Contacts of the helix formed by residues 927 - 947 (chain A) in PDB entry 3GTL
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 VAL 927 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923A LEU* 3.6 22.0 - - + +
924A LYS* 3.3 14.6 - - + +
925A LEU 3.3 0.2 - - - -
926A GLN* 1.3 81.0 - - - +
928A LEU* 1.3 63.2 - - + +
930A ASP* 4.0 2.9 - - - +
931A GLU* 2.8 28.5 + - - +
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Residues in contact with LEU 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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924A LYS 3.5 7.4 + - - +
925A LEU* 3.8 29.4 - - + -
927A VAL* 1.3 82.5 - - + +
929A LEU* 1.3 51.3 + - + +
931A GLU* 2.8 16.6 + - + +
932A GLU* 2.7 33.6 + - - +
983A ILE* 5.0 1.6 - - + +
984A LYS* 4.1 26.9 - - + -
987A VAL* 3.7 35.0 - - + +
988A LEU* 5.0 14.1 - - + -
991A LYS* 5.7 7.4 - - + +
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Residues in contact with LEU 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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897A TYR 5.6 0.2 - - - +
898A ARG* 4.7 3.8 + - - +
899A VAL* 3.0 53.8 - - + +
901A LEU* 4.9 1.6 - - + -
925A LEU 3.1 21.4 + - - +
926A GLN* 3.7 9.4 - - - +
927A VAL 4.0 0.2 - - - +
928A LEU* 1.3 74.8 - - - +
930A ASP* 1.3 64.9 + - - +
932A GLU* 3.4 13.1 + - - +
933A TYR* 3.2 21.9 + - + +
983A ILE* 2.9 36.3 - - + -
987A VAL* 4.1 3.8 - - + -
1028A THR* 3.8 20.4 - - + +
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Residues in contact with ASP 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A ARG* 3.3 28.8 + - - +
926A GLN* 2.8 36.8 + - - +
927A VAL* 4.0 4.5 - - - +
929A LEU* 1.3 75.7 - - - +
931A GLU* 1.3 64.5 + - - +
933A TYR* 3.1 4.0 + - - +
934A LYS* 3.0 36.4 + - - +
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Residues in contact with GLU 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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927A VAL* 2.8 18.8 + - + +
928A LEU* 2.8 22.2 + - + +
930A ASP* 1.3 75.5 - - - +
932A GLU* 1.3 61.0 + - - +
934A LYS* 3.6 9.5 + - - +
935A GLN* 3.3 24.9 + - - +
987A VAL* 6.0 2.5 - - + -
991A LYS* 4.8 18.9 + - - +
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Residues in contact with GLU 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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897A TYR 4.2 14.6 - - - +
899A VAL* 4.6 0.3 - - - +
928A LEU 2.7 13.9 + - - +
929A LEU* 3.5 18.7 - - - +
930A ASP 3.1 0.4 + - - -
931A GLU* 1.3 71.5 - - - +
933A TYR* 1.3 67.3 + - - +
935A GLN* 3.0 10.4 + - - +
936A LEU* 3.0 43.9 + - + +
986A ILE* 5.1 1.0 - - - +
987A VAL* 4.2 11.8 - - + +
1026A LEU 4.4 3.5 - - - +
1027A ALA* 3.7 5.6 - - - +
1028A THR* 2.8 50.7 + - - -
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Residues in contact with TYR 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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890A ASP 5.5 0.2 + - - -
893A PHE* 3.8 25.2 - + - -
894A GLU* 3.3 33.5 + - - +
897A TYR* 3.5 24.7 - - + +
898A ARG* 3.4 55.9 - - - +
899A VAL 5.8 0.4 - - - +
929A LEU* 3.2 8.6 + - + +
930A ASP* 3.1 6.8 + - - +
932A GLU* 1.3 81.8 - - - +
934A LYS* 1.3 66.2 + - - +
936A LEU* 3.4 9.3 + - + +
937A VAL* 3.3 30.8 + - + +
