Contacts of the helix formed by residues 868 - 876 (chain A) in PDB entry 5WRZ
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 ASN 868 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767A ASN* 3.0 42.8 + - - +
770A ASP* 3.6 31.6 - - - +
771A ILE* 4.8 1.0 - - - +
864A SER* 2.7 26.2 + - - +
865A ARG* 2.9 23.7 + - - +
867A THR* 1.3 84.2 + - - +
869A PHE* 1.3 59.1 + - - +
870A ALA 3.3 2.2 - - - -
871A GLY* 3.2 7.6 + - - -
872A ILE* 3.0 29.9 + - + +
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Residues in contact with PHE 869 (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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676A ILE* 3.9 17.9 - - + -
862A HIS 4.7 0.7 - - - -
864A SER* 3.5 39.0 - - - -
865A ARG 3.4 16.2 - - - -
866A THR* 3.1 13.5 + - - +
867A THR 3.4 0.4 - - - -
868A ASN* 1.3 76.4 - - - +
870A ALA* 1.3 61.0 + - - +
872A ILE* 3.8 11.8 - - + +
873A LEU* 2.8 43.8 + - + +
918A LEU* 3.7 36.1 - - + -
919A ILE* 4.2 0.9 - - - -
920A LEU* 3.6 28.9 - - + -
1002A LEU* 3.4 32.1 - - + -
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Residues in contact with ALA 870 (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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676A ILE* 4.2 20.5 + - + +
677A PHE* 4.0 24.5 - - + -
774A ALA* 3.6 27.6 - - + -
777A LEU* 4.5 3.5 - - + +
797A LEU* 4.0 12.8 - - + +
867A THR 5.0 1.0 + - - +
868A ASN 3.3 0.6 - - - -
869A PHE* 1.3 77.1 - - - +
871A GLY* 1.3 53.7 + - - +
873A LEU 3.5 0.2 + - - -
874A SER* 2.8 37.9 + - - -
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Residues in contact with GLY 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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770A ASP* 4.2 22.4 + - - -
773A VAL* 4.0 18.7 - - - +
868A ASN 3.2 8.7 + - - -
870A ALA* 1.3 77.5 - - - +
872A ILE* 1.3 64.6 + - - +
874A SER* 3.8 4.9 - - - -
875A GLN* 2.9 30.6 + - - +
876A GLY 4.1 0.4 - - - +
878A ARG* 5.3 0.2 - - - -
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Residues in contact with ILE 872 (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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770A ASP* 4.4 9.6 + - - +
841A ARG* 3.6 1.6 - - - -
862A HIS* 4.9 0.4 - - - +
864A SER* 3.9 29.2 - - - +
868A ASN* 3.0 29.3 + - + +
869A PHE* 3.3 19.0 + - + +
871A GLY* 1.3 74.9 - - - +
873A LEU* 1.3 62.9 + - + +
876A GLY* 2.6 39.8 + - - +
877A LEU* 3.8 27.6 - - + -
920A LEU* 3.7 24.9 - - + -
999A LEU* 4.1 11.8 - - + +
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Residues in contact with LEU 873 (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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672A LEU* 5.3 1.8 - - + -
676A ILE* 4.4 11.0 - - + -
797A LEU* 3.3 29.5 - - + +
799A THR* 2.9 29.6 + - + +
801A ILE* 4.6 11.7 - - + -
839A ILE* 4.3 24.9 - - + -
841A ARG* 2.7 24.7 - - + +
869A PHE* 2.8 31.6 + - + +
871A GLY 3.3 0.2 - - - -
872A ILE* 1.3 84.5 - - + +
874A SER* 1.3 56.1 + - - +
920A LEU* 4.7 8.7 - - + -
999A LEU* 4.8 4.5 - - + -
1002A LEU* 4.3 20.6 - - + -
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Residues in contact with SER 874 (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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773A VAL* 3.7 11.4 - - - +
777A LEU* 3.6 26.5 - - - +
796A LYS 4.2 7.9 - - - -
797A LEU* 3.5 16.7 + - - +
798A LYS* 5.5 3.7 - - - +
841A ARG* 3.0 14.5 + - - -
870A ALA 2.8 22.9 + - - -
871A GLY 3.5 2.9 + - - -
873A LEU* 1.3 78.7 - - - +
875A GLN* 1.3 71.4 + - - +
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Residues in contact with GLN 875 (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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773A VAL* 4.3 17.1 - - + +
777A LEU* 5.6 4.4 - - - +
841A ARG* 3.3 12.8 + - - +
847A ARG* 4.5 7.1 + - - -
871A GLY 2.9 16.6 + - - +
874A SER* 1.3 95.2 + - - +
876A GLY* 1.3 62.3 + - - +
877A LEU 4.6 0.3 - - - +
878A ARG* 3.9 44.9 + - - +
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Residues in contact with GLY 876 (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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841A ARG* 3.2 26.5 - - - -
844A GLU* 4.4 2.9 - - - -
847A ARG* 5.0 1.1 - - - -
871A GLY 4.1 0.3 - - - +
872A ILE* 2.6 37.2 + - - +
875A GLN* 1.3 77.4 - - - +
877A LEU* 1.3 65.4 + - - -
878A ARG* 3.6 9.5 + - - +
999A LEU* 4.6 2.7 - - - -
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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