Contacts of the helix formed by residues 924 - 940 (chain A) in PDB entry 5A7R
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 THR 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A CYS 3.4 8.4 + - - -
712A GLU* 3.5 19.5 - - + +
713A LYS 3.4 12.8 - - - +
714A PRO* 4.6 2.0 - - + -
715A LEU* 5.1 2.0 - - - -
922A LYS 4.3 7.4 - - - +
923A LEU* 1.3 77.3 - - - +
925A VAL* 1.3 64.7 + - - +
927A ASP* 3.1 25.9 + - - +
928A VAL* 3.0 23.9 + - - +
1975A GOL 2.6 29.3 + - - +
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Residues in contact with VAL 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A TRP* 3.7 36.1 - - + +
711A CYS* 3.7 26.9 - - + -
713A LYS* 3.0 22.8 + - + +
715A LEU* 4.5 7.8 - - + +
888A LEU* 4.0 25.5 - - + +
891A ALA* 3.7 28.9 - - + -
892A ALA 4.5 1.8 - - - +
924A THR* 1.3 72.0 - - - +
926A GLY* 1.3 58.4 + - - +
928A VAL* 3.2 3.6 + - - +
929A TYR* 2.9 27.9 + - + +
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Residues in contact with GLY 926 (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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708A TRP 3.2 20.6 - - - -
709A GLU* 3.6 13.4 - - - +
711A CYS 2.8 19.3 + - - -
924A THR* 3.8 0.7 - - - -
925A VAL* 1.3 75.7 - - - +
927A ASP* 1.3 65.4 + - - +
929A TYR* 3.4 1.3 + - - +
930A LYS* 3.0 29.3 + - - +
1975A GOL 4.0 3.8 - - - -
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Residues in contact with ASP 927 (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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922A LYS 4.4 1.4 - - - +
923A LEU* 3.6 24.7 - - + +
924A THR* 3.1 42.0 + - - +
926A GLY* 1.3 75.1 - - - +
928A VAL* 1.3 62.9 + - - +
930A LYS* 3.5 6.7 + - - +
931A LEU* 3.2 27.6 + - - +
1975A GOL 2.7 30.6 + - - -
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Residues in contact with VAL 928 (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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715A LEU* 4.9 3.8 - - + -
884A LEU* 4.1 26.9 - - + -
888A LEU* 3.8 30.7 - - + -
918A LEU* 4.1 27.1 - - + -
923A LEU* 4.3 16.8 - - + +
924A THR 3.0 14.4 + - - +
925A VAL 3.7 5.8 - - - +
927A ASP* 1.3 73.8 - - - +
929A TYR* 1.3 67.1 + - - +
931A LEU* 3.0 21.8 + - + +
932A LEU* 3.1 14.5 + - + +
956A ILE* 5.5 1.8 - - + -
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Residues in contact with TYR 929 (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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708A TRP* 3.8 19.1 - + + +
709A GLU* 3.5 39.7 - - + -
838A PRO* 4.4 6.6 + - - +
841A MET* 5.0 9.2 - - + -
842A ARG* 4.0 30.5 + - + +
845A LEU* 3.8 30.7 - - + -
888A LEU* 4.2 5.6 - - + +
925A VAL* 2.9 18.7 + - + +
926A GLY 3.8 2.7 - - - +
928A VAL* 1.3 76.6 - - - +
930A LYS* 1.3 62.0 + - - +
932A LEU* 3.1 19.2 + - + +
933A LEU* 3.1 56.7 + - + +
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Residues in contact with LYS 930 (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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709A GLU* 3.8 24.5 + - + +
926A GLY 3.0 21.4 + - - +
927A ASP* 3.8 7.2 - - - +
929A TYR* 1.3 76.8 - - - +
931A LEU* 1.3 56.6 + - - +
933A LEU* 3.3 14.8 + - + +
934A ARG* 3.0 36.0 + - - +
1975A GOL 2.5 37.8 + - - -
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Residues in contact with LEU 931 (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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918A LEU* 5.0 2.0 - - + -
923A LEU* 4.1 14.4 - - + -
927A ASP 3.2 14.1 + - - +
928A VAL* 3.0 13.9 + - + +
930A LYS* 1.3 77.6 - - + +
932A LEU* 1.3 58.8 + - - +
934A ARG* 3.3 31.0 + - - +
935A TYR* 3.0 24.6 + - - +
955A PHE* 3.8 9.8 - - + -
956A ILE* 4.2 28.0 - - + +
959A ALA* 3.9 21.8 - - + -
960A VAL* 3.7 26.7 - - + -
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Residues in contact with LEU 932 (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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836A PHE* 6.0 0.8 - - + -
