Contacts of the helix formed by residues 929 - 946 (chain A) in PDB entry 5AMN
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 929 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A VAL* 3.4 19.3 - - - +
903A ASP 3.5 22.4 - - - +
904A SER* 3.8 12.3 - - - -
921A GLU* 4.8 3.4 + - + +
927A ILE* 4.3 11.9 + - + +
928A TYR* 1.3 81.5 - - - +
930A THR* 1.3 63.7 + - - +
931A GLN* 3.2 20.5 + - - +
932A SER* 2.6 35.6 + - - -
933A ASP 3.1 6.2 + - - -
992A PRO* 5.4 1.9 - - - +
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Residues in contact with THR 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ALA* 3.5 38.5 + - + +
869A LYS* 5.4 1.9 - - - -
870A LEU 4.8 2.9 + - - -
871A VAL* 3.9 11.1 - - - +
899A VAL* 5.3 4.4 - - - +
903A ASP 5.1 0.8 + - - -
929A THR* 1.3 75.1 - - - +
931A GLN* 1.3 69.7 + - - +
933A ASP* 3.1 13.6 + - + +
934A VAL* 3.0 23.9 + - - +
998A PHE* 4.0 11.7 - - + -
2015A FMT 3.8 11.0 - - - +
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Residues in contact with GLN 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A THR* 3.1 10.4 + - - +
930A THR* 1.3 92.8 - - - +
932A SER* 1.3 58.4 + - - +
934A VAL* 3.2 29.8 - - - +
935A TRP 3.3 2.1 + - - -
992A PRO* 3.2 42.0 - - + +
993A ASP* 4.8 4.1 - - - +
995A ARG* 2.9 38.6 + - - +
996A PRO 3.5 9.2 - - - +
997A VAL* 3.9 21.8 - - - +
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Residues in contact with SER 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A VAL* 4.7 1.4 - - - +
919A ALA* 3.9 7.0 + - - +
921A GLU* 3.5 17.2 + - - -
922A SER* 3.6 18.4 - - - -
927A ILE 4.4 0.9 - - - -
928A TYR* 3.5 8.6 - - - +
929A THR* 2.6 40.1 + - - -
931A GLN* 1.3 74.5 - - - +
933A ASP* 1.3 64.8 + - - +
934A VAL 3.1 1.6 - - - -
935A TRP* 3.2 12.5 + - - +
936A SER* 3.2 14.7 + - - -
995A ARG* 3.8 8.4 - - - +
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Residues in contact with ASP 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A MET* 3.7 16.6 - - + +
870A LEU 4.3 1.2 - - - +
871A VAL* 3.2 20.5 - - - +
872A HIS* 2.9 25.3 + - - +
873A ARG* 2.9 28.2 + - - -
874A ASP 4.6 0.3 + - - -
875A LEU* 3.6 15.4 + - + +
929A THR 3.1 6.4 + - - +
930A THR* 3.2 16.2 - - - +
932A SER* 1.3 78.1 + - - +
934A VAL* 1.3 54.2 + - - +
936A SER* 3.3 6.9 + - - +
937A PHE* 3.0 23.2 + - - +
998A PHE* 3.9 14.6 - - + -
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Residues in contact with VAL 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A THR 3.0 18.8 + - - +
931A GLN* 3.2 22.7 - - - +
932A SER 3.1 0.2 - - - -
933A ASP* 1.3 74.5 - - - +
935A TRP* 1.3 65.3 + - - +
937A PHE* 3.2 6.1 + - - +
938A GLY 3.1 15.6 + - - -
987A CYS* 3.5 33.7 - - + +
995A ARG* 4.2 7.4 - - + -
996A PRO* 3.4 27.8 - - + +
998A PHE* 3.8 30.1 - - + +
1001A ILE* 4.2 6.1 - - + -
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Residues in contact with TRP 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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916A LYS 5.4 1.0 + - - -
917A TRP 3.7 13.1 + - - -
