Contacts of the helix formed by residues 862 - 873 (chain A) in PDB entry 1R4X
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 GLU 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783A PHE* 3.9 3.6 - - - -
834A PHE* 3.6 25.4 - - - -
835A ARG 4.4 5.2 - - - +
836A GLY* 5.4 0.9 - - - -
838A HIS* 3.1 35.9 - - + +
860A SER* 3.2 24.5 + - - +
861A LEU* 1.3 81.1 - - - +
863A GLU* 1.3 67.6 + - - +
864A LEU* 3.4 13.1 - - + +
865A PRO* 3.3 21.6 - - + +
866A VAL* 4.1 2.4 - - - +
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Residues in contact with GLU 863 (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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783A PHE* 3.6 47.0 - - + -
785A LYS* 2.8 31.1 + - - +
862A GLU* 1.3 73.3 - - - +
864A LEU* 1.3 64.6 + - - +
866A VAL* 3.1 7.0 + - + +
867A ASP* 3.1 32.0 + - - +
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Residues in contact with LEU 864 (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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717A PRO* 3.7 48.5 - - + +
718A THR* 4.1 10.3 - - + -
834A PHE* 3.8 23.1 - - + -
835A ARG* 4.6 10.3 - - - +
862A GLU* 4.1 12.2 - - + +
863A GLU* 1.3 78.0 - - - +
865A PRO* 1.3 62.8 - - + +
867A ASP* 3.2 7.9 + - + +
868A ILE* 2.9 39.5 + - + +
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Residues in contact with PRO 865 (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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764A ILE* 6.3 0.7 - - + -
834A PHE* 3.7 39.0 - - + -
838A HIS* 5.7 0.2 - - + -
840A ILE* 4.0 16.6 - - + -
860A SER* 3.6 13.7 - - - +
862A GLU* 3.3 33.9 - - + +
864A LEU* 1.3 91.4 - - + +
866A VAL* 1.3 58.0 + - - +
868A ILE* 3.3 12.6 + - + +
869A ILE* 2.9 33.8 + - - +
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Residues in contact with VAL 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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783A PHE* 3.4 28.7 - - + +
785A LYS* 3.7 32.3 - - + -
840A ILE* 4.2 5.2 - - + -
858A ALA* 3.9 19.5 - - + +
859A ARG 3.8 6.5 - - - -
860A SER* 3.7 32.1 - - - +
862A GLU 4.1 4.3 - - - +
863A GLU* 3.1 9.9 + - - +
865A PRO* 1.3 77.2 - - - +
867A ASP* 1.3 64.9 + - - +
869A ILE* 3.3 2.1 + - - +
870A LEU* 3.2 23.9 + - + +
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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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718A THR* 4.0 19.4 - - + +
785A LYS* 2.7 41.1 + - - +
863A GLU* 3.1 21.8 + - - +
864A LEU* 3.2 10.5 + - - +
866A VAL* 1.3 76.0 - - - +
868A ILE* 1.3 63.4 + - - +
870A LEU* 3.4 4.9 + - - +
871A ALA* 3.0 27.3 + - - +
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Residues in contact with ILE 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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717A PRO 3.9 3.1 - - - +
718A THR* 3.8 24.7 - - - +
720A VAL* 3.8 25.8 - - + -
760A VAL* 3.6 27.4 - - + -
763A HIS* 6.0 0.7 - - + -
764A ILE* 5.6 1.8 - - + -
834A PHE* 3.6 37.0 - - + -
835A ARG* 4.6 0.2 - - - +
864A LEU* 2.9 30.6 + - + +
865A PRO* 3.6 5.8 - - + +
867A ASP* 1.3 73.8 - - - +
869A ILE* 1.3 68.6 + - + +
871A ALA* 3.3 4.8 + - - +
872A SER* 2.8 33.1 + - - +
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Residues in contact with ILE 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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760A VAL* 4.5 3.8 - - + -
764A ILE* 3.9 25.8 - - + -
808A LEU* 3.8 22.7 - - + -
810A MET* 4.1 12.8 - - - -
840A ILE* 3.9 18.6 - - + -
842A VAL* 3.8 28.5 - - + -
856A VAL* 4.5 9.9 - - + -
858A ALA* 4.3 9.4 - - + -
865A PRO 2.9 21.5 + - - +
866A VAL 3.3 4.5 + - - +
868A ILE* 1.3 77.1 - - + +
870A LEU* 1.3 59.7 + - + +
872A SER* 3.1 3.5 + - - -
873A VAL* 2.9 38.6 + - + +
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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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785A LYS* 3.5 44.9 - - + +
786A GLU 4.2 7.4 - - - +
787A GLU* 4.0 25.7 - - + +
789A PHE* 3.4 26.1 - - + -
856A VAL* 3.8 41.5 - - + +
858A ALA* 4.9 4.3 - - + -
866A VAL* 3.2 17.0 + - + +
867A ASP* 4.0 4.9 - - - +
869A ILE* 1.3 80.7 - - + +
871A ALA* 1.3 60.4 + - - +
872A SER 3.6 0.2 + - - -
873A VAL* 3.9 3.2 + - - -
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Residues in contact with ALA 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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718A THR* 4.6 19.1 - - + +
867A ASP 3.0 18.0 + - - +
868A ILE* 3.8 5.6 - - - +
870A LEU* 1.3 77.0 - - - +
872A SER* 1.3 62.9 + - - +
873A VAL 4.5 2.3 - - - -
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Residues in contact with SER 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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718A THR 5.1 1.9 + - - -
720A VAL* 4.1 7.8 - - - +
760A VAL* 3.9 21.7 - - - +
807A PHE* 3.3 35.8 - - - -
808A LEU* 4.8 1.6 - - - -
868A ILE* 2.8 28.6 + - - +
869A ILE* 3.7 3.8 - - - -
871A ALA* 1.3 78.7 - - - +
873A VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 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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789A PHE* 3.7 44.2 - - + -
804A ILE* 5.3 7.0 - - + -
807A PHE* 4.5 6.1 - - + -
808A LEU* 4.1 32.8 - - + -
854A MET* 3.5 31.1 - - + +
856A VAL* 4.3 8.5 - - + -
869A ILE* 2.9 24.3 + - + +
870A LEU* 3.9 2.7 + - - -
871A ALA 3.5 3.1 - - - -
872A SER* 1.3 81.8 - - - +
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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