Contacts of the helix formed by residues 871 - 888 (chain A) in PDB entry 5M9O
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 871 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A PHE* 3.6 31.0 - + + -
831A GLU* 3.5 48.2 - - + -
832A HIS* 4.4 4.0 - + + -
866A ARG* 3.7 27.4 - - + +
868A GLU* 2.8 56.3 + - + +
870A GLN* 1.3 96.5 - - + +
872A GLN* 1.3 55.4 + - - -
873A LYS 3.5 1.6 - - - -
874A VAL* 3.0 12.2 - - + +
875A ILE* 2.8 36.0 + - + +
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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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866A ARG 5.8 0.9 - - - -
867A LYS 5.8 2.0 - - - +
868A GLU 3.5 3.6 + - - +
869A LYS* 3.0 22.0 + - + +
870A GLN 3.5 0.8 - - - -
871A PHE* 1.3 74.1 - - - +
873A LYS* 1.3 64.1 + - - +
875A ILE* 4.5 4.5 - - - +
876A THR* 3.0 41.5 + - + +
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Residues in contact with LYS 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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869A LYS 4.7 0.8 + - - -
870A GLN 5.2 2.2 + - - +
871A PHE 3.5 0.4 - - - -
872A GLN* 1.3 77.7 - - - +
874A VAL* 1.3 59.1 + - - +
876A THR* 4.3 2.7 + - - -
877A GLU* 3.1 31.1 + - - +
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Residues in contact with VAL 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A PHE* 3.5 33.2 - - + -
831A GLU* 5.7 0.7 - - - +
841A THR* 5.2 2.9 - - + -
850A ASP* 4.5 6.1 - - - +
870A GLN 5.0 1.8 + - - +
871A PHE* 3.0 33.3 + - + +
873A LYS* 1.3 78.6 - - - +
875A ILE* 1.3 58.9 + - + +
877A GLU* 3.2 9.2 - - - +
878A TYR* 2.9 59.8 + - + +
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Residues in contact with ILE 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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800A PHE* 3.5 36.8 - - + -
863A VAL* 4.5 4.9 - - + -
864A GLU 3.6 19.1 - - - +
865A VAL* 4.3 6.7 - - + -
866A ARG 3.7 31.9 - - - +
871A PHE* 2.8 31.5 + - + +
872A GLN* 4.4 2.5 - - - +
874A VAL* 1.3 68.6 - - + +
876A THR* 1.3 73.8 + - + +
877A GLU 2.9 1.1 - - - -
878A TYR* 2.6 18.4 + - + +
879A LEU* 2.8 30.4 + - + +
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Residues in contact with THR 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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872A GLN* 3.0 27.8 + - + +
873A LYS* 4.3 2.9 + - - -
875A ILE* 1.3 82.1 - - + +
877A GLU* 1.3 60.0 + - - +
879A LEU* 3.3 14.5 + - + +
880A ASN* 3.1 37.0 + - - +
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Residues in contact with GLU 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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853A LEU* 3.7 28.7 - - + +
873A LYS 3.1 25.7 + - - +
874A VAL* 3.2 9.4 - - - +
876A THR* 1.3 77.7 + - - +
878A TYR* 1.3 70.4 + - + +
879A LEU 3.0 1.8 - - - -
880A ASN* 2.8 24.2 + - + +
881A ALA* 3.0 11.0 + - + +
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Residues in contact with TYR 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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799A ALA 4.1 7.1 + - - -
800A PHE* 3.7 36.5 - + + -
801A ILE* 4.1 8.7 - - + -
841A THR* 4.1 12.3 - - - +
850A ASP* 2.8 33.6 + - - -
852A GLY* 4.0 3.2 - - - -
853A LEU* 3.5 39.8 + - + -
856A VAL* 3.5 20.6 - - + +
863A VAL* 3.5 16.9 - - + +
874A VAL* 2.9 48.0 + - + +
875A ILE* 2.6 12.7 + - - +
877A GLU* 1.3 72.2 - - + +
879A LEU* 1.3 55.5 + - - +
881A ALA* 3.2 4.6 + - - +
882A GLN 3.0 23.7 + - - -
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Residues in contact with LEU 879 (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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863A VAL* 3.8 22.0 - - + -
865A VAL* 4.0 23.6 - - + -
875A ILE* 2.8 22.2 + - + +
876A THR* 3.4 16.2 - - + +
