Contacts of the helix formed by residues 931 - 950 (chain A) in PDB entry 1TXD
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 PRO 931 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A GLN* 3.3 34.1 - - + +
895A LEU* 5.1 2.9 - - + -
927A LYS 3.0 25.4 - - - +
928A ASP* 3.5 10.3 - - - +
929A ILE 3.2 4.3 - - - -
930A ILE* 1.3 92.5 - - + +
932A THR* 1.3 60.5 + - - -
933A GLN 3.3 1.3 - - - -
934A MET* 3.7 7.1 + - + +
935A GLN* 3.3 21.5 + - - +
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Residues in contact with THR 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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802A HIS* 3.7 8.1 + - - -
805A THR* 3.6 31.5 - - + +
806A LEU* 4.5 10.6 - - - +
809A LEU* 4.9 1.2 - - - +
928A ASP 4.4 4.3 - - - +
929A ILE* 2.7 32.7 + - + +
930A ILE 2.9 2.8 + - - -
931A PRO* 1.3 75.7 - - - +
933A GLN* 1.4 67.9 + - - +
935A GLN* 3.3 7.1 + - - +
936A ARG* 3.1 24.1 + - - +
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Residues in contact with GLN 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A HIS* 2.9 28.1 + - - -
806A LEU* 3.7 4.8 - - + +
838A ILE* 3.6 30.5 - - + +
842A HIS* 2.8 29.8 + - - -
880A LEU* 4.7 1.8 - - - +
884A ALA* 4.2 6.3 - - + +
887A PHE* 3.6 31.4 - - + -
888A CYS* 3.7 17.0 - - - -
930A ILE 3.5 2.0 + - - +
931A PRO 3.3 0.6 - - - -
932A THR* 1.4 77.6 + - - +
934A MET* 1.3 66.6 + - - +
935A GLN 3.2 0.3 + - - -
936A ARG* 3.3 5.7 + - - +
937A LEU* 3.3 37.2 + - + +
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Residues in contact with MET 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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888A CYS* 3.6 15.7 - - + -
891A GLN* 4.9 9.6 - - - +
931A PRO* 3.7 10.5 + - + +
932A THR 3.5 0.2 - - - -
933A GLN* 1.3 78.1 - - - +
935A GLN* 1.3 64.7 + - - +
937A LEU* 3.1 14.1 + - + -
938A THR* 3.3 22.4 + - + +
971A LEU* 3.5 22.7 - - + -
974A VAL* 4.0 25.4 - - + -
975A ASN* 3.1 27.4 - - - +
978A VAL* 4.1 18.2 - - + -
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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
----------------------------------------------------------
931A PRO 3.3 12.0 + - - +
932A THR* 3.3 10.7 + - - +
933A GLN 3.2 0.8 - - - -
934A MET* 1.3 79.3 - - - +
936A ARG* 1.3 62.5 + - - +
938A THR* 2.4 42.5 + - - +
939A LYS* 3.4 38.3 + - + +
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Residues in contact with ARG 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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795A LEU* 3.4 11.7 + - - +
798A THR* 3.0 37.2 + - - -
799A GLU* 2.7 46.2 + - - +
802A HIS* 3.4 46.6 - - + +
842A HIS* 4.4 2.2 - - + -
932A THR 3.1 5.7 + - - +
933A GLN 3.5 5.8 - - - +
934A MET 3.3 0.2 - - - -
935A GLN* 1.3 77.0 - - - +
937A LEU* 1.3 57.2 - - + +
939A LYS* 3.0 34.4 + - - +
940A TYR* 3.4 39.0 + - + +
943A LEU* 3.6 15.7 - - - +
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Residues in contact with LEU 937 (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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842A HIS* 4.9 0.2 - - - +
880A LEU* 4.2 12.1 - - + -
884A ALA* 3.5 25.8 - - + -
888A CYS* 5.0 1.8 - - - -
933A GLN* 3.3 34.6 + - + +
934A MET* 3.1 17.5 + - + +
936A ARG* 1.3 81.5 - - + +
938A THR* 1.3 62.4 + - - +
939A LYS 3.4 0.5 + - - -
940A TYR* 3.8 19.3 + - + +
941A PRO* 3.5 14.4 - - - +
967A CYS 5.2 1.0 - - - +
970A ILE* 4.3 18.2 - - + +
971A LEU* 4.0 15.5 - - + +
974A VAL* 3.7 28.0 - - + -
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Residues in contact with THR 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 MET* 3.4 30.3 - - + +
935A GLN* 2.4 45.1 + - - +
937A LEU* 1.3 75.8 - - - +
939A LYS* 1.3 60.6 + - - +
940A TYR 3.6 0.2 - - - -
941A PRO* 3.3 14.3 - - - +
942A LEU* 3.9 14.9 - - - +
971A LEU* 4.1 17.8 - - + +
975A ASN* 6.1 0.4 - - - +
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Residues in contact with LYS 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 GLN* 3.5 44.3 - - + +
936A ARG* 3.0 20.7 + - - +
938A THR* 1.3 79.6 + - - +
940A TYR* 1.3 66.8 + - - +
941A PRO* 3.3 3.1 - - - -
942A LEU* 3.1 21.0 + - + +
943A LEU* 3.1 36.9 + - + +
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Residues in contact with TYR 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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795A LEU* 4.1 15.0 - - + -
799A GLU* 2.6 30.7 + - - -
842A HIS* 3.2 21.4 - + - -
845A LEU* 3.8 4.2 - - + +
872A PHE* 3.8 32.3 - + - -
880A LEU* 4.3 19.1 - - + -
936A ARG* 3.4 44.4 + - + -
937A LEU* 3.8 19.9 + - + +
939A LYS* 1.3 77.8 - - - +
941A PRO* 1.3 69.4 - - + +
