Contacts of the helix formed by residues 285 - 295 (chain A) in PDB entry 4UAL
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 SER 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ALA* 3.9 0.8 - - - +
284A GLU* 1.3 80.6 - - - +
286A LEU* 1.3 66.0 + - - +
287A VAL* 4.0 8.1 + - - +
288A GLU* 2.9 38.6 + - - +
289A THR* 3.0 24.8 + - - -
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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
----------------------------------------------------------
240A PRO* 4.5 14.4 - - + -
285A SER* 1.3 71.5 - - - +
287A VAL* 1.3 63.9 + - + +
289A THR* 3.1 9.4 + - - -
290A TYR* 2.8 87.2 + - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SER* 3.2 7.2 + - - +
286A LEU* 1.3 87.9 - - + +
288A GLU* 1.3 64.2 + - + +
290A TYR* 3.4 6.6 + - + +
291A GLY* 2.9 25.5 + - - -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 3.7 15.7 - - + -
284A GLU* 4.4 9.6 + - - +
285A SER* 2.9 34.1 + - - +
287A VAL* 1.3 84.1 - - + +
289A THR* 1.3 63.2 + - - +
291A GLY* 3.3 2.4 + - - +
292A LYS* 3.1 31.1 + - - +
299A ARG* 5.1 0.3 + - - -
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PRO* 4.3 12.1 - - + +
241A ASP* 4.1 18.3 + - - +
281A PHE* 3.2 28.0 + - + +
283A ALA* 3.3 20.0 + - - +
285A SER 3.0 10.1 + - - -
286A LEU* 3.3 11.8 - - - -
288A GLU* 1.3 73.8 - - - +
290A TYR* 1.3 70.8 + - + +
292A LYS* 3.2 3.8 + - - +
293A ILE* 3.0 38.9 + - + +
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PRO* 3.8 30.5 - - + +
243A ILE* 4.1 8.4 - - + +
248A LEU* 3.8 39.7 - - + -
251A MET* 5.4 8.2 - - + +
286A LEU* 2.8 64.2 + - + +
287A VAL* 3.9 6.1 - - + +
289A THR* 1.3 77.5 - - + +
291A GLY* 1.3 58.1 + - - +
293A ILE* 3.3 3.7 + - + +
294A MET* 2.9 40.9 + - - +
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL 2.9 16.0 + - - -
288A GLU* 3.3 4.0 + - - -
289A THR 3.1 0.4 - - - -
290A TYR* 1.3 76.2 - - - +
292A LYS* 1.3 58.3 + - - +
294A MET* 4.9 2.9 - - - -
295A ASN* 2.7 41.6 + - - +
299A ARG* 4.0 5.4 + - - -
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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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280A PRO 5.2 2.2 - - - +
281A PHE* 3.6 27.9 - - + +
282A TYR 2.7 29.2 + - - +
283A ALA* 3.6 18.3 - - - +
288A GLU* 3.1 14.6 + - - +
289A THR 3.2 5.1 + - - +
291A GLY* 1.3 74.3 - - - +
293A ILE* 1.3 66.9 + - - +
295A ASN 3.4 1.4 - - - -
296A HIS* 3.0 23.7 + - - -
299A ARG* 3.2 39.9 - - + +
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Residues in contact with ILE 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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240A PRO 3.6 24.2 - - - +
241A ASP 4.8 2.0 - - - +
243A ILE* 3.6 30.3 - - + +
245A PRO* 3.6 22.5 - - + +
248A LEU* 3.7 16.4 - - + -
265A TRP* 4.0 4.5 - - + +
281A PHE* 3.5 32.8 - - + -
289A THR* 3.0 26.4 + - + +
290A TYR* 3.6 6.7 - - + +
292A LYS* 1.3 77.7 - - - +
294A MET* 1.3 63.0 + - - +
295A ASN 3.2 0.3 + - - -
296A HIS* 3.1 25.5 + - - +
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Residues in contact with MET 294 (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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245A PRO* 4.7 11.5 - - + +
248A LEU* 3.8 25.1 - - + -
249A GLN* 3.9 39.3 - - + +
252A GLU* 3.6 38.1 - - - +
290A TYR* 2.9 29.6 + - - +
291A GLY* 4.3 3.8 - - - +
293A ILE* 1.3 74.4 - - + +
295A ASN* 1.3 65.4 + - - +
296A HIS* 3.6 7.4 + - - -
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Residues in contact with ASN 295 (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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291A GLY* 2.7 32.3 + - - +
292A LYS 3.4 3.6 - - - -
293A ILE 3.1 0.4 - - - -
294A MET* 1.3 84.4 - - - +
296A HIS* 1.3 62.9 + - - -
297A GLU* 3.1 4.7 + - - +
298A GLU* 3.3 7.5 + - + -
299A ARG* 2.9 41.8 + - + +
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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