878A TYR* 1.3 76.6 - - - +
880A ASN* 1.3 58.2 + - - +
882A GLN* 3.6 27.8 + - - +
883A GLU* 3.3 30.2 + - - +
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Residues in contact with ASN 880 (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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876A THR* 3.1 23.4 + - - +
877A GLU* 2.8 16.7 + - + +
879A LEU* 1.3 72.7 - - - +
881A ALA* 1.3 60.1 + - - +
883A GLU* 3.4 12.7 + - - +
884A SER* 3.3 17.5 + - - -
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Residues in contact with ALA 881 (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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853A LEU* 3.7 20.9 - - + -
856A VAL* 3.8 7.4 - - + -
857A LYS* 3.4 37.2 - - + +
877A GLU* 3.0 7.4 + - + +
878A TYR 3.2 8.9 + - - +
880A ASN* 1.3 72.9 - - - +
882A GLN* 1.3 64.3 + - - +
883A GLU 3.2 1.6 - - - -
884A SER* 3.2 9.3 + - - +
885A ALA* 3.1 21.3 + - - +
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Residues in contact with GLN 882 (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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856A VAL* 3.5 17.1 - - + +
861A VAL 5.3 0.9 - - - +
862A MET* 3.2 16.1 - - - +
863A VAL* 2.9 31.6 + - + +
878A TYR 3.0 12.6 + - - +
879A LEU* 3.6 33.9 + - - +
881A ALA* 1.3 75.1 - - - +
883A GLU* 1.3 59.9 + - - +
885A ALA* 3.3 2.6 + - - +
886A LYS* 2.9 46.3 + - + +
893A TRP* 3.7 24.1 - - + +
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Residues in contact with GLU 883 (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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879A LEU 3.3 16.0 + - - +
880A ASN* 3.4 15.3 - - - +
881A ALA 3.2 0.6 - - - -
882A GLN* 1.3 78.4 + - - +
884A SER* 1.3 64.2 + - - +
886A LYS* 3.8 29.4 + - - +
887A SER* 3.0 30.6 + - - +
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Residues in contact with SER 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LYS* 4.9 9.4 + - - +
880A ASN 3.3 9.0 + - - -
881A ALA* 3.2 14.2 + - - -
883A GLU* 1.3 77.9 - - - +
885A ALA* 1.3 57.4 + - - +
887A SER* 3.4 5.6 + - - -
888A ALA* 3.1 29.2 + - - +
890A LEU* 5.5 0.4 - - - -
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Residues in contact with ALA 885 (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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856A VAL 3.4 26.2 - - - +
857A LYS 3.4 14.8 + - - +
858A GLU 4.3 0.7 - - - -
859A GLY* 3.5 17.9 - - - +
881A ALA 3.1 6.5 + - - +
882A GLN 3.6 7.4 - - - +
883A GLU 3.2 0.2 - - - -
884A SER* 1.3 75.2 - - - +
886A LYS* 1.3 64.8 + - - +
888A ALA 3.5 0.9 + - - -
889A ARG 3.1 17.3 + - - -
890A LEU* 3.2 17.5 + - + -
893A TRP* 3.5 7.0 - - + +
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Residues in contact with LYS 886 (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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882A GLN* 2.9 34.5 + - + +
883A GLU* 3.8 29.4 + - - +
885A ALA* 1.3 74.8 - - - +
887A SER* 1.3 55.2 + - - +
889A ARG* 2.7 38.5 + - - -
893A TRP* 3.4 59.0 - - + +
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Residues in contact with SER 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A GLU* 3.0 19.6 + - - +
884A SER* 3.7 5.8 - - - -
886A LYS* 1.3 74.8 - - - +
888A ALA* 1.3 60.7 + - - +
889A ARG* 3.1 21.7 + - - +
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Residues in contact with ALA 888 (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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884A SER 3.1 16.1 + - - +
885A ALA 3.5 0.2 + - - -
886A LYS 3.5 0.2 - - - -
887A SER* 1.3 72.7 - - - +
889A ARG* 1.3 70.9 + - - +
890A LEU* 3.3 33.0 + - + +
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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