Contacts of the helix formed by residues 872 - 878 (chain A) in PDB entry 6M0X
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 PHE 872 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A ILE* 4.1 18.4 - - + -
861A PHE* 3.4 58.3 - + - -
864A ILE* 3.7 25.8 - - + -
865A TYR* 4.1 11.0 - - + -
869A LYS* 3.1 20.7 + - - +
870A SER 3.4 6.1 - - - +
871A LYS* 1.3 78.6 - - - +
873A LEU* 1.3 64.0 + - - +
874A MET* 3.3 4.2 + - + +
875A TYR* 3.3 19.3 + - - +
876A ARG* 3.6 3.8 + - - +
882A PHE* 3.7 26.5 - + + -
935A LEU* 4.4 15.3 - - + -
936A LYS 3.7 8.5 - - - +
937A TYR* 3.9 11.2 - + + -
938A TYR* 5.0 0.2 - - - -
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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
----------------------------------------------------------
831A ARG* 4.9 0.9 - - + -
846A LEU* 3.7 27.8 - - + -
871A LYS 3.5 8.1 - - - +
872A PHE* 1.3 72.1 - - - +
874A MET* 1.3 57.6 + - - +
876A ARG* 3.3 2.5 + - - +
877A HIS* 2.8 35.9 + - + +
936A LYS* 3.1 25.2 + - + +
937A TYR* 3.6 7.6 - - - -
938A TYR* 3.5 54.1 - - + +
41B C 3.5 44.4 - - - +
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Residues in contact with MET 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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872A PHE* 3.2 2.8 - - + +
873A LEU* 1.3 75.7 - - - +
875A TYR* 1.3 61.7 + - - +
876A ARG 3.0 1.6 - - - -
878A ASP* 2.6 50.5 + - + +
881A THR* 3.7 25.4 - - - -
882A PHE* 3.6 27.8 - - + -
886A ILE* 3.4 33.4 - - + -
922A LYS* 5.9 0.4 - - - -
932A ILE* 4.6 5.8 - - + -
935A LEU* 3.8 26.2 - - + -
936A LYS 4.7 1.0 + - - -
41B C 3.1 29.6 + - - +
42B U 5.2 5.6 - - - +
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Residues in contact with TYR 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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869A LYS* 3.3 55.4 + - + +
870A SER* 3.7 25.4 - - - -
872A PHE* 3.3 8.8 + - + +
874A MET* 1.3 81.0 - - - +
876A ARG* 1.3 63.5 + - + +
879A PRO* 3.7 22.0 - - + +
882A PHE* 3.4 44.7 - + + -
883A GLU* 5.3 4.0 - - - -
887A GLU* 5.0 0.2 - - - -
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Residues in contact with ARG 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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833A ALA* 3.9 15.2 - - - +
834A LYS* 2.8 33.7 + - - +
835A VAL* 3.7 15.6 - - - +
870A SER* 2.6 50.5 + - - +
872A PHE 3.6 2.4 + - - +
873A LEU* 3.3 7.7 + - - +
874A MET 3.0 0.4 - - - -
875A TYR* 1.3 89.0 - - + +
877A HIS* 1.3 76.8 + - + +
879A PRO* 4.0 7.0 - - - +
938A TYR* 3.7 21.2 + - - -
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Residues in contact with HIS 877 (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 LEU* 2.8 26.3 + - + +
876A ARG* 1.3 90.4 + - + +
878A ASP* 1.3 61.9 + - - +
879A PRO* 3.7 3.3 - - - +
938A TYR* 3.8 17.4 + - - -
39B A 4.7 11.0 + - - +
40B G 3.8 43.4 + - - -
41B C 3.5 43.5 + - + +
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Residues in contact with ASP 878 (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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874A MET* 2.6 30.9 + - + +
877A HIS* 1.3 77.9 - - - +
879A PRO* 1.3 68.2 - - - +
880A GLN* 3.0 15.8 + - - +
881A THR* 2.3 42.2 + - - -
882A PHE 3.2 7.8 + - - -
922A LYS* 3.0 32.1 + - - +
923A TYR* 5.6 0.7 - - - +
31B U 5.2 6.8 + - - +
41B C 3.5 12.2 + - - +
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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