Contacts of the helix formed by residues 274 - 286 (chain A) in PDB entry 2B6U
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 LEU 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A ARG* 5.0 2.9 + - - +
270A LEU* 4.0 12.3 - - + -
272A ASN 3.0 14.4 + - - +
273A GLN* 1.4 79.5 - - - +
275A PHE* 1.4 69.3 + - + +
276A ILE* 3.8 26.2 - - + +
277A ALA* 3.1 24.4 - - + +
278A LYS* 4.3 0.7 + - - +
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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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15A CYS* 4.3 0.4 - - - -
17A ARG* 3.5 46.4 - - + +
18A ASP* 5.1 8.3 - - - -
168A SER* 2.6 56.9 + - - +
169A SER* 3.8 1.1 - - - +
268A CYS* 3.5 42.0 - - + -
269A ARG 4.0 11.0 + - - -
270A LEU* 3.6 40.9 - - + +
273A GLN 3.7 0.6 + - - -
274A LEU* 1.4 74.8 - - + +
276A ILE* 1.4 63.1 + - + +
277A ALA 3.1 0.9 + - - -
278A LYS* 3.3 4.2 + - - +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.6 20.2 - - - +
18A ASP* 4.3 18.8 - - - +
22A VAL* 5.9 6.1 - - + -
274A LEU* 3.2 19.7 - - + -
275A PHE* 1.4 81.9 - - + +
277A ALA* 1.3 66.2 + - - +
279A GLU* 2.8 39.2 + - - +
280A THR* 3.2 21.2 + - + -
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Residues in contact with ALA 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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253A ALA* 4.9 4.3 - - - +
273A GLN* 3.4 25.6 - - + -
274A LEU* 3.1 28.1 + - + +
275A PHE 3.1 0.2 + - - -
276A ILE* 1.3 78.1 - - - +
278A LYS* 1.4 60.5 + - - +
280A THR* 3.4 13.0 + - - -
281A THR* 3.8 9.5 - - - +
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Residues in contact with LYS 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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167A PRO* 4.0 9.9 - - + -
168A SER* 3.4 13.2 - - - -
172A LYS* 3.5 9.2 - - - +
250A PHE 4.5 1.6 - - - +
253A ALA* 3.4 41.0 + - + -
254A ARG* 3.4 45.6 - - + +
257A TYR* 3.8 3.8 - - - +
269A ARG* 3.6 18.6 - - - +
273A GLN* 3.0 26.7 + - - +
274A LEU 5.5 0.4 - - - +
275A PHE 3.3 3.3 + - - +
276A ILE 3.2 0.2 - - - -
277A ALA* 1.4 76.4 - - + +
279A GLU* 1.4 65.9 + - - +
280A THR 3.6 0.2 - - - -
281A THR* 4.0 14.6 - - + -
282A LEU* 3.4 21.2 + - + +
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Residues in contact with GLU 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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17A ARG* 3.0 15.8 + - - -
22A VAL* 3.3 15.7 - - - +
26A PHE* 3.6 18.5 - - - -
168A SER* 2.7 20.1 + - - +
169A SER* 2.8 22.2 + - - +
172A LYS* 3.2 10.6 - - - +
276A ILE* 2.8 29.5 + - - +
278A LYS* 1.4 73.7 - - - +
280A THR* 1.3 75.1 + - - +
281A THR 3.2 0.5 + - - -
283A PHE* 2.9 54.0 + - + -
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Residues in contact with THR 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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26A PHE* 6.1 2.7 - - + -
276A ILE* 3.3 29.7 + - + +
277A ALA* 3.4 9.0 + - - -
279A GLU* 1.3 86.1 - - - +
281A THR* 1.3 63.0 + - - +
283A PHE* 3.5 4.9 + - - +
284A LEU* 3.0 39.8 + - - +
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Residues in contact with THR 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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246A CYS 4.8 0.2 - - - +
249A PRO* 2.7 17.9 + - - +
250A PHE* 2.6 44.0 + - + +
253A ALA* 4.0 12.3 - - + -
277A ALA 3.8 17.3 - - - +
278A LYS* 3.9 12.3 - - + +
280A THR* 1.3 81.6 + - - +
282A LEU* 1.4 70.1 + - - +
284A LEU* 3.0 11.7 + - - +
285A ALA* 2.9 22.3 + - - +
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Residues in contact with LEU 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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102A PHE* 3.1 47.0 - - + -
106A MET* 4.7 4.0 - - + -
167A PRO* 4.0 12.6 - - + -
172A LYS* 3.1 26.5 - - + +
173A CYS 4.9 2.9 - - - +
174A ALA* 3.8 29.4 - - + -
250A PHE* 3.5 37.9 - - + -
254A ARG* 3.8 16.2 - - - +
278A LYS* 3.4 8.0 + - + +
279A GLU 3.2 3.2 + - - -
281A THR* 1.4 81.4 - - - +
283A PHE* 1.4 60.2 + - - +
285A ALA* 3.5 5.2 + - + +
286A ALA 3.2 9.5 + - - -
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Residues in contact with PHE 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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26A PHE* 3.2 46.7 - + + -
29A LEU* 4.8 7.1 - - + +
30A TYR* 2.8 33.3 + + + -
79A ILE* 5.1 0.4 - - + -
169A SER* 4.7 3.8 - - - -
171A LYS* 3.2 58.3 - - + -
172A LYS* 2.8 35.9 - - + +
279A GLU* 2.9 46.7 + - + +
280A THR* 3.8 5.2 - - - +
282A LEU* 1.4 74.5 - - - +
284A LEU* 1.4 66.7 - - - +
286A ALA* 3.2 3.8 + - - -
287A THR* 3.8 4.3 + - - -
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Residues in contact with LEU 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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245A VAL 5.6 2.7 - - - +
246A CYS* 4.6 11.3 - - - +
249A PRO* 5.2 13.5 - - + -
280A THR* 3.0 32.6 + - - +
281A THR* 3.4 10.5 - - - +
283A PHE* 1.4 74.3 - - - +
285A ALA* 1.3 58.7 + - - +
287A THR* 2.8 34.3 + - - +
288A ASN 4.4 0.3 + - - -
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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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102A PHE* 4.4 3.4 - - + -
106A MET* 4.6 1.3 - - + -
246A CYS* 3.4 28.9 + - - +
247A PHE* 3.6 11.5 - - + -
250A PHE* 4.5 7.4 - - + -
281A THR 2.9 15.9 + - - +
282A LEU* 3.6 20.9 - - + +
284A LEU* 1.3 76.7 - - - +
286A ALA* 1.4 57.0 - - - +
287A THR 3.1 0.4 - - - -
288A ASN* 2.9 32.0 + - - +
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Residues in contact with ALA 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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30A TYR* 2.8 35.0 + - + +
33A VAL* 4.2 4.0 - - - +
71A MET* 4.6 1.4 - - - +
75A LEU* 4.7 8.7 - - + -
79A ILE* 5.6 0.4 - - + -
102A PHE* 3.4 31.8 - - + -
282A LEU 3.2 1.6 + - - +
283A PHE 3.2 3.2 + - - +
285A ALA* 1.4 74.6 - - - +
287A THR* 1.4 54.2 + - - +
288A ASN* 3.1 14.4 - - - +
289A ILE* 2.9 24.3 - - - +
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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