Contacts of the helix formed by residues 873 - 886 (chain A) in PDB entry 4O3M
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 LYS 873 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870A LYS* 2.9 25.0 + - + +
872A LYS* 1.3 79.3 - - - +
874A VAL* 1.3 64.5 + - - +
875A ALA 3.3 2.7 - - - -
876A PHE* 3.1 19.3 + - + +
877A ASP* 3.0 29.9 + - - +
7P G 4.1 2.4 + - - +
8P A 5.7 4.9 - - - +
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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
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869A LYS* 4.2 19.5 - - + +
870A LYS 2.9 12.3 + - - +
871A PRO 3.4 17.3 - - - +
872A LYS 3.8 0.2 - - - -
873A LYS* 1.3 74.3 - - - +
875A ALA* 1.4 58.5 + - + +
877A ASP* 3.1 11.1 + - - +
878A CYS* 2.9 38.9 + - - -
900A GLU* 5.6 4.0 - - - +
904A MET* 4.4 9.4 - - + -
964A ALA* 3.8 24.7 - - + +
992A PHE* 4.0 29.8 - - + -
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Residues in contact with ALA 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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873A LYS 3.3 0.8 - - - -
874A VAL* 1.4 80.7 - - + +
876A PHE* 1.4 61.6 + - + +
878A CYS* 3.4 2.3 + - - +
879A LEU* 3.0 28.6 + - - +
903A THR* 5.1 6.1 - - + +
904A MET* 3.6 32.5 - - + +
907A THR* 3.7 30.7 - - + +
908A LEU* 3.8 5.0 - - - +
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Residues in contact with PHE 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 LYS 4.9 5.4 - - - -
873A LYS* 3.1 23.8 + - + +
875A ALA* 1.4 77.6 - - + +
877A ASP* 1.3 62.3 + - - +
879A LEU* 3.6 20.6 - - + +
880A GLU* 3.0 30.7 + - - +
907A THR* 4.1 21.1 - - + -
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Residues in contact with ASP 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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868A PRO 5.6 1.0 - - - +
870A LYS* 3.9 21.3 + - - +
873A LYS* 3.0 26.2 + - - +
874A VAL* 3.3 12.8 - - - +
876A PHE* 1.3 74.9 - - - +
878A CYS* 1.4 63.4 + - - +
880A GLU* 3.6 3.9 + - - +
881A TRP* 3.1 26.0 + - - +
992A PHE* 4.2 23.9 - - + -
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Residues in contact with CYS 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 VAL* 2.9 22.5 + - - +
875A ALA 3.8 4.9 - - - +
877A ASP* 1.4 73.3 - - - +
879A LEU* 1.3 53.5 + - - +
881A TRP* 3.4 4.0 + - - +
882A ILE* 2.8 41.6 + - - +
893A ILE* 4.0 22.7 - - + -
904A MET* 3.9 22.0 - - - -
908A LEU* 5.1 0.2 - - + -
962A ILE* 3.8 23.1 - - + -
964A ALA* 4.8 0.9 - - - -
992A PHE* 3.7 25.6 - - - -
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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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875A ALA 3.0 16.8 + - - +
876A PHE* 3.6 26.2 - - + +
878A CYS* 1.3 76.0 - - - +
880A GLU* 1.4 58.3 + - - +
882A ILE* 3.5 5.8 + - - +
883A ARG* 3.1 38.2 + - + +
907A THR* 4.7 10.3 - - + +
908A LEU* 3.7 22.6 - - + +
911A ASP* 3.4 50.0 - - + +
913A LEU* 4.0 16.8 - - + -
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Residues in contact with GLU 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 PHE 3.0 17.4 + - - +
877A ASP* 4.1 4.9 - - - +
879A LEU* 1.4 72.6 - - - +
881A TRP* 1.3 60.0 + - - +
883A ARG* 3.3 5.9 + - - +
884A LYS* 3.0 33.3 + - + +
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Residues in contact with TRP 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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865A TYR* 5.8 3.8 - + - -
867A LEU* 5.5 6.5 - - + +
877A ASP 3.1 18.7 + - - +
878A CYS* 3.7 4.3 - - - +
880A GLU* 1.3 75.3 - - - +
882A ILE* 1.4 62.2 + - + +
884A LYS* 4.4 3.1 - - - -
885A HIS* 2.9 68.3 + + + +
886A HIS* 3.3 35.2 - + - -
960A PHE* 3.7 22.9 - + + -
962A ILE* 3.8 20.6 - - + -
988A HIS* 3.7 34.5 - + + -
990A LEU* 3.6 33.3 - - + +
992A PHE* 5.5 2.0 - + + -
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Residues in contact with ILE 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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878A CYS 2.8 28.1 + - - +
879A LEU 3.9 3.8 - - - +
881A TRP* 1.4 85.4 - - + +
883A ARG* 1.3 60.2 + - - +
886A HIS* 2.8 44.7 + - - +
887A PRO* 3.1 9.6 - - + -
893A ILE* 3.7 24.5 - - + -
908A LEU* 4.1 13.7 - - + -
913A LEU* 3.9 19.5 - - + -
941A GLN* 3.9 11.4 - - - +
942A VAL* 4.5 2.2 - - + -
960A PHE* 3.7 35.2 - - + -
962A ILE* 4.1 2.7 - - + -
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Residues in contact with ARG 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* 3.1 21.7 + - + +
880A GLU* 3.3 4.9 + - - +
882A ILE* 1.3 74.9 - - - +
884A LYS* 1.3 60.8 + - - +
887A PRO* 3.4 29.4 - - + +
911A ASP* 2.8 48.7 + - - +
912A GLY* 3.4 14.6 + - - -
913A LEU* 3.4 35.6 - - + +
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Residues in contact with LYS 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A GLU* 3.0 19.0 + - + +
881A TRP* 3.8 5.2 - - - +
883A ARG* 1.3 77.9 - - - +
885A HIS* 1.3 87.7 + - + +
887A PRO* 4.5 2.2 - - - +
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Residues in contact with HIS 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A TRP* 2.9 63.9 + + + +
884A LYS* 1.3 108.9 - - + +
886A HIS* 1.3 85.2 + - + +
887A PRO* 3.7 4.7 - - - +
889A ASP* 4.5 0.9 - - - +
988A HIS* 5.5 10.1 - + + +
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Residues in contact with HIS 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A TRP* 3.3 34.9 - + - -
882A ILE* 2.8 18.7 + - + +
885A HIS* 1.3 86.9 + - + +
887A PRO* 1.4 64.4 - - - +
888A TYR 3.1 4.6 + - - -
889A ASP* 3.1 34.7 + - + +
941A GLN* 3.3 15.1 + - - -
959A ARG* 3.6 22.9 + - + +
960A PHE* 3.8 18.8 - + + -
986A ILE 5.2 1.3 - - - -
988A HIS* 3.2 38.0 + + - -
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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