943A LEU* 3.3 3.3 + - + -
944A LEU* 3.0 29.8 + - + +
967A CYS* 3.7 19.5 - - + -
970A ILE* 6.5 0.4 - - + -
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Residues in contact with PRO 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 LEU 3.5 10.5 - - - +
938A THR 3.3 14.4 - - - +
939A LYS 3.3 4.9 - - - -
940A TYR* 1.3 93.0 - - + +
942A LEU* 1.3 59.5 + - + +
944A LEU* 3.5 3.1 + - + +
945A ASP* 2.9 35.4 + - - +
964A ALA* 4.3 5.7 - - - +
967A CYS* 4.1 19.0 - - + -
968A ARG* 4.0 38.6 - - + +
971A LEU* 4.4 11.4 - - + -
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Residues in contact with LEU 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 THR 3.9 20.0 - - - +
939A LYS* 3.1 22.3 + - + +
941A PRO* 1.3 78.8 - - + +
943A LEU* 1.3 67.5 + - + +
945A ASP* 3.3 12.9 + - - +
946A ASN* 3.0 30.8 + - - +
968A ARG* 5.5 1.6 - - - +
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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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791A VAL* 4.9 3.1 - - - +
794A GLU* 3.7 31.6 - - + +
795A LEU* 4.2 30.7 - - + +
798A THR* 4.1 6.1 - - + +
936A ARG* 3.6 27.6 - - - +
939A LYS* 3.1 28.0 + - + +
940A TYR* 3.7 8.7 - - - +
942A LEU* 1.3 80.0 - - + +
944A LEU* 1.3 66.0 + - + +
946A ASN* 3.4 8.6 + - - +
947A ILE* 3.2 27.7 + - - +
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Residues in contact with LEU 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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795A LEU* 4.5 17.5 - - + -
868A LEU* 4.2 18.8 - - + -
872A PHE* 3.8 31.9 - - + -
940A TYR* 3.0 26.2 + - - +
941A PRO 4.0 0.2 - - - +
943A LEU* 1.3 80.3 - - + +
945A ASP* 1.3 68.0 + - - +
946A ASN 3.1 1.8 - - - -
947A ILE* 3.2 6.0 + - + -
948A ALA* 3.0 18.2 + - - +
960A VAL* 3.3 12.9 - - + +
963A ALA* 3.7 38.1 - - + -
964A ALA* 3.7 16.8 - - + +
967A CYS* 3.9 5.8 - - - -
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Residues in contact with ASP 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 PRO 2.9 18.7 + - - +
942A LEU* 3.3 12.9 + - - +
944A LEU* 1.3 77.0 - - - +
946A ASN* 1.3 59.1 + - - +
948A ALA* 3.3 8.8 + - - +
949A LYS* 2.9 26.5 + - - +
961A LYS* 5.7 2.4 - - - +
964A ALA* 3.5 13.3 - - - +
968A ARG* 2.4 36.5 + - - -
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Residues in contact with ASN 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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791A VAL* 4.0 22.9 - - + +
942A LEU* 3.0 20.1 + - - +
943A LEU* 3.7 8.3 - - - +
945A ASP* 1.3 75.5 - - - +
947A ILE* 1.3 68.2 + - - +
949A LYS* 3.3 27.8 + - - +
950A TYR* 3.3 24.3 - - - -
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Residues in contact with ILE 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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788A ARG* 4.5 5.0 - - + +
791A VAL* 3.7 31.9 - - + +
792A ILE* 4.0 26.7 - - + +
795A LEU* 3.9 28.5 - - + -
864A ILE* 4.4 9.9 - - + -
868A LEU* 4.7 9.9 - - + -
943A LEU 3.2 16.0 + - - +
944A LEU* 3.2 12.3 + - + +
946A ASN* 1.3 77.5 - - - +
948A ALA* 1.3 60.6 + - - +
950A TYR* 3.2 12.3 + - - +
951A THR* 2.8 24.8 + - - +
960A VAL* 4.1 17.5 - - + -
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Residues in contact with ALA 948 (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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944A LEU 3.0 8.8 + - - +
945A ASP* 3.4 12.3 - - - +
947A ILE* 1.3 76.8 - - - +
949A LYS* 1.3 62.7 + - - +
951A THR* 3.1 26.2 + - - +
957A ARG* 3.9 12.4 + - + +
960A VAL* 3.4 23.0 - - + +
961A LYS* 3.6 30.3 - - + +
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Residues in contact with LYS 949 (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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945A ASP 2.9 13.9 + - - +
946A ASN* 3.3 26.1 + - - +
948A ALA* 1.3 78.0 - - - +
950A TYR* 1.3 92.8 + - + +
951A THR 3.3 3.9 + - - +
957A ARG* 5.3 3.1 + - - -
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Residues in contact with TYR 950 (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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784A CYS* 4.0 16.9 - - + +
785A GLU* 5.1 0.5 - - - +
787A LYS* 3.7 41.0 - - + +
788A ARG* 3.2 39.2 - - + +
791A VAL* 4.1 22.2 - - + -
946A ASN* 3.3 26.4 + - - +
947A ILE 3.2 7.6 + - - +
949A LYS* 1.3 112.8 + - + +
951A THR* 1.3 59.4 + - - +
952A GLU* 4.0 7.5 + - - +
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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
------------------------------------------------------------
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