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Residues in contact with LYS 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 ASP* 3.0 27.4 + - - +
931A GLU* 3.7 11.6 - - - +
933A TYR* 1.3 78.7 - - - +
935A GLN* 1.3 51.8 + - - +
937A VAL* 2.7 31.0 + - + +
938A LYS* 2.8 20.7 + - + +
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Residues in contact with GLN 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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931A GLU* 3.3 17.8 + - - +
932A GLU* 3.0 11.6 + - - +
934A LYS* 1.3 80.8 - - - +
936A LEU* 1.3 57.1 + - + +
937A VAL 3.2 0.4 - - - -
938A LYS* 3.5 23.3 + - - +
939A ASP* 3.0 39.3 + - - -
1023A ARG* 3.5 40.6 - - - +
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Residues in contact with LEU 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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885A THR* 4.0 6.0 - - + +
893A PHE* 3.3 22.4 - - + -
897A TYR* 3.2 40.6 - - + +
932A GLU* 3.0 44.1 + - + +
933A TYR* 3.7 12.6 - - - +
934A LYS 3.1 0.6 + - - -
935A GLN* 1.3 75.3 - - + +
937A VAL* 1.3 58.3 + - - +
939A ASP* 3.9 9.9 - - + +
940A ARG* 3.6 10.2 + - - +
1020A CYS 5.7 0.2 - - - +
1023A ARG* 3.6 44.6 - - + +
1024A SER* 4.3 5.2 - - - +
1027A ALA* 4.4 3.8 - - + -
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Residues in contact with VAL 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A PHE* 4.5 11.4 - - + -
933A TYR* 3.3 30.9 + - + +
934A LYS* 2.7 11.8 + - + +
936A LEU* 1.3 78.1 - - - +
938A LYS* 1.3 66.2 + - - +
939A ASP 2.8 6.0 + - - -
940A ARG* 3.7 7.0 - - + +
941A LYS* 3.2 24.2 + - + +
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Residues in contact with LYS 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 LYS* 2.8 17.8 + - + +
935A GLN* 3.5 30.1 - - - +
937A VAL* 1.3 77.9 - - - +
939A ASP* 1.3 59.4 + - - +
941A LYS* 4.2 0.5 - - - +
942A PHE* 3.2 25.9 + - + +
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Residues in contact with ASP 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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885A THR* 4.7 7.6 - - + -
935A GLN* 3.0 24.6 + - - +
936A LEU* 4.1 9.2 - - + +
937A VAL 2.8 1.2 - - - -
938A LYS* 1.3 77.2 - - - +
940A ARG* 1.3 67.6 + - - +
941A LYS 3.0 2.0 - - - -
942A PHE* 2.7 19.2 + - - +
943A LEU* 2.8 17.3 + - + +
1020A CYS* 3.5 30.3 - - + +
1023A ARG* 2.7 43.7 + - - +
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Residues in contact with ARG 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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885A THR* 2.8 35.2 + - + +
886A ILE* 4.3 0.6 - - - +
887A GLY 2.8 11.7 + - - -
888A GLY 2.3 36.4 + - - -
889A SER 3.3 8.0 + - - -
890A ASP* 3.2 39.9 + - - +
893A PHE* 3.3 26.8 - - + +
936A LEU 3.6 17.0 + - - +
937A VAL* 3.3 9.5 + - + +
939A ASP* 1.3 77.0 - - - +
941A LYS* 1.3 58.5 + - - +
943A LEU* 4.2 3.9 - - - +
944A ARG* 2.9 58.6 + - - +
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Residues in contact with LYS 941 (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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937A VAL* 3.2 13.7 + - + +
938A LYS 5.1 0.4 - - - +
939A ASP 3.0 0.6 - - - -
940A ARG* 1.3 77.8 - - + +
942A PHE* 1.3 64.8 + - - +
943A LEU 3.1 1.1 - - - -
