Contacts of the helix formed by residues 937 - 958 (chain A) in PDB entry 1FVR
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 SER 937 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935A THR 4.1 0.6 + - - -
936A LEU* 1.3 76.0 - - - +
938A SER* 1.3 64.0 + - - +
939A GLN* 3.3 10.2 + - - +
940A GLN* 2.8 36.9 + - - +
941A LEU* 3.0 24.8 + - - +
1105A THR* 4.4 6.1 - - - -
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Residues in contact with SER 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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937A SER* 1.3 74.0 - - - +
939A GLN* 1.3 63.9 + - - +
941A LEU* 3.3 3.9 + - - +
942A LEU* 3.0 29.6 + - - +
1101A THR* 4.0 16.1 - - - -
1102A TYR* 3.3 11.1 + - - +
1103A VAL* 2.9 52.9 + - - +
1105A THR* 4.5 4.8 + - - +
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Residues in contact with GLN 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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937A SER* 3.2 9.2 + - - +
938A SER* 1.3 80.5 - - - +
940A GLN* 1.3 58.5 + - + +
942A LEU* 3.4 2.7 + - - +
943A HIS* 2.9 49.7 + - + -
1095A MET 4.5 1.2 - - - +
1096A LEU* 3.1 53.0 + - - +
1098A GLU 4.0 9.0 - - - +
1100A LYS 5.1 3.5 - - - +
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Residues in contact with GLN 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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935A THR 3.8 6.0 + - - +
936A LEU* 3.4 25.7 - - + +
937A SER* 2.8 42.1 + - - +
939A GLN* 1.3 76.2 - - + +
941A LEU* 1.3 65.8 + - - +
943A HIS* 3.3 9.8 + - + +
944A PHE* 3.1 31.7 + - + -
976A TYR* 6.3 0.4 - - - -
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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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914A LEU* 3.8 28.7 - - + -
936A LEU* 3.9 22.7 - - + +
937A SER 3.0 19.1 + - - +
938A SER* 3.7 5.6 - - - +
940A GLN* 1.3 77.2 - - - +
942A LEU* 1.3 62.8 + - - +
944A PHE* 3.1 17.9 + - + +
945A ALA* 3.2 9.0 + - - +
1031A ILE* 3.5 28.1 - - + +
1034A LEU* 4.1 15.3 - - + -
1103A VAL* 3.6 33.9 - - + -
1105A THR* 4.0 19.5 - - + -
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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 SER* 3.0 21.2 + - - +
939A GLN* 5.4 2.0 - - - +
941A LEU* 1.3 78.0 - - - +
943A HIS* 1.3 57.1 + - - +
945A ALA* 3.1 8.2 + - + +
946A ALA* 2.8 28.9 + - - +
1028A LEU* 5.1 3.8 - - + -
1031A ILE* 6.3 0.7 - - + -
1032A VAL* 5.9 0.4 - - + -
1067A VAL* 4.7 14.4 - - + -
1092A LEU* 4.3 23.6 - - + +
1095A MET* 4.2 20.9 - - + -
1096A LEU* 3.5 30.1 - - + +
1102A TYR* 3.9 26.7 - - + -
1103A VAL* 3.9 20.6 - - + -
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Residues in contact with HIS 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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939A GLN* 2.9 48.7 + - + +
940A GLN* 3.6 10.1 - - + +
941A LEU 3.2 0.4 - - - -
942A LEU* 1.3 73.6 - - - +
944A PHE* 1.3 61.2 + - + +
946A ALA* 3.7 7.0 - - - +
947A ASP* 2.9 39.7 + - - +
950A ARG* 5.5 4.2 + - - -
1096A LEU* 3.5 25.9 - - + +
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Residues in contact with PHE 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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910A LEU* 3.8 26.0 - - + -
913A PHE* 3.8 32.1 - + - -
914A LEU* 4.8 2.0 - - + -
936A LEU* 4.1 19.5 - - + -
