Contacts of the helix formed by residues 871 - 888 (chain A) in PDB entry 1OY6
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 ASN 871 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870A GLY* 1.3 68.4 - - - -
872A GLN* 1.3 66.8 + - - +
873A ALA 3.2 0.4 - - - -
874A PRO* 3.1 28.0 - - - +
875A SER* 4.3 3.8 + - - -
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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
----------------------------------------------------------
458A PHE 3.3 11.3 + - - -
459A PHE* 3.1 10.5 + - - -
460A GLY* 2.9 46.1 + - - +
463A THR* 3.5 17.6 - - - +
467A TYR* 3.6 18.8 - - + -
869A SER 5.0 2.2 - - - +
870A GLY* 4.3 7.4 - - - -
871A ASN* 1.3 75.6 - - - +
873A ALA* 1.3 64.9 + - - +
875A SER* 3.2 16.7 + - - -
876A LEU* 3.2 36.1 + - + +
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Residues in contact with ALA 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR* 5.4 0.9 - - + -
869A SER* 4.9 8.1 - - - +
870A GLY 3.3 9.9 + - - +
871A ASN 3.2 0.4 - - - -
872A GLN* 1.3 77.7 - - + +
874A PRO* 1.3 76.4 - - + +
876A LEU* 2.8 27.7 + - + +
877A TYR* 3.1 26.3 + - + -
928A GLN* 4.2 23.6 - - - +
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Residues in contact with PRO 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A GLY 3.4 8.3 - - - +
871A ASN* 3.1 27.8 - - - +
873A ALA* 1.3 95.4 - - + +
875A SER* 1.3 61.0 + - - +
877A TYR* 4.9 2.0 - - + +
878A ALA* 3.6 16.3 + - - +
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Residues in contact with SER 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ASN 4.7 2.8 + - - -
872A GLN 3.2 8.5 + - - -
873A ALA 2.9 1.8 + - - -
874A PRO* 1.3 78.8 - - - +
876A LEU* 1.3 67.2 + - - +
877A TYR 3.4 0.2 - - - -
878A ALA* 3.2 19.6 - - - +
879A ILE* 3.0 22.7 - - - +
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Residues in contact with LEU 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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455A PRO 3.8 8.2 - - - +
456A MET* 3.5 46.7 - - + +
458A PHE* 3.3 29.6 - - + +
467A TYR* 3.9 14.6 - - + -
872A GLN* 3.2 44.0 + - + +
873A ALA* 2.8 15.3 + - + +
875A SER* 1.3 75.2 - - - +
877A TYR* 1.3 63.0 + - + +
879A ILE* 3.2 21.4 + - + +
880A SER* 3.3 12.8 + - - -
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Residues in contact with TYR 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A VAL* 6.4 0.2 - - + -
456A MET* 4.5 10.4 - - + -
873A ALA* 3.1 24.2 + - + +
874A PRO* 4.9 2.2 - - + +
876A LEU* 1.3 79.4 - - + +
878A ALA* 1.3 59.5 + - - +
879A ILE 3.2 0.2 - - - -
880A SER* 3.0 19.3 + - - -
881A LEU* 2.9 39.4 + - + +
928A GLN* 3.3 54.2 + - + +
931A LEU* 4.8 7.1 - - + +
932A LEU* 3.7 24.4 - - + +
935A ILE* 5.2 12.3 - - + -
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Residues in contact with ALA 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A PRO 3.6 15.8 + - - +
875A SER* 3.2 19.1 + - - +
876A LEU 3.2 0.2 - - - -
877A TYR* 1.3 79.2 - - - +
879A ILE* 1.3 58.6 + - + +
881A LEU* 3.4 19.6 + - - +
882A ILE* 3.2 24.8 - - + +
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Residues in contact with ILE 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A PRO* 3.4 31.9 - - + +
458A PHE* 4.4 21.8 - - + -
875A SER* 3.0 27.1 - - - +
876A LEU* 3.2 8.7 + - + +
877A TYR 3.2 0.4 - - - -
878A ALA* 1.3 74.8 - - + +
880A SER* 1.3 61.4 + - - +
881A LEU 3.2 0.9 - - - -
882A ILE* 3.3 15.1 + - + +
883A VAL* 3.1 40.7 + - + +
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Residues in contact with SER 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ALA 3.2 14.7 - - - +
