Contacts of the helix formed by residues 272 - 282 (chain A) in PDB entry 2CUY
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 GLU 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLU* 3.3 6.5 - - - -
271A GLY* 1.3 75.5 - - - +
273A VAL* 1.3 66.4 + - - +
275A LYS* 3.1 31.5 + - + +
276A GLY* 3.1 18.2 + - - -
289A SER* 3.1 29.4 - - - +
291A GLN* 3.7 11.9 + - - +
13B ARG* 3.9 4.9 + - - -
14B VAL* 4.1 26.7 + - + +
15B GLY* 3.6 21.0 - - - +
18B ARG* 2.8 36.7 + - - -
46B TRP 4.8 4.2 - - - +
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Residues in contact with VAL 273 (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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10A GLY 5.5 0.2 - - - -
11A SER* 3.6 28.3 - - - +
160A GLN* 6.2 0.2 - - - +
267A GLU* 3.6 2.9 + - - +
271A GLY* 3.6 1.7 - - - -
272A GLU* 1.3 80.2 - - - +
274A LEU* 1.3 70.0 + - + +
276A GLY* 3.0 12.9 + - - -
277A LEU* 3.1 27.4 + - + +
14B VAL* 4.3 14.1 - - + -
50B GLU* 3.7 39.3 - - + +
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Residues in contact with LEU 274 (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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5A LEU* 3.9 20.4 - - + -
6A PHE 3.3 45.3 - - - +
7A PRO* 3.4 7.6 - - + -
8A GLY 5.5 0.4 - - - +
11A SER* 5.9 0.2 - - - +
88A HIS* 3.8 23.6 - - + -
250A TRP* 3.9 18.3 + - + -
267A GLU* 2.9 27.1 + - + +
273A VAL* 1.3 77.6 - - + +
275A LYS* 1.3 62.5 + - - +
277A LEU* 3.1 22.5 + - + +
278A VAL* 2.9 28.8 + - - +
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Residues in contact with LYS 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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5A LEU* 5.9 0.2 - - - -
267A GLU* 2.8 17.1 + - + +
272A GLU* 3.1 38.1 + - + +
274A LEU* 1.3 76.8 - - - +
276A GLY* 1.3 63.2 + - - +
278A VAL* 3.3 3.9 + - - +
279A LEU* 3.2 38.9 + - + +
287A ALA* 3.6 40.2 - - + +
288A LEU* 4.8 4.5 - - - +
289A SER* 3.5 17.9 - - - +
18B ARG* 4.4 13.9 - - - +
46B TRP 5.5 3.7 + - - +
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Residues in contact with GLY 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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272A GLU 3.1 6.7 + - - -
273A VAL* 3.0 8.4 + - - -
275A LYS* 1.3 78.5 - - - +
277A LEU* 1.3 63.9 + - - +
279A LEU* 3.5 6.9 + - - +
280A ARG* 3.1 36.8 + - - +
14B VAL* 5.8 1.3 - - - -
47B GLU* 4.2 21.1 - - - -
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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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88A HIS* 4.5 3.4 - - + -
156A ASN* 3.6 36.3 - - + +
157A ALA* 4.1 1.1 - - + -
160A GLN* 3.2 38.1 - - - +
250A TRP* 3.6 30.5 - - + +
254A LEU* 4.1 1.6 - - - -
273A VAL* 3.1 22.7 + - + +
274A LEU* 3.1 23.1 + - + +
276A GLY* 1.3 78.6 - - - +
278A VAL* 1.3 61.6 + - - +
280A ARG* 3.3 6.5 + - - +
281A THR* 2.9 31.0 + - - -
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Residues in contact with VAL 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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5A LEU* 3.5 28.7 - - + -
250A TRP* 5.3 0.2 - - - +
254A LEU* 3.8 22.2 - - + -
265A PHE* 3.9 26.2 - - + -
274A LEU 2.9 18.7 + - - +
275A LYS* 3.5 8.5 - - - +
276A GLY 3.3 0.2 - - - -
277A LEU* 1.3 76.3 - - - +
279A LEU* 1.3 57.5 + - + +
281A THR 3.1 0.3 + - - -
282A LEU* 2.6 40.4 + - + +
285A ALA* 4.2 13.7 - - + -
287A ALA* 3.7 21.5 - - + -
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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
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275A LYS* 3.2 41.1 + - + +
276A GLY* 4.0 6.3 - - - +
278A VAL* 1.3 78.2 - - + +
280A ARG* 1.3 61.1 + - - +
282A LEU 3.4 17.0 - - - +
283A LYS* 3.7 17.8 + - - +
285A ALA 3.8 22.7 - - - +
286A GLU* 4.7 0.4 - - - -
287A ALA* 3.9 21.5 - - + +
47B GLU* 5.7 10.8 - - + -
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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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157A ALA* 4.2 10.5 - - + -
158A PRO* 3.9 19.9 - - + +
159A GLU 6.1 0.2 - - - -
160A GLN* 2.7 45.3 + - - +
273A VAL 5.7 0.2 + - - -
276A GLY* 3.1 33.7 + - - +
277A LEU* 3.8 7.5 - - - +
279A LEU* 1.3 76.9 - - - +
281A THR* 1.3 59.1 + - - +
283A LYS* 3.1 30.3 + - - +
47B GLU* 2.5 41.8 + - - +
48B GLY 3.6 1.8 + - - -
49B PRO* 3.6 25.2 - - - +
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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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156A ASN 3.8 0.9 + - - -
157A ALA* 3.4 12.6 - - - +
158A PRO* 3.3 22.1 - - + +
251A VAL* 4.3 9.6 - - + -
254A LEU* 3.6 27.0 - - + +
255A ARG* 3.6 38.3 + - - +
277A LEU 2.9 18.2 + - - -
280A ARG* 1.3 79.0 - - - +
282A LEU* 1.4 67.8 + - + +
283A LYS* 4.1 6.7 + - - +
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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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254A LEU* 3.7 35.4 - - + +
255A ARG* 4.0 21.3 - - + +
258A GLU* 3.2 29.4 - - + +
265A PHE* 3.5 34.3 - - + -
278A VAL* 2.6 28.4 + - + +
279A LEU* 3.4 10.6 - - - +
281A THR* 1.4 90.2 - - + +
283A LYS* 1.3 63.3 + - - +
284A GLU 3.6 0.9 - - - +
285A ALA* 3.6 19.3 - - + +
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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