940A GLN* 3.1 23.0 + - + -
941A LEU* 3.1 20.4 + - + +
943A HIS* 1.3 75.7 - - + +
945A ALA* 1.3 64.9 + - - +
947A ASP* 3.2 7.8 + - - +
948A VAL* 3.1 27.7 + - - +
972A VAL* 4.4 13.5 - - + -
976A TYR* 3.4 29.4 - + + -
978A ALA* 4.1 15.8 - - + +
1031A ILE* 4.0 13.2 - - + -
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Residues in contact with ALA 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 LEU 3.2 8.0 + - - +
942A LEU* 3.1 11.6 + - + +
944A PHE* 1.3 80.0 - - - +
946A ALA* 1.3 62.0 + - - +
948A VAL* 3.4 1.8 + - - -
949A ALA* 3.0 14.2 + - - +
1024A TYR* 2.7 32.6 + - - +
1028A LEU* 3.7 25.4 - - + -
1031A ILE* 3.7 12.7 - - + +
1092A LEU* 3.6 10.5 - - + -
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Residues in contact with ALA 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 LEU 2.8 15.9 + - - +
943A HIS* 3.7 9.6 - - - +
945A ALA* 1.3 76.0 - - - +
947A ASP* 1.3 58.3 + - - +
949A ALA 3.2 0.9 + - - -
950A ARG* 2.8 49.1 + - - +
1089A LEU* 3.6 14.9 - - + +
1092A LEU* 3.5 15.8 - - + +
1093A ASN* 4.6 1.8 - - - +
1096A LEU* 4.2 15.9 - - + -
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Residues in contact with ASP 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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884A ASN* 3.2 30.7 + - - +
943A HIS* 2.9 29.2 + - - +
944A PHE* 3.4 7.9 - - - +
946A ALA* 1.3 76.4 - - - +
948A VAL* 1.3 58.5 + - - +
950A ARG* 2.9 24.0 + - - +
951A GLY 3.0 22.9 + - - -
976A TYR 4.3 3.3 - - - +
977A VAL* 3.9 8.7 - - - +
978A ALA* 3.1 31.6 + - + +
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Residues in contact with VAL 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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884A ASN* 5.4 0.2 - - - -
910A LEU* 5.0 4.3 - - + -
944A PHE 3.1 15.9 + - - +
945A ALA* 3.9 6.5 - - - +
947A ASP* 1.3 75.7 - - - +
949A ALA* 1.3 53.9 + - - +
951A GLY 3.2 0.7 + - - -
952A MET* 2.8 39.0 + - + +
965A LEU* 4.5 2.7 - - + -
970A ILE* 4.0 48.0 - - + -
978A ALA* 4.4 4.7 - - + -
980A ILE* 3.6 15.2 - - + +
1024A TYR* 3.9 22.7 - - + -
1027A LEU* 4.1 13.0 - - + -
1031A ILE* 5.4 1.3 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.3 + - - +
946A ALA 3.7 3.8 - - - +
948A VAL* 1.3 76.2 - - - +
950A ARG* 1.3 57.2 + - - +
953A ASP* 3.0 29.5 + - - +
1024A TYR* 3.9 16.5 - - + +
1085A PHE* 3.8 23.3 - - + +
1088A ILE* 3.9 20.2 - - + -
1089A LEU* 4.4 8.1 - - + +
1092A LEU* 4.1 6.1 - - + -
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Residues in contact with ARG 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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882A HIS* 3.9 17.5 + - + +
884A ASN* 2.8 28.3 + - - +
943A HIS* 5.5 4.9 + - - -
946A ALA* 2.8 31.7 + - - +
947A ASP* 2.9 25.3 + - - +
949A ALA* 1.3 75.4 - - - +
951A GLY* 1.3 62.9 + - - +
953A ASP* 3.4 5.6 + - - +
954A TYR* 3.2 21.7 + - - +
1089A LEU* 4.0 30.6 - - + +
1093A ASN* 4.7 6.3 + - - +
1096A LEU* 6.2 0.2 - - - +
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Residues in contact with GLY 951 (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 HIS* 4.1 8.5 - - - -
884A ASN* 3.7 22.6 - - - +
885A ILE* 4.2 2.2 - - - +
947A ASP 3.0 10.9 + - - -
948A VAL 3.6 3.1 - - - -
950A ARG* 1.3 78.3 - - - +
952A MET* 1.3 56.2 + - - +
954A TYR* 3.4 4.2 + - - +
955A LEU* 3.1 31.0 + - - +
980A ILE* 3.6 12.6 - - - -
