Contacts of the helix formed by residues 275 - 285 (chain A) in PDB entry 6DMY
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 VAL 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A TYR* 4.1 13.9 - - + +
216A MET* 4.1 20.0 - - + -
265A LEU* 3.1 37.5 - - + +
268A LEU* 5.4 6.7 - - + +
269A LYS* 5.2 9.7 - - + +
273A TYR* 3.9 12.3 + - + +
274A GLN* 1.3 75.9 - - - +
276A ASP* 1.3 63.9 + - - +
277A SER 3.3 2.5 - - - +
278A TRP* 3.7 23.7 + - + -
279A GLU* 3.6 18.8 + - - +
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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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269A LYS* 5.9 0.7 - - - +
274A GLN* 3.2 28.7 + - + +
275A VAL* 1.3 76.1 - - - +
277A SER* 1.3 58.5 + - - +
279A GLU* 3.3 14.2 + - - +
280A GLU* 2.9 28.1 + - - +
878A ASP* 3.9 20.7 - - + +
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Residues in contact with SER 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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275A VAL 3.3 0.8 - - - -
276A ASP* 1.3 77.3 - - - +
278A TRP* 1.3 65.3 + - - +
280A GLU* 3.0 18.4 + - - +
281A MET* 2.7 34.4 + - - +
878A ASP* 4.5 10.6 + - - -
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Residues in contact with TRP 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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209A LEU* 4.2 13.2 - - + -
211A THR* 3.6 36.1 - - + -
213A THR* 4.5 5.8 - - + +
216A MET* 3.3 39.3 - - + +
220A ILE* 4.4 14.4 - - + -
265A LEU* 4.1 23.6 - - + -
275A VAL* 3.9 18.6 - - + +
276A ASP 3.4 0.6 - - - -
277A SER* 1.3 85.6 - - - +
279A GLU* 1.3 57.8 + - - +
281A MET* 3.1 38.2 + - + +
282A LEU* 2.9 35.6 + - + +
1808A Y01 3.6 26.9 - - + -
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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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262A LEU* 5.3 9.4 - - + -
265A LEU* 4.5 14.6 - - + +
266A GLU* 5.0 3.4 - - - +
269A LYS* 2.4 36.1 + - - -
275A VAL 3.6 9.4 + - - +
276A ASP* 3.3 15.3 + - - +
277A SER 3.2 0.6 - - - -
278A TRP* 1.3 76.2 - - - +
280A GLU* 1.3 59.3 + - - +
282A LEU* 3.9 6.5 - - - +
283A ASN* 2.9 51.8 + - - +
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Residues in contact with GLU 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* 2.9 18.5 + - - +
277A SER* 3.0 17.5 + - - +
279A GLU* 1.3 77.2 - - - +
281A MET* 1.3 53.9 + - - +
283A ASN* 3.8 5.6 - - - +
284A LYS* 2.9 42.0 + - + +
878A ASP* 4.1 13.0 - - - +
879A ASP* 3.0 29.1 - - - +
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Residues in contact with MET 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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209A LEU* 4.9 7.2 - - + -
277A SER* 2.7 17.1 + - - +
278A TRP* 3.1 42.1 + - + +
280A GLU* 1.3 72.9 - - - +
282A LEU* 1.3 75.8 + - + +
284A LYS* 4.1 4.7 - - + -
285A ALA* 2.8 32.9 + - + +
931A PRO* 5.9 4.9 - - - -
932A VAL* 4.3 31.2 - - + -
1808A Y01 3.9 27.1 - - + -
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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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261A PRO* 3.8 27.6 - - + +
262A LEU* 3.9 27.4 - - + -
265A LEU* 4.1 21.1 - - + -
278A TRP* 2.9 21.4 + - + +
279A GLU* 4.2 3.6 - - - +
281A MET* 1.3 84.0 - - + +
283A ASN* 1.3 61.1 + - - +
285A ALA 3.0 14.2 - - - +
286A GLU* 3.6 2.4 - - - +
287A VAL* 3.5 33.5 + - + +
288A GLY* 4.0 5.8 + - - +
1808A Y01 3.7 37.2 - - + -
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Residues in contact with ASN 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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262A LEU* 5.0 13.1 - - - +
279A GLU* 2.9 45.8 + - - +
280A GLU* 4.0 5.2 - - - +
282A LEU* 1.3 80.1 - - - +
284A LYS* 1.3 64.7 + - - +
286A GLU* 4.1 12.9 - - - +
288A GLY* 6.1 0.5 - - - -
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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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280A GLU* 2.9 32.5 + - + +
281A MET* 3.1 6.5 + - + +
283A ASN* 1.3 77.2 - - - +
285A ALA* 1.3 62.0 + - + +
286A GLU* 3.2 6.9 + - - +
333A LYS* 3.7 17.5 - - + +
334A TYR* 4.7 13.2 + - - +
850A ASP* 5.9 1.4 + - - -
854A GLY* 6.0 4.2 - - - -
930A ASP* 6.2 0.4 - - - +
932A VAL* 6.1 3.8 - - + -
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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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281A MET* 2.8 16.0 + - + +
282A LEU 3.0 9.5 - - - +
284A LYS* 1.3 70.7 - - - +
286A GLU* 1.3 53.0 + - - +
287A VAL* 2.6 27.0 + - - +
331A SER* 4.4 2.7 - - - -
333A LYS* 5.0 0.7 - - - -
334A TYR* 3.6 35.0 - - + -
932A VAL* 4.4 13.2 - - + -
1808A Y01 4.3 22.2 - - + +
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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