Contacts of the helix formed by residues 915 - 935 (chain A) in PDB entry 1FO4
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 GLY 915 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A PHE* 5.0 0.9 - - - -
877A ILE* 3.6 22.7 - - - -
881A ALA* 3.6 18.9 - - - +
914A PHE* 1.3 69.9 - - - +
916A GLY* 1.3 63.3 + - - +
918A GLN* 3.2 18.1 - - - +
919A ALA 3.2 17.0 + - - -
3007A GOL 2.7 16.1 + - - -
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Residues in contact with GLY 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ARG* 4.0 12.6 - - - +
884A HIS* 4.4 11.7 - - - -
913A GLY 2.9 13.2 + - - -
914A PHE 3.3 2.4 + - - -
915A GLY* 1.3 76.8 - - - +
917A PRO* 1.3 54.6 - - - +
919A ALA* 3.1 3.3 + - - +
920A LEU* 2.7 47.4 + - - +
1005A PHE* 4.4 8.1 - - - -
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Residues in contact with PRO 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A ARG* 4.0 7.9 - - - +
913A GLY* 3.3 32.1 - - - +
915A GLY 3.6 2.5 - - - -
916A GLY* 1.3 87.4 - - - +
918A GLN* 1.3 63.2 + - - +
920A LEU* 4.2 2.4 - - + -
921A PHE* 2.9 32.2 + - - +
1005A PHE* 4.8 2.9 - - + -
1205A LEU* 4.4 12.3 - - + -
1206A PHE* 4.2 7.3 - - + -
1261A GLU 6.0 0.2 - - - +
1264A LEU* 3.8 29.4 - - + -
1265A PHE* 3.9 20.9 - - + +
3007A GOL 4.0 0.4 - - - +
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Residues in contact with GLN 918 (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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736A ILE* 3.2 30.1 - - + +
737A GLY 6.1 0.4 - - - +
839A ARG* 3.4 15.3 - - - +
840A HIS 3.2 22.3 + - - +
842A PHE* 3.6 34.5 - - + -
915A GLY* 3.2 24.3 - - - +
916A GLY 3.2 0.2 - - - -
917A PRO* 1.3 79.0 - - + +
919A ALA* 1.3 63.8 + - - +
922A ILE* 3.1 30.6 + - - +
1205A LEU* 6.0 0.4 - - + -
3007A GOL 3.1 37.1 + - - -
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Residues in contact with ALA 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A HIS* 4.5 8.0 + - - +
881A ALA* 2.9 46.6 - - + +
884A HIS* 4.1 5.2 - - + +
885A MET* 4.1 13.3 - - - +
915A GLY 3.2 1.6 + - - -
916A GLY 3.1 6.5 + - - +
918A GLN* 1.3 77.5 - - - +
920A LEU* 1.3 65.5 + - - +
922A ILE* 3.4 11.1 + - - +
923A ALA* 3.1 23.4 + - - +
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Residues in contact with LEU 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A HIS* 3.3 32.8 - - + +
887A ASN* 3.5 32.9 + - - +
916A GLY* 2.7 36.5 + - - +
917A PRO* 4.2 0.7 - - + -
919A ALA* 1.3 72.6 - - - +
921A PHE* 1.3 63.0 + - - +
923A ALA* 3.4 4.3 + - - +
924A GLU* 3.0 20.3 + - - +
1003A THR* 3.6 19.1 - - - +
1004A LYS 4.4 9.4 - - - +
1005A PHE* 4.8 8.7 - - + -
1262A PRO 6.1 0.2 - - - +
1265A PHE* 3.3 42.7 - - + -
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Residues in contact with PHE 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A LEU* 3.4 30.3 - - + -
735A TYR 4.2 2.2 - - - -
736A ILE* 3.4 28.7 - - + -
917A PRO 2.9 19.7 + - - +
918A GLN 3.6 2.9 - - - +
920A LEU* 1.3 74.0 - - - +
922A ILE* 1.3 64.7 + - - +
924A GLU* 3.4 2.1 + - - +
925A ASN* 3.0 22.5 + - + +
1206A PHE* 3.7 25.4 - + + -
1265A PHE* 3.3 8.9 - + - -
1268A ALA* 5.1 0.7 - - + -
1271A PHE* 3.5 49.1 - + - -
1272A PHE* 4.1 14.1 - + - -
1296A LEU 4.3 4.0 - - - -
1298A SER* 3.6 23.8 - - - -
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Residues in contact with ILE 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A LEU* 3.8 19.3 - - + +
736A ILE* 4.1 12.6 - - + -
842A PHE* 4.3 11.4 - - + -
844A ALA* 3.4 35.2 - - + -
846A TYR* 5.0 8.9 - - + -
861A VAL* 4.0 17.0 - - + -
863A HIS* 3.5 24.0 - - + +
918A GLN 3.1 19.0 + - - +
919A ALA* 3.7 6.1 - - - +
920A LEU 3.3 0.2 - - - -
921A PHE* 1.3 76.0 - - - +
923A ALA* 1.3 66.3 + - - +
925A ASN* 3.1 10.9 + - - +
926A TRP* 3.2 21.4 + - + +
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Residues in contact with ALA 923 (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 MET 3.6 22.9 - - - +
886A ASP 4.8 0.9 - - - +
887A ASN* 4.4 15.3 - - + +
889A TYR* 5.6 2.2 - - + -
919A ALA 3.1 14.1 + - - +
920A LEU* 3.5 11.0 - - - +
921A PHE 3.3 0.2 - - - -
922A ILE* 1.3 78.7 - - - +
924A GLU* 1.3 63.9 + - - +
925A ASN 3.1 0.7 + - - -
926A TRP* 3.2 26.6 + - + +
927A MET* 3.0 21.4 + - - +
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Residues in contact with GLU 924 (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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887A ASN* 2.7 25.2 + - - +
889A TYR* 2.7 22.4 + - - -
920A LEU 3.0 12.2 + - - +
921A PHE 3.9 0.7 - - - +
923A ALA* 1.3 75.5 - - - +
925A ASN* 1.3 57.8 + - - +
927A MET* 3.6 5.9 - - - +
928A SER* 2.9 29.3 + - - -
942A ARG* 2.7 34.9 + - - -
1001A ILE* 3.9 11.9 - - + -
1002A PRO* 3.8 4.3 - - - +
1265A PHE* 3.5 26.9 - - + -
1272A PHE* 3.5 25.7 - - + -
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Residues in contact with ASN 925 (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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734A LEU* 3.4 45.8 - - + +
846A TYR* 3.3 32.9 + - - -
921A PHE* 3.0 12.2 + - + +
922A ILE 3.4 4.6 + - - +
923A ALA 3.1 0.4 - - - -
924A GLU* 1.3 74.7 - - - +
926A TRP* 1.3 64.1 + - - +
928A SER* 2.6 22.5 + - - -
929A GLU* 3.2 12.9 + - - +
1271A PHE* 5.6 1.0 - - - -
1272A PHE* 3.7 9.7 - - + -
1275A LYS* 3.1 26.9 + - - -
1296A LEU 4.7 2.3 + - - +
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Residues in contact with TRP 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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846A TYR* 3.8 28.3 - + + -
848A VAL* 4.2 20.5 - - + +
856A ILE* 3.7 26.7 - - + -
859A LEU* 3.4 45.8 - - + +
861A VAL* 4.4 6.2 - - + +
885A MET 4.4 2.8 + - - -
886A ASP 5.5 0.2 - - - -
889A TYR* 4.5 7