Contacts of the helix formed by residues 278 - 290 (chain A) in PDB entry 5FA5
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 CYS 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 3.0 40.9 - - - +
38A PHE* 5.5 0.2 - - - -
276A GLU* 3.4 38.8 - - - -
277A PHE* 1.3 74.6 - - - +
279A SER* 1.4 52.0 + - - +
280A TYR 3.2 0.9 - - - -
281A LEU* 2.9 14.8 + - + +
282A GLN* 2.7 44.5 + - + +
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 5.4 6.1 - - - -
244A PRO* 3.4 30.4 - - - +
272A HIS* 4.9 2.1 - - - +
275A LYS* 4.5 11.4 - - - +
276A GLU* 2.9 23.3 + - - -
277A PHE 4.2 1.2 + - - -
278A CYS* 1.4 77.8 - - - +
280A TYR* 1.4 62.1 + - - +
282A GLN* 3.2 19.2 + - - +
283A TYR* 2.9 30.3 + - - +
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 5.9 0.4 - - + -
233A THR* 3.6 40.7 - - + -
236A PHE* 3.8 25.8 - + + -
244A PRO* 3.6 26.9 - - + +
266A ILE* 4.3 21.3 - - + -
270A ASN* 3.3 18.4 - - - -
271A HIS* 3.0 22.3 + - - +
272A HIS* 2.8 25.9 + + + -
277A PHE* 3.3 38.1 - + + +
278A CYS 3.2 0.4 - - - -
279A SER* 1.4 81.5 + - - +
281A LEU* 1.3 61.3 + - - +
283A TYR* 3.5 5.2 + - - +
284A LEU* 3.4 23.9 + - - +
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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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14A VAL* 4.8 3.7 - - + +
16A SER* 3.4 33.4 - - - +
36A GLN 3.5 23.1 - - - +
37A GLY* 3.6 24.2 - - - +
38A PHE* 3.6 23.8 - - + +
266A ILE* 3.6 20.6 - - + -
277A PHE 4.5 0.2 + - - -
278A CYS* 2.9 16.2 + - + +
280A TYR* 1.3 76.5 - - - +
282A GLN* 1.4 56.6 + - + +
284A LEU* 3.1 9.1 + - + +
285A GLU* 3.0 33.6 + - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 4.5 8.5 + - - +
278A CYS* 2.7 32.9 + - + +
279A SER* 3.4 24.1 + - - +
281A LEU* 1.4 72.3 - - + +
283A TYR* 1.3 58.0 + - - +
285A GLU* 3.3 8.6 + - - +
286A TYR* 3.0 29.0 + - - +
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PHE* 4.0 19.3 - + + -
244A PRO 3.6 20.0 - - - +
245A VAL* 3.6 20.9 - - + +
246A LEU* 3.2 33.5 + - + -
251A GLN* 3.2 33.3 + - - -
279A SER 2.9 15.6 + - - +
280A TYR* 3.6 7.2 - - - +
281A LEU 3.2 0.2 - - - -
282A GLN* 1.3 77.2 - - - +
284A LEU* 1.3 56.8 + - + +
286A TYR* 3.3 28.9 + + - +
287A LEU* 3.1 53.2 + - + +
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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
----------------------------------------------------------
14A VAL* 4.0 15.9 - - + +
16A SER* 4.5 5.8 - - - +
231A LEU* 3.8 27.1 - - + -
236A PHE* 4.8 4.0 - - + -
246A LEU* 4.6 13.9 - - + -
254A ILE* 4.4 20.5 - - + +
258A LEU* 5.2 1.9 - - - +
264A PHE* 3.7 34.5 - - + -
266A ILE* 4.1 18.6 - - + -
280A TYR 3.4 10.9 + - - +
281A LEU* 3.1 10.5 + - + +
283A TYR* 1.3 76.3 - - + +
285A GLU* 1.4 58.6 + - - +
287A LEU* 3.6 6.9 + - + +
288A SER* 3.0 28.6 + - - -
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Residues in contact with GLU 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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13A ARG* 3.4 34.0 + - - +
14A VAL* 3.2 34.4 + - + +
281A LEU* 3.0 20.2 + - + +
282A GLN* 3.3 11.4 + - - +
284A LEU* 1.4 72.1 - - - +
286A TYR* 1.3 55.2 + - - +
288A SER* 3.2 5.8 + - - -
289A GLN* 2.8 52.8 + - + +
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Residues in contact with TYR 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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251A GLN* 6.0 0.2 - - - -
282A GLN 3.0 12.9 + - - +
283A TYR* 3.3 30.5 - + - +
285A GLU* 1.3 74.3 - - - +
287A LEU* 1.4 78.2 + - + +
289A GLN* 3.2 5.6 + - - -
290A ASN* 2.9 65.0 + - + +
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Residues in contact with LEU 287 (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 LEU* 4.3 1.8 - - + -
251A GLN* 4.1 26.9 - - + +
254A ILE* 3.9 37.2 - - + -
255A PHE* 3.2 38.1 - - + -
258A LEU* 4.6 0.2 - - - -
283A TYR* 3.1 56.3 + - + +
284A LEU* 3.8 9.2 - - + +
285A GLU 3.4 0.2 - - - -
286A TYR* 1.4 88.6 - - + +
288A SER* 1.4 57.1 + - - +
290A ASN* 3.0 19.0 + - + -
291A ARG 3.4 0.2 + - - -
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Residues in contact with SER 288 (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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13A ARG 3.9 12.0 + - - -
14A VAL* 3.7 19.6 - - - +
258A LEU* 4.0 15.6 - - - +
284A LEU 3.0 15.5 + - - -
285A GLU* 3.2 11.2 + - - -
287A LEU* 1.4 75.7 - - - +
289A GLN* 1.3 66.4 + - - +
291A ARG* 3.1 45.0 + - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.9 9.9 + - - +
285A GLU* 2.8 43.3 + - + +
286A TYR* 3.8 5.8 - - - +
288A SER* 1.3 81.5 + - - +
290A ASN* 1.3 64.0 + - - +
291A ARG* 3.4 8.3 + - - +
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Residues in contact with ASN 290 (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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255A PHE* 3.7 13.2 - - + -
286A TYR* 2.9 61.9 + - + +
287A LEU* 3.0 12.4 + - + +
289A GLN* 1.3 82.5 - - - +
291A ARG* 1.3 57.3 + - - +
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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