Contacts of the helix formed by residues 868 - 872 (chain A) in PDB entry 6A5T
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 LEU 868 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A ASP 4.7 0.7 - - - +
855A GLY* 3.0 22.4 - - - +
866A GLN* 3.1 3.9 - - - +
867A PHE* 1.3 82.1 - - - +
869A TYR* 1.3 54.7 + - - +
870A GLY 2.8 1.4 + - - -
871A GLU* 2.3 36.9 + - - -
872A ASP* 3.4 28.9 - - - +
873A GLY* 4.1 7.2 - - - +
1001A VAL* 3.8 9.6 - - + -
1002A LEU* 3.6 44.6 - - + -
1012A ALA 5.9 0.2 - - - +
1016A ALA* 4.4 12.6 - - + -
207E TYR* 3.2 16.3 + - + -
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Residues in contact with TYR 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A VAL* 4.3 17.0 - - + -
855A GLY* 3.3 13.9 + - - +
857A THR* 4.0 18.6 + - + +
866A GLN* 3.9 7.6 - - - -
868A LEU* 1.3 70.9 - - + +
870A GLY* 1.3 65.4 + - - +
871A GLU 3.2 0.2 + - - -
872A ASP* 2.7 26.2 + - - +
873A GLY* 4.9 2.0 - - - +
874A LEU 4.7 4.7 - - - -
875A ASP* 5.1 1.8 - - - -
876A GLY 5.2 1.1 + - - -
1060A VAL* 3.4 47.1 - - + -
1066A VAL* 3.3 38.4 - - + +
1369A ARG* 4.0 37.6 + - + +
1370A HIS* 4.5 10.4 + - - -
1373A LEU* 4.6 11.1 - - + +
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Residues in contact with GLY 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A GLN* 2.4 34.4 + - - -
868A LEU 2.8 0.6 + - - -
869A TYR* 1.3 73.7 - - - +
871A GLU* 1.3 67.8 + - - +
872A ASP* 2.9 16.4 + - - +
1368A TYR* 5.1 3.5 - - - -
1369A ARG* 4.2 22.1 + - - +
1372A ALA* 5.0 3.1 - - - -
203E THR* 4.1 9.7 + - - -
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Residues in contact with GLU 871 (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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866A GLN* 5.4 4.2 + - - +
868A LEU* 2.3 30.6 + - - +
870A GLY* 1.3 70.2 - - - +
872A ASP* 1.3 53.7 + - - +
1016A ALA* 4.7 7.1 - - - +
1348A ARG* 3.4 24.7 + - - -
1368A TYR* 4.0 19.1 + - - -
1372A ALA* 5.8 1.0 - - - +
1376A ASP* 5.2 2.1 - - - +
199E ARG* 3.7 5.5 + - - +
201E SER* 3.3 28.9 + - - +
203E THR* 4.7 0.7 - - - +
204E SER* 2.6 32.2 + - - +
207E TYR* 3.2 56.2 - - + -
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Residues in contact with ASP 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A LEU* 3.4 17.7 + - - +
869A TYR 2.7 15.1 - - - +
870A GLY 2.9 5.6 + - - +
871A GLU* 1.3 83.3 - - - +
873A GLY* 1.3 80.6 + - - +
874A LEU* 2.7 39.2 + - + +
1001A VAL* 3.4 15.2 - - - +
1016A ALA* 4.3 6.4 - - - +
1017A THR* 5.4 1.0 - - - +
1369A ARG* 2.5 42.0 + - - -
203E THR* 4.7 6.9 + - - +
204E SER* 4.4 12.1 - - - -
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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