Contacts of the helix formed by residues 865 - 876 (chain A) in PDB entry 5ZR1
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 865 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A THR* 3.4 6.3 - - - +
863A ILE 3.4 0.2 + - - -
864A ILE* 1.3 85.2 + - - +
866A TRP* 1.3 61.3 + - - +
867A ASP* 3.6 6.0 + - - -
868A PHE* 3.8 14.6 - - - -
869A VAL* 3.2 23.9 + - - +
330D THR* 2.9 27.0 + - - -
331D PHE* 3.5 41.5 - - - -
372D LEU* 5.8 1.8 - - - +
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Residues in contact with TRP 866 (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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804A PHE* 3.6 28.2 - + - -
822A LEU* 3.7 44.9 - - + -
826A VAL* 3.9 22.3 - - + +
829A ILE* 4.7 5.6 - - + +
862A ARG* 3.8 40.4 - - + -
863A ILE* 3.2 37.7 + - + +
865A SER* 1.3 75.8 - - - +
867A ASP* 1.3 71.3 + - + +
868A PHE 3.2 0.2 - - - -
869A VAL* 3.9 3.3 - - + +
870A LEU* 3.2 40.8 + - + +
887A ASP* 4.6 13.7 - - + -
177E GLN* 5.3 7.6 - - - -
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Residues in contact with ASP 867 (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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865A SER* 4.1 5.5 + - - -
866A TRP* 1.3 88.3 + - + +
868A PHE* 1.3 70.2 + - - +
870A LEU* 4.1 4.0 - - - -
871A ASN* 2.6 33.5 + - - +
331D PHE* 5.5 1.4 - - - -
177E GLN* 3.3 50.2 + - + +
180E SER* 3.5 13.8 + - - +
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Residues in contact with PHE 868 (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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865A SER* 3.8 17.5 - - - -
866A TRP 3.2 0.8 - - - -
867A ASP* 1.3 84.4 + - - +
869A VAL* 1.3 66.8 + - + +
871A ASN 3.4 1.2 + - - -
872A GLN* 2.8 43.6 + - + +
104D ARG 5.7 3.8 - - - -
331D PHE* 3.5 50.5 - + + -
333D SER* 3.7 23.1 - - - -
336D THR* 4.2 3.6 - - + -
180E SER* 3.6 25.4 - - - -
181E THR* 3.5 33.9 - - + +
183E CYS* 3.8 16.2 - - - -
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Residues in contact with VAL 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A SER* 5.0 1.3 - - - +
800A THR* 3.7 30.3 - - + +
801A ALA* 4.0 25.6 - - + +
804A PHE* 4.7 14.4 - - + -
863A ILE* 5.7 0.4 - - + -
865A SER* 3.2 22.2 + - - +
866A TRP* 3.9 8.5 - - + +
868A PHE* 1.3 80.0 - - + +
870A LEU* 1.3 67.3 + - - +
872A GLN* 3.6 14.9 - - - +
873A LEU* 3.2 30.1 + - + +
330D THR 3.9 14.1 - - - +
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Residues in contact with LEU 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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804A PHE* 3.6 29.8 - - + -
822A LEU* 4.3 11.2 - - + -
866A TRP* 3.2 41.7 + - + +
867A ASP* 4.5 3.8 - - - +
868A PHE 3.3 0.2 - - - -
869A VAL* 1.3 78.3 - - - +
871A ASN* 1.3 69.4 + - - +
873A LEU* 3.6 3.1 + - - +
874A LEU* 3.2 40.0 + - + +
879A LEU* 3.8 14.8 - - + -
881A LYS* 3.8 31.9 - - + -
892A VAL* 4.8 2.0 - - + -
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Residues in contact with ASN 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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867A ASP* 2.6 24.6 + - - +
868A PHE 3.4 1.0 + - - -
870A LEU* 1.3 85.3 - - - +
872A GLN* 1.3 60.6 + - - +
874A LEU* 3.9 12.2 - - - +
875A ASP* 3.0 36.9 + - - +
881A LYS* 5.8 0.7 - - - -
177E GLN 2.4 31.9 + - - +
178E ARG* 4.2 16.4 - - - +
180E SER* 4.0 5.5 - - - -
181E THR* 3.8 19.1 - - + +
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Residues in contact with GLN 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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793A PHE* 4.7 7.2 - - + -
797A LEU* 3.7 24.9 - - - +
798A SER* 5.1 2.4 + - - +
801A ALA* 4.4 8.4 - - - +
868A PHE* 2.8 31.9 + - + +
869A VAL* 3.8 23.0 - - - +
870A LEU 3.3 0.4 - - - -
871A ASN* 1.3 78.1 - - - +
873A LEU* 1.3 58.9 + - + +
875A ASP* 3.7 4.0 + - - +
876A ALA* 3.3 26.0 + - - +
103D PRO* 4.6 26.7 - - + +
277D GLN* 5.0 2.2 - - - +
331D PHE 4.7 6.1 + - - +
332D ARG 5.8 1.6 + - - -
181E THR* 4.1 9.9 - - + -
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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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793A PHE* 5.0 2.7 - - + -
794A MET* 5.7 0.2 - - + -
797A LEU* 3.9 28.7 - - + -
801A ALA* 4.4 11.4 - - + +
804A PHE* 3.8 22.7 - - + -
805A ILE* 3.8 29.6 - - + -
869A VAL 3.2 17.9 + - - +
870A LEU 4.2 0.2 - - - +
872A GLN* 1.3 79.9 - - + +
874A LEU* 1.3 63.6 + - - +
876A ALA* 3.7 2.4 + - - -
877A GLY 3.5 1.2 + - - -
878A ILE* 3.3 34.6 + - + +
879A LEU* 3.1 40.8 + - + -
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Residues in contact with LEU 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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870A LEU* 3.2 33.4 + - + +
871A ASN* 4.1 11.2 - - - +
872A GLN 3.4 0.2 - - - -
873A LEU* 1.3 76.1 - - - +
875A ASP* 1.3 67.0 + - - +
877A GLY* 3.4 6.4 + - - -
879A LEU* 3.7 40.9 - - + +
881A LYS* 3.7 50.0 - - + +
253D LYS* 3.3 15.9 + - - -
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Residues in contact with ASP 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ASN* 3.0 24.7 + - - +
872A GLN* 4.1 4.4 - - - +
873A LEU 3.4 0.2 - - - -
874A LEU* 1.3 78.0 - - - +
876A ALA* 1.3 63.0 + - - +
104D ARG* 3.8 28.6 + - + +
252D THR* 3.4 29.8 - - + +
253D LYS* 3.4 21.5 + - - +
181E THR* 3.1 23.9 + - - +
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Residues in contact with ALA 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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793A PHE* 3.9 30.3 - - + -
872A GLN 3.3 16.5 + - - +
873A LEU* 4.1 5.4 - - - +
874A LEU 3.3 0.6 - - - -
875A ASP* 1.3 78.7 - - - +
877A GLY* 1.3 59.2 + - - +
878A ILE* 3.6 10.4 + - + -
103D PRO* 6.4 0.9 - - + -
252D THR* 3.8 13.4 - - + +
253D LYS* 4.1 1.3 - - - -
254D LEU* 3.0 36.1 + - + +
255D ASN* 4.8 0.3 - - - +
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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