Contacts of the helix formed by residues 274 - 281 (chain A) in PDB entry 5KFR
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 TYR 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A PHE 3.8 4.7 - - - +
248A SER 3.6 25.6 - - - +
249A GLN* 3.4 35.0 + - + -
250A MET 3.2 9.9 - - - +
251A PRO* 3.9 9.2 - - + -
252A ILE* 3.7 10.7 - - - +
273A GLU* 1.3 108.9 + - + +
275A MET* 1.3 67.1 + - - +
276A GLY 3.2 1.3 - - - +
277A GLU* 3.0 43.4 + - + +
278A LEU 4.1 1.2 + - - -
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Residues in contact with MET 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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247A PHE* 3.6 36.8 + - + +
250A MET* 2.8 19.7 + - + +
252A ILE* 3.7 12.8 - - - +
255A ILE* 3.8 23.1 - - + -
258A LEU* 4.0 24.0 - - + -
274A TYR* 1.3 71.3 - - - +
276A GLY* 1.3 62.6 + - - +
278A LEU* 3.1 46.9 + - + +
298A LEU* 4.5 3.4 - - + -
301A MET* 3.9 33.7 - - + -
302A CYS* 3.6 11.1 - - - +
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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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247A PHE* 2.9 20.0 + - - -
274A TYR* 3.2 0.8 + - - +
275A MET* 1.3 77.1 - - - +
277A GLU* 1.3 60.5 + - - +
278A LEU 3.0 1.4 + - - -
279A THR* 3.1 28.2 + - - +
302A CYS 5.1 0.7 - - - -
503A GOL 3.1 40.1 + - - -
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Residues in contact with GLU 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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248A SER 5.7 0.7 - - - +
271A GLY 4.7 1.6 - - - +
272A ILE* 3.6 33.2 - - + +
273A GLU* 2.9 24.1 + - - +
274A TYR* 3.0 36.7 + - + +
276A GLY* 1.3 77.4 - - - +
278A LEU* 1.3 61.6 + - - +
279A THR 3.2 0.7 + - - -
280A GLN* 3.5 15.9 + - - +
281A PHE* 3.6 12.8 - - - -
503A GOL 3.6 5.8 + - - +
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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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252A ILE* 4.9 2.2 - - + -
258A LEU* 5.5 0.4 - - + -
266A VAL* 3.9 11.2 - - + -
270A LEU* 3.7 20.0 - - + -
272A ILE* 3.7 23.1 - - + -
274A TYR 4.9 0.2 - - - +
275A MET* 3.1 48.9 + - + +
276A GLY 3.0 1.6 - - - -
277A GLU* 1.3 74.4 - - - +
279A THR* 1.3 62.1 + - - +
280A GLN 3.0 7.0 + - - -
281A PHE* 3.2 22.7 + - - +
286A LEU* 4.1 21.7 - - + +
298A LEU* 3.9 22.2 - - + +
302A CYS* 3.5 17.9 - - + -
303A ARG* 4.8 0.3 + - - -
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Residues in contact with THR 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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276A GLY 3.1 17.5 + - - +
278A LEU* 1.3 77.6 - - - +
280A GLN* 1.3 77.0 + - - +
281A PHE 3.2 3.9 + - - +
302A CYS* 3.7 34.8 - - + +
303A ARG* 3.0 38.6 + - + +
503A GOL 4.2 19.8 - - - +
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Residues in contact with GLN 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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277A GLU* 3.5 12.8 + - - +
278A LEU 3.0 1.6 + - - -
279A THR* 1.3 106.8 + - - +
281A PHE* 1.3 70.1 + - + +
282A THR* 5.6 0.7 - - - +
285A GLN* 4.2 2.8 - - - +
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Residues in contact with PHE 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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270A LEU* 3.8 54.5 - - + -
272A ILE* 4.2 12.6 - - + -
277A GLU 3.6 17.7 - - - -
278A LEU* 3.2 21.4 + - - +
279A THR 3.2 6.9 - - - +
280A GLN* 1.3 88.6 - - + +
282A THR* 1.3 64.5 + - - +
285A GLN* 3.2 26.5 - - + +
286A LEU* 3.8 24.0 - - + +
289A HIS* 6.1 0.2 - - - -
299A TYR* 3.7 17.0 - - - -
303A ARG* 4.5 0.2 + - - -
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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