918A MET 3.2 10.1 + - - -
919A ALA* 3.5 27.6 - - + -
920A ILE* 4.0 22.7 - - + -
931A GLN 3.3 3.0 + - - -
932A SER 3.2 11.5 + - - +
934A VAL* 1.3 78.4 - - - +
936A SER* 1.3 59.1 + - - +
938A GLY* 2.9 17.7 + - - -
939A VAL* 3.3 16.8 + - + +
952A TYR* 4.5 7.8 + - - -
964A LEU* 4.2 24.7 - - + +
969A ARG* 3.6 29.4 - - - -
987A CYS 3.4 12.1 - - - +
988A TRP* 3.3 41.8 + + - -
989A LYS 3.7 2.0 - - - -
995A ARG* 3.2 38.1 - - - +
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Residues in contact with SER 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A ARG 5.2 5.5 + - - -
874A ASP* 5.6 0.2 - - - -
875A LEU* 3.6 37.2 + - - +
913A ILE* 6.0 1.2 - - - +
917A TRP* 2.7 28.6 + - - +
918A MET* 4.6 2.4 - - - -
919A ALA 5.1 0.2 + - - -
932A SER 3.2 8.6 + - - -
933A ASP* 3.6 11.1 + - - -
934A VAL 3.3 0.2 - - - -
935A TRP* 1.3 79.9 - - - +
937A PHE* 1.3 56.6 + - - +
939A VAL* 3.2 7.7 + - - +
940A LEU* 2.9 26.3 + - - +
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Residues in contact with PHE 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A ALA* 3.7 27.4 - - + -
858A ILE* 4.1 18.6 - - + -
859A SER* 4.0 13.2 - - - -
875A LEU* 3.8 12.9 - - + +
933A ASP 3.0 14.0 + - - +
934A VAL 3.2 8.7 + - - +
936A SER* 1.3 76.1 - - - +
938A GLY* 1.3 53.6 + - - +
940A LEU* 3.2 13.9 + - + +
941A LEU* 2.8 61.6 + - + +
944A ILE* 6.3 0.9 - - + -
987A CYS* 4.5 2.9 - - - -
998A PHE* 3.9 18.8 - + + -
1001A ILE* 3.5 42.0 - - + -
1005A LEU* 4.1 4.9 - - + -
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Residues in contact with GLY 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 VAL 3.1 5.9 + - - -
935A TRP 2.9 10.6 + - - -
937A PHE* 1.3 75.1 - - - +
939A VAL* 1.3 62.4 + - - +
941A LEU* 3.4 10.7 - - - +
942A TRP 3.2 15.4 + - - -
984A MET* 3.8 4.2 - - - +
987A CYS* 3.9 18.4 - - - -
988A TRP* 3.3 25.2 - - - -
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Residues in contact with VAL 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A LYS 4.0 15.9 - - - +
917A TRP* 3.8 24.2 - - + +
935A TRP* 3.8 24.9 - - + +
936A SER 3.2 6.8 + - - +
938A GLY* 1.3 73.1 - - - +
940A LEU* 1.3 61.0 + - - +
942A TRP* 3.1 5.0 + - - +
943A GLU* 3.0 26.7 + - - +
951A PRO* 3.6 35.2 - - + -
952A TYR* 5.1 3.1 - - - +
970A MET* 4.2 9.0 - - + -
988A TRP* 3.8 18.4 - - + +
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Residues in contact with LEU 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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812A LEU* 4.6 4.0 - - + -
858A ILE* 3.8 28.9 - - + -
875A LEU* 3.8 27.4 - - + -
876A ALA* 4.8 5.6 - - - +
877A ALA* 3.3 42.4 - - + +
880A ILE* 4.2 4.3 - - + -
917A TRP* 5.1 0.4 - - - +
936A SER 2.9 13.9 + - - +
937A PHE* 3.3 17.9 - - + +
938A GLY 3.2 0.2 - - - -
939A VAL* 1.3 74.8 - - - +
941A LEU* 1.3 64.6 + - - +
943A GLU* 3.2 6.8 + - - +
944A ILE* 3.1 38.2 + - + +
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Residues in contact with LEU 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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855A ALA* 3.8 28.7 - - + -