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Residues in contact with MET 952 (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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948A VAL* 2.8 27.0 + - + +
949A ALA 4.0 0.2 - - - +
951A GLY* 1.3 71.3 - - - +
953A ASP* 1.3 61.6 + - - +
955A LEU* 3.7 19.5 - - + +
956A SER* 2.8 38.1 + - - +
960A PHE* 5.2 2.7 - - + +
962A HIS* 4.2 11.0 - - + +
965A LEU* 3.8 33.0 - - + -
980A ILE* 3.7 18.6 - - + -
1020A ASP* 3.7 23.8 - - - +
1085A PHE* 3.6 40.6 - - + -
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Residues in contact with ASP 953 (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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949A ALA 3.0 18.1 + - - +
950A ARG* 3.6 8.4 - - - +
951A GLY 3.3 0.2 - - - -
952A MET* 1.3 75.6 - - - +
954A TYR* 1.3 64.0 + - - +
956A SER* 3.4 2.7 + - - -
957A GLN* 2.8 51.9 + - - +
1085A PHE* 3.8 14.8 - - + +
1086A ALA* 3.6 31.5 + - - +
1089A LEU* 5.6 5.3 - - + +
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Residues in contact with TYR 954 (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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879A LEU 2.6 29.6 + - - -
880A GLY* 3.4 0.5 - - - -
881A HIS 3.2 28.8 + - - -
882A HIS* 3.6 43.5 - + + +
885A ILE* 4.1 9.2 - - + -
950A ARG 3.2 5.9 + - - +
951A GLY 3.4 8.1 - - - +
952A MET 3.2 0.2 - - - -
953A ASP* 1.3 84.7 + - - +
955A LEU* 1.3 74.3 + - + +
957A GLN* 3.6 5.9 + - - +
958A LYS* 3.0 52.8 + - + +
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Residues in contact with LEU 955 (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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879A LEU* 4.1 20.6 - - + -
885A ILE* 4.0 22.0 - - + -
951A GLY 3.1 20.3 + - - +
952A MET* 4.0 26.7 - - + +
953A ASP 3.3 0.2 - - - -
954A TYR* 1.3 90.4 - - + +
956A SER* 1.3 60.7 + - - +
958A LYS* 2.9 17.9 + - - -
959A GLN 3.4 0.2 + - - -
960A PHE* 3.0 47.8 + - + +
980A ILE* 4.2 13.7 - - + -
982A ASP* 5.1 3.1 - - + -
985A LEU* 4.5 14.4 - - + -
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Residues in contact with SER 956 (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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952A MET* 2.8 30.8 + - - +
953A ASP* 3.4 6.8 + - - -
955A LEU* 1.3 72.9 - - - +
957A GLN* 1.3 62.7 + - - +
959A GLN* 2.8 25.1 + - - -
960A PHE 3.7 11.8 + - - -
1017A THR* 3.5 30.4 - - - +
1085A PHE* 3.8 16.2 - - - +
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Residues in contact with GLN 957 (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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953A ASP* 2.8 47.3 + - - +
954A TYR* 3.6 7.4 - - - +
956A SER* 1.3 79.5 + - - +
958A LYS* 1.3 61.1 - - + +
959A GLN* 3.3 11.4 + - - +
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Residues in contact with LYS 958 (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 LYS 2.9 27.3 + - - -
879A LEU 3.2 7.2 + - - -
880A GLY* 3.9 4.9 - - - +
954A TYR* 3.0 55.7 + - + +
955A LEU 2.9 9.7 + - - +
957A GLN* 1.3 82.1 - - + +
959A GLN* 1.3 70.0 + - - +
960A PHE* 3.2 12.6 + - + -
987A ARG* 3.1 27.1 + - - +
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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
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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