3 - - - +
299A ACT 2.9 22.2 - - - +
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Residues in contact with GLU 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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32A ARG* 3.2 35.0 + - - +
284A ARG* 3.1 28.5 + - - +
285A VAL 3.9 4.0 - - - +
286A LEU 3.2 0.2 - - - -
287A ALA* 1.3 78.5 - - + +
289A THR* 1.3 58.2 + - - +
299A ACT 3.6 22.6 - - + +
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Residues in contact with THR 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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29A ALA* 4.1 20.8 - - + +
32A ARG* 4.9 4.7 + - - -
55A ARG* 3.4 46.3 + - - +
57A VAL* 4.2 6.1 - - + -
285A VAL* 2.7 31.3 + - - +
286A LEU* 3.3 5.4 + - - -
288A GLU* 1.3 79.9 - - - +
290A LEU* 1.3 68.8 + - + +
291A GLY 4.8 0.7 - - - +
299A ACT 4.3 3.8 - - - +
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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