937A PHE* 2.8 39.1 + - + +
938A GLY* 3.4 13.5 - - - +
939A VAL 3.3 0.2 - - - -
940A LEU* 1.3 73.6 - - - +
942A TRP* 1.3 60.6 + - - +
944A ILE* 3.5 7.5 + - + +
945A VAL* 3.1 29.1 + - + +
980A MET* 3.7 22.7 - - + -
983A LEU* 3.5 33.9 - - + -
984A MET* 3.9 23.8 - - + +
987A CYS* 4.8 0.9 - - - -
1005A LEU* 4.7 2.9 - - + -
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Residues in contact with TRP 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A GLY 3.2 9.7 + - - +
939A VAL 3.1 10.9 + - - +
940A LEU 3.1 0.4 - - - -
941A LEU* 1.3 77.5 - - - +
943A GLU* 1.3 70.6 + - - +
945A VAL* 3.4 1.4 + - - -
946A THR* 3.1 47.8 + - + +
949A GLY* 3.3 17.0 - - - -
950A ASN 3.1 42.8 - - - -
951A PRO* 3.4 14.6 - - + -
953A PRO* 4.3 14.8 - - + -
970A MET* 3.6 33.8 - - + +
971A GLU 3.9 11.0 + - - -
973A PRO* 3.3 29.3 - - + +
984A MET* 4.1 20.6 - - - -
988A TRP* 4.5 3.1 - + - -
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Residues in contact with GLU 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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813A ARG* 3.4 23.2 + - - -
816A LEU* 4.5 0.9 - - - -
876A ALA* 3.7 1.2 - - - -
877A ALA* 2.8 48.3 + - + +
878A ARG* 4.7 1.6 + - - -
917A TRP* 3.0 34.8 + - - +
939A VAL 3.0 14.5 + - - +
940A LEU* 3.2 11.2 + - - +
942A TRP* 1.3 76.2 - - + +
944A ILE* 1.3 61.4 + - - +
946A THR* 3.2 7.1 + - - -
947A LEU 3.0 4.0 + - - -
948A GLY* 2.6 32.8 + - - -
949A GLY 4.1 12.8 - - - +
951A PRO* 4.5 7.9 - - + -
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Residues in contact with ILE 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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812A LEU* 4.1 28.3 - - + -
816A LEU* 3.7 11.6 - - + +
851A LEU* 3.7 41.8 - - + +
854A PHE* 4.7 5.4 - - + -
855A ALA* 4.2 32.8 - - + +
858A ILE* 4.5 3.8 - - + -
937A PHE* 6.3 0.7 - - + -
940A LEU* 3.1 28.5 + - + +
941A LEU* 3.7 10.3 - - + +
943A GLU* 1.3 75.7 - - - +
945A VAL* 1.3 61.7 + - + +
947A LEU* 2.9 28.4 + - - +
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Residues in contact with VAL 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A LEU* 4.6 13.9 - - + +
941A LEU* 3.1 17.2 + - + +
942A TRP 4.0 2.9 - - - +
943A GLU 3.4 0.2 - - - -
944A ILE* 1.3 84.7 - - + +
946A THR* 1.3 59.4 + - - +
947A LEU* 3.2 5.3 + - - +
973A PRO* 4.0 11.6 - - + +
975A ASN* 3.1 35.7 - - - +
976A CYS* 3.2 21.5 - - + -
980A MET* 3.9 30.3 - - + -
984A MET* 4.2 5.8 - - + -
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Residues in contact with THR 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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820A ARG* 3.4 12.0 + - - -
942A TRP* 3.1 41.2 + - + +
943A GLU 3.2 1.6 + - - -
945A VAL* 1.3 75.4 - - - +
947A LEU* 1.3 69.8 + - - +
949A GLY* 2.8 34.3 + - - -
973A PRO* 3.7 29.2 - - + -
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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