Contacts of the helix formed by residues 922 - 927 (chain A) in PDB entry 5UAK
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 VAL 922 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A GLY* 4.1 22.0 - - - +
315A PHE* 4.3 5.2 - - + +
340A ILE* 3.7 41.1 - - + -
344A ILE* 5.1 7.0 - - + -
918A ILE* 2.8 27.0 + - + +
919A TYR* 3.0 17.3 - - - +
920A VAL 4.1 0.4 - - - -
921A GLY* 1.3 67.8 - - - +
923A ALA* 1.3 62.0 + - - +
924A ASP* 4.1 12.3 - - + -
925A THR* 3.4 25.9 + - - +
926A LEU 3.3 9.4 + - - -
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Residues in contact with ALA 923 (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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920A VAL 4.4 6.5 - - - +
921A GLY 3.1 10.5 + - - +
922A VAL* 1.3 69.8 - - - +
924A ASP* 1.3 60.7 + - - +
925A THR 3.2 0.2 - - - -
926A LEU* 4.3 4.9 - - + -
927A LEU* 2.8 57.1 + - + +
1000A ILE* 4.1 11.1 - - + +
1004A ALA* 4.7 11.2 - - + -
1135A LEU* 4.7 11.7 - - + -
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Residues in contact with ASP 924 (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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310A PHE* 5.8 0.2 - - - -
311A PHE* 2.9 50.0 - - - +
314A GLY* 4.5 3.7 + - - -
344A ILE* 5.9 5.6 - - + +
347A ARG* 2.7 35.8 + - - -
922A VAL* 3.2 13.2 - - + -
923A ALA* 1.3 79.2 - - - +
925A THR* 1.3 55.7 + - - +
927A LEU 4.4 0.2 - - - +
928A ALA* 3.2 19.7 - - - +
996A GLN* 4.6 0.5 + - - -
1000A ILE* 3.6 21.1 - - + +
1142A THR* 5.1 4.3 - - - +
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Residues in contact with THR 925 (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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311A PHE 3.7 6.2 + - - -
312A PHE* 3.6 38.6 + - + +
314A GLY 3.9 0.2 - - - -
315A PHE* 3.1 45.6 + - + +
316A PHE* 5.7 1.8 - - + -
919A TYR* 4.2 19.6 + - + -
922A VAL* 3.4 12.6 + - - +
923A ALA 3.2 0.2 - - - -
924A ASP* 1.3 79.2 - - - +
926A LEU* 1.3 66.0 + - - +
927A LEU 3.6 0.2 - - - -
928A ALA* 3.7 14.6 + - - +
933A ARG* 5.2 1.7 + - - -
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Residues in contact with LEU 926 (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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873A GLU* 3.2 44.1 - - + +
877A SER* 3.6 23.8 - - - +
919A TYR* 3.5 53.1 + - + +
920A VAL* 4.4 15.5 - - + +
922A VAL 3.3 7.1 + - - +
923A ALA* 4.3 4.0 - - + +
925A THR* 1.3 80.2 - - - +
927A LEU* 1.3 85.4 + - + +
928A ALA 3.1 8.0 + - - +
933A ARG* 4.9 1.7 + - - -
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Residues in contact with LEU 927 (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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870A PHE* 3.8 30.5 - - + +
873A GLU* 5.1 4.0 - - + -
874A VAL* 4.4 22.9 - - + +
923A ALA* 2.8 30.9 + - + +
924A ASP 4.4 0.2 - - - +
926A LEU* 1.3 94.1 - - + +
928A ALA* 1.3 61.1 + - - +
996A GLN* 3.5 9.4 + - - -
999A LEU* 5.4 2.4 - - - +
1000A ILE* 3.8 28.1 + - - +
1003A GLY* 3.5 10.3 - - - +
1004A ALA* 3.5 32.1 - - - +
1007A VAL* 5.5 4.3 - - + -
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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