841A MET* 3.9 35.5 - - + +
845A LEU* 5.3 1.6 - - + -
881A LEU* 4.2 12.8 - - + -
884A LEU* 4.3 15.7 - - + -
885A ILE* 4.7 11.7 - - + -
888A LEU* 4.3 21.8 - - + -
928A VAL* 3.1 17.6 + - + +
929A TYR* 3.1 18.1 + - + +
931A LEU* 1.3 75.7 - - - +
933A LEU* 1.3 61.9 + - - +
935A TYR* 3.3 7.8 + - - +
936A TYR* 3.1 18.2 + - - +
952A LEU* 3.9 33.7 - - + -
956A ILE* 4.6 3.1 - - + -
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Residues in contact with LEU 933 (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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709A GLU* 5.4 3.8 - - + -
838A PRO* 3.7 34.8 - - + -
841A MET* 4.2 7.6 - - + -
929A TYR* 3.1 47.9 + - + +
930A LYS* 3.6 17.0 - - + +
932A LEU* 1.3 74.6 - - - +
934A ARG* 1.3 60.2 + - + +
936A TYR* 3.3 6.5 + - - +
937A ASN* 3.0 34.3 + - - +
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Residues in contact with ARG 934 (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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930A LYS* 3.0 21.7 + - - +
931A LEU* 3.6 26.4 - - - +
933A LEU* 1.3 74.6 - - + +
935A TYR* 1.3 59.6 + - - +
937A ASN* 3.3 5.7 + - - -
938A GLU* 2.8 58.4 + - + +
955A PHE* 3.8 9.6 - - + -
959A ALA* 3.8 32.5 + - - +
963A CYS* 6.2 1.8 - - - +
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Residues in contact with TYR 935 (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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832A TYR* 5.0 1.4 + - - -
836A PHE* 3.6 37.0 - + - -
931A LEU 3.0 13.9 + - - +
932A LEU 3.3 8.7 + - - +
934A ARG* 1.3 75.5 - - - +
936A TYR* 1.3 57.5 + - - +
939A GLU* 2.9 53.5 + - + +
940A CYS* 3.5 19.9 + - - -
948A PRO* 3.2 17.3 - - - +
950A ILE 2.6 30.0 + - - -
951A LYS* 3.6 12.7 - - - -
952A LEU* 3.5 33.6 + - + -
955A PHE* 3.5 33.7 - + + -
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Residues in contact with TYR 936 (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 LEU 5.6 0.7 - - - -
836A PHE* 3.3 31.4 - - + +
837A VAL* 3.9 24.7 - - + +
838A PRO* 3.4 28.5 - - + -
841A MET* 4.8 0.2 - - + -
932A LEU 3.1 13.4 + - - +
933A LEU* 3.5 9.0 - - - +
934A ARG 3.3 0.2 - - - -
935A TYR* 1.3 76.7 - - - +
937A ASN* 1.3 71.2 + - - +
940A CYS* 3.0 23.7 + - + -
941A ARG* 2.9 76.4 + - + +
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Residues in contact with ASN 937 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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933A LEU* 3.0 22.6 + - - +
934A ARG* 3.6 9.6 - - - +
936A TYR* 1.3 87.4 - - - +
938A GLU* 1.3 65.6 + - + +
939A GLU 3.8 0.2 + - - -
941A ARG* 3.3 44.7 + - - +
942A ASN* 4.6 11.3 + - - +
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Residues in contact with GLU 938 (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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934A ARG* 2.8 49.5 + - - +
937A ASN* 1.3 79.5 - - + +
939A GLU* 1.3 72.8 + - + +
942A ASN* 6.2 0.4 - - - -
955A PHE* 3.4 30.4 - - + -
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Residues in contact with GLU 939 (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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935A TYR* 2.9 45.4 + - + +
938A GLU* 1.3 91.6 - - + +
940A CYS* 1.3 59.5 + - - +
942A ASN 5.4 0.4 - - - -
943A CYS* 3.6 14.8 - - - +
948A PRO* 3.5 20.3 - - + +
949A ASP* 3.8 31.1 + - - +
950A ILE* 4.1 17.4 - - + +
955A PHE* 4.1 16.0 - - + -
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Residues in contact with CYS 940 (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 LEU* 3.9 32.9 - - + +
836A PHE* 3.8 19.1 - - + -
935A TYR* 3.5 38.8 - - - -
936A TYR* 3.0 25.6 + - + +
939A GLU* 1.3 81.4 - - - +
941A ARG* 1.3 64.7 + - - +
942A ASN 3.3 2.2 - - - -
943A CYS* 3.1 21.2 + - - +
948A PRO* 4.6 0.7 - - - -
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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