944A ARG* 4.2 13.7 - - + +
945A GLU* 3.0 27.5 + - - +
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Residues in contact with PHE 942 (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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938A LYS 3.2 21.0 + - - +
939A ASP* 2.7 14.8 + - - +
941A LYS* 1.3 73.2 - - - +
943A LEU* 1.3 82.0 + - + +
945A GLU* 3.2 22.1 - - + +
946A VAL* 3.3 23.4 + - + +
1016A THR* 3.6 30.1 - - + -
1017A LEU* 5.5 1.6 - - + -
1020A CYS* 4.1 9.6 - - - -
201E LYS* 4.6 4.5 - - - -
206E GLY* 3.7 22.4 - - - -
207E ARG* 3.6 41.5 - - + -
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Residues in contact with LEU 943 (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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883A LEU* 4.1 27.4 - - + -
885A THR* 4.3 15.7 - - - -
886A ILE* 3.0 35.4 - - + -
939A ASP 2.8 15.7 + - - +
940A ARG 4.2 0.7 - - - +
942A PHE* 1.3 86.0 - - + +
944A ARG* 1.3 54.4 + - - +
945A GLU 2.8 4.3 - - - -
946A VAL* 2.6 24.0 + - - +
947A PHE* 2.7 28.7 + - + -
1017A LEU* 4.9 4.9 - - + -
1020A CYS* 3.7 41.1 - - + -
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Residues in contact with ARG 944 (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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886A ILE* 3.2 34.5 + - + +
887A GLY 3.8 1.6 + - - -
888A GLY 3.2 4.0 + - - -
890A ASP* 4.9 2.4 + - - -
940A ARG* 2.9 65.9 + - - +
941A LYS* 3.6 16.1 + - + +
943A LEU* 1.3 76.6 - - - +
945A GLU* 1.3 61.2 + - - +
947A PHE 4.8 2.2 - - - +
948A VAL* 3.6 20.8 - - - +
1292A PRO* 3.8 22.1 - - - +
1296A GLY* 3.0 29.0 + - - -
1297A GLU* 5.0 0.2 - - - +
1298A TYR* 3.4 32.0 + - - +
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Residues in contact with GLU 945 (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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941A LYS* 3.0 21.2 + - - +
942A PHE* 3.2 14.8 - - - +
943A LEU 2.7 0.4 + - - -
944A ARG* 1.3 77.1 - - - +
946A VAL* 1.3 64.0 + - + +
948A VAL* 3.3 18.7 - - - +
201E LYS* 3.1 30.8 + - + +
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Residues in contact with VAL 946 (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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942A PHE* 3.3 29.1 + - + +
943A LEU* 2.6 11.4 + - - +
945A GLU* 1.3 77.2 - - + +
947A PHE* 1.3 90.2 + - + +
948A VAL* 3.3 8.5 + - - +
949A ASP* 5.0 0.5 - - - +
201E LYS* 3.4 42.6 - - + +
202E SER 4.2 17.0 - - - +
203E GLU* 4.9 0.9 - - + +
206E GLY* 4.5 3.4 - - - +
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Residues in contact with PHE 947 (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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883A LEU* 4.7 5.4 - - + -
886A ILE* 5.1 7.6 - - + +
943A LEU* 2.7 33.6 + - + +
944A ARG* 4.1 5.5 - - - +
946A VAL* 1.3 91.6 - - + +
948A VAL* 1.3 51.2 + - - +
949A ASP* 2.7 23.9 + - - +
950A GLY* 3.0 13.9 + - - -
951A GLU 3.9 12.6 - - - +
954A TRP* 2.9 57.7 - + + +
1017A LEU* 3.6 26.7 - - + -
1298A TYR* 4.6 2.3 + - - -
203E GLU* 3.4 38.1 - - + -
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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
------------------------------------------------------------
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