452A VAL* 3.2 31.7 + - - -
455A PRO* 3.3 11.2 - - - +
456A MET* 4.0 3.5 + - - +
876A LEU 3.3 7.7 + - - -
877A TYR* 3.0 26.3 + - - -
879A ILE* 1.3 77.6 - - - +
881A LEU* 1.3 61.8 + - - +
882A ILE 3.5 0.2 + - - -
884A VAL* 3.0 31.4 + - - +
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Residues in contact with LEU 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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877A TYR* 2.9 27.0 + - + +
878A ALA* 3.6 15.0 - - + +
879A ILE 3.2 0.6 - - - -
880A SER* 1.3 80.1 - - - +
882A ILE* 1.3 62.9 + - + +
884A VAL* 4.5 3.8 - - - +
885A PHE* 4.1 14.9 + - - +
902A MET* 5.2 18.2 - - + +
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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 ALA* 3.2 22.0 - - + +
879A ILE* 3.3 18.6 + - + +
880A SER 3.2 0.2 - - - -
881A LEU* 1.3 80.1 - - + +
883A VAL* 1.3 69.8 + - + +
884A VAL 3.2 1.6 + - - -
885A PHE* 3.3 3.8 + - - +
886A LEU* 3.3 40.9 + - + +
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Residues in contact with VAL 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A SER* 4.4 5.8 - - - +
451A ALA* 3.4 26.5 - - + +
455A PRO* 4.3 8.1 - - + -
879A ILE* 3.1 32.1 + - + +
882A ILE* 1.3 75.1 - - + +
884A VAL* 1.3 65.3 + - - +
886A LEU* 4.6 6.3 - - + -
887A CYS* 3.0 36.5 + - - -
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Residues in contact with VAL 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 3.8 17.4 - - + +
451A ALA* 3.4 15.0 - - + +
452A VAL* 3.2 30.5 - - + -
880A SER 3.0 24.3 + - - +
881A LEU* 4.7 3.8 - - - +
882A ILE 3.2 0.8 - - - -
883A VAL* 1.3 78.6 - - - +
885A PHE* 1.3 52.7 + - - +
887A CYS 3.3 1.0 + - - -
888A LEU* 2.7 45.1 + - + +
901A VAL* 4.5 7.0 - - + -
902A MET* 4.0 24.9 - - + -
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Residues in contact with PHE 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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881A LEU 4.1 11.8 + - - +
882A ILE* 3.3 9.6 + - - +
884A VAL* 1.3 82.2 - - + +
886A LEU* 1.3 71.3 + - + +
888A LEU* 3.5 7.5 + - - +
889A ALA* 3.3 19.2 + - - +
895A TRP* 4.2 32.3 - + - -
898A PRO* 3.3 42.7 - - + +
899A PHE* 3.4 38.4 - + - -
902A MET* 5.0 9.4 - - + -
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Residues in contact with LEU 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 ILE* 3.3 31.7 + - + +
883A VAL* 4.0 6.5 - - + +
884A VAL 3.2 0.4 - - - -
885A PHE* 1.3 90.4 - - + +
887A CYS* 1.3 59.7 + - - +
888A LEU 3.1 4.9 - - - -
889A ALA* 3.3 6.3 + - - +
890A ALA* 3.1 25.3 + - - +
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Residues in contact with CYS 887 (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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447A MET* 3.3 52.1 - - + +
448A VAL* 3.8 9.0 - - - +
450A SER* 4.9 1.3 - - - -
883A VAL* 3.0 39.8 + - - +
884A VAL 3.8 2.7 - - - +
886A LEU* 1.3 76.2 - - - +
888A LEU* 1.3 59.3 + - - +
889A ALA 3.2 3.5 + - - -
890A ALA* 3.7 17.9 + - - +
891A LEU* 4.3 4.3 + - - +
892A TYR* 3.8 14.7 - - - -
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Residues in contact with LEU 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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448A VAL* 3.4 36.1 - - + -
884A VAL* 2.7 21.3 + - + +
885A PHE* 3.6 9.4 - - - +
886A LEU 3.1 0.6 - - - -
887A CYS* 1.3 76.0 - - - +
889A ALA* 1.3 56.3 + - - +
892A TYR* 3.2 38.4 - - + +
897A ILE* 3.1 31.4 - - + +
898A PRO* 3.4 27.3 - - + +
901A VAL* 3.4 27.6 - - + -
943A ILE* 4.1 15.7 - - + -
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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