Contacts of the helix formed by residues 284 - 293 (chain A) in PDB entry 2FYT
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 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A CYS* 2.8 22.7 + - - -
282A GLY 3.1 2.0 + - - -
283A THR* 1.3 78.9 - - - +
285A ILE* 1.3 65.5 + - - +
286A LEU 3.3 2.7 - - - -
287A SER* 3.2 8.7 + - - -
288A MET* 2.9 29.9 + - - +
310A ALA* 4.4 4.5 - - - -
314A ILE* 4.0 12.6 - - - -
325A LEU* 5.2 0.9 - - - -
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Residues in contact with ILE 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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251A LEU* 3.8 25.4 - - + -
256A ARG* 4.5 2.0 - - - +
257A THR* 4.3 4.9 - - + -
281A CYS 4.0 0.2 + - - -
283A THR* 3.4 13.7 + - - +
284A GLY* 1.3 76.8 - - - +
286A LEU* 1.3 76.1 + - + +
288A MET* 3.3 19.0 + - + +
289A PHE* 3.1 53.2 + - + -
549A SAH 3.3 37.0 - - - +
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Residues in contact with LEU 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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256A ARG* 5.2 3.1 - - - +
257A THR* 5.6 1.3 - - + -
260A TYR* 3.7 55.0 - - + -
264A ILE* 4.2 2.4 - - + +
278A ASP* 3.5 16.7 + - - +
281A CYS 5.0 0.4 + - - -
284A GLY 3.3 0.6 - - - -
285A ILE* 1.3 84.1 - - + +
287A SER* 1.3 58.3 + - - +
289A PHE* 3.3 21.5 + - + +
290A ALA 3.0 23.9 + - - -
344A ILE* 3.7 22.3 - - + +
345A SER* 4.3 5.2 - - - +
346A GLU* 3.9 15.0 - - + +
549A SAH 3.6 29.4 - - - +
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Residues in contact with SER 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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278A ASP* 2.7 36.5 + - - +
281A CYS* 4.1 1.6 - - - +
284A GLY* 3.2 12.3 + - - -
286A LEU* 1.3 77.2 - - - +
288A MET* 1.3 56.6 - - - +
290A ALA* 3.4 5.0 + - - +
291A ALA* 3.0 22.5 + - - +
298A VAL* 3.5 24.0 - - - +
300A GLY* 3.9 10.0 - - - -
323A ILE* 3.5 25.7 - - - +
325A LEU* 5.5 0.7 - - - -
344A ILE* 4.8 0.2 - - - -
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Residues in contact with MET 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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283A THR* 4.6 0.7 - - - +
284A GLY 2.9 22.2 + - - +
285A ILE* 3.9 23.8 - - + +
287A SER* 1.3 76.0 - - - +
289A PHE* 1.3 60.3 + - + +
291A ALA* 3.3 2.2 + - - +
292A LYS* 3.0 35.4 + - + +
313A ILE* 3.5 28.3 - - + +
314A ILE* 3.7 16.8 - - + -
317A ASN* 3.5 31.9 - - - +
319A LEU* 3.7 19.9 - - + +
323A ILE* 3.8 7.9 - - + -
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Residues in contact with PHE 289 (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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257A THR* 4.0 16.2 - - + -
261A ARG* 3.6 52.0 - - + -
264A ILE* 3.4 26.3 - - + +
265A TYR* 3.3 32.1 - + + -
285A ILE* 3.1 49.5 + - + -
286A LEU* 3.4 25.4 - - + +
288A MET* 1.3 74.3 - - + +
290A ALA* 1.3 62.4 + - - +
293A ALA 3.0 17.8 + - - -
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Residues in contact with ALA 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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264A ILE* 3.9 10.3 - - + +
271A PHE* 4.0 21.7 - - + +
276A VAL* 4.3 5.2 - - + -
286A LEU 3.0 13.1 + - - +
287A SER* 3.6 9.4 - - - +
288A MET 3.2 0.4 - - - -
289A PHE* 1.3 75.4 - - - +
291A ALA* 1.3 62.3 + - - +
293A ALA* 3.3 4.5 + - - +
294A GLY 3.2 5.9 + - - -
295A ALA* 3.1 22.8 + - + +
298A VAL* 4.1 13.7 - - + -
344A ILE* 4.3 13.0 - - + -
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Residues in contact with ALA 291 (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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287A SER 3.0 15.8 + - - +
288A MET 3.3 5.4 + - - +
290A ALA* 1.3 75.3 - - - +
292A LYS* 1.3 59.7 + - - +
294A GLY* 2.9 21.3 + - - -
295A ALA* 3.8 11.0 + - - +
298A VAL* 4.3 0.6 - - + +
319A LEU* 4.2 17.7 - - + -
322A THR* 3.9 20.7 - - + +
323A ILE* 3.8 18.2 - - + -
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Residues in contact with LYS 292 (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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265A TYR* 3.6 27.4 - - + +
288A MET* 3.0 22.0 + - + +
289A PHE 3.8 1.6 - - - +
291A ALA* 1.3 75.9 - - - +
293A ALA* 1.3 59.2 + - - +
294A GLY* 3.2 1.8 + - - -
317A ASN* 5.5 4.2 + - - -
319A LEU* 4.3 29.9 - - + +
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Residues in contact with ALA 293 (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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264A ILE* 3.7 32.1 - - + +
265A TYR* 4.5 6.5 - - + -
268A PRO* 3.8 20.5 - - + +
271A PHE* 3.9 11.0 - - + -
272A LYS* 3.8 17.0 + - - +
289A PHE 3.0 15.5 + - - +
290A ALA 3.3 5.4 + - - +
291A ALA 3.2 0.2 - - - -
292A LYS* 1.3 74.4 - - - +
294A GLY* 1.3 58.1 + - - +
295A ALA 3.7 0.4 - - - -
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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