Contacts of the helix formed by residues 277 - 284 (chain A) in PDB entry 3K5M
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 GLY 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLY 3.1 14.1 + - - -
223A TRP* 4.0 13.7 - - - -
275A ILE 3.5 2.4 + - - -
276A ASP* 1.3 72.1 + - - +
278A ILE* 1.3 65.8 + - - +
280A ALA* 3.9 2.4 - - - +
281A LEU* 2.9 31.1 + - - +
343A PHE* 3.8 26.7 - - - -
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A TRP* 3.5 43.2 - - + +
224A ASN* 4.7 14.1 - - + +
276A ASP* 3.2 16.1 + - - +
277A GLY* 1.3 76.6 - - - +
279A GLU* 1.3 66.6 + - + +
281A LEU* 3.8 1.2 - - - +
282A LYS* 3.0 55.1 + - + +
291A PHE* 3.7 24.4 - - + +
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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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226A VAL* 5.6 4.3 - - - +
227A GLN* 6.0 1.4 - - - +
276A ASP* 3.1 30.4 + - + +
278A ILE* 1.3 78.7 - - + +
280A ALA* 1.3 58.5 + - - +
282A LYS* 3.2 8.7 + - + +
283A SER* 2.7 31.4 + - - -
366A HIS* 3.7 26.4 + - + +
800T G 5.7 3.1 + - - -
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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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275A ILE* 3.9 19.3 - - + -
276A ASP 3.0 17.5 + - - +
277A GLY* 3.9 6.3 - - - +
279A GLU* 1.3 77.1 - - - +
281A LEU* 1.3 63.6 + - - +
283A SER* 2.6 21.5 + - - -
284A ALA 3.1 4.3 + - - -
343A PHE* 5.3 0.2 - - + -
348A ILE* 3.5 29.3 - - + +
352A LEU* 4.2 6.5 - - + -
366A HIS* 3.7 14.2 - - - +
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Residues in contact with LEU 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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223A TRP* 3.8 25.4 - - + -
277A GLY* 2.9 22.0 + - - +
278A ILE 3.8 2.7 - - - +
280A ALA* 1.3 76.0 - - + +
282A LYS* 1.3 65.0 + - - +
284A ALA 3.0 9.0 + - - -
286A TRP* 3.0 41.1 + - + -
288A PHE* 4.3 15.5 - - + -
291A PHE* 4.0 10.8 - - + -
296A VAL* 4.7 0.9 - - + -
342A ILE* 4.1 15.9 - - + -
343A PHE* 6.2 1.1 - - + -
346A THR* 3.8 32.1 - - + +
348A ILE* 4.0 20.6 - - + -
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Residues in contact with LYS 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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278A ILE* 3.0 44.5 + - + +
279A GLU* 3.6 7.9 - - + +
281A LEU* 1.3 75.5 - - - +
283A SER* 1.3 57.9 + - - +
285A PHE* 2.9 23.7 + - - -
286A TRP 4.3 7.4 - - - +
291A PHE* 3.4 37.3 - - + +
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Residues in contact with SER 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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279A GLU 2.7 15.1 + - - -
280A ALA* 2.6 17.5 + - - -
282A LYS* 1.3 78.3 - - - +
284A ALA* 1.3 55.0 + - - +
285A PHE* 3.1 22.6 + - - -
351A PHE* 3.9 9.5 - - - -
352A LEU* 3.9 11.6 - - - +
355A ARG* 6.0 1.5 - - - -
366A HIS* 3.4 34.3 + - - -
491A ALA* 5.0 0.3 - - - +
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Residues in contact with ALA 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 ALA 3.1 0.4 + - - +
281A LEU 3.0 2.8 + - - -
283A SER* 1.3 76.3 + - - +
285A PHE* 1.3 77.1 + - - +
286A TRP* 3.3 26.5 + - + +
348A ILE* 3.8 11.9 - - + -
351A PHE* 3.4 42.6 - - + -
487A PRO* 3.7 13.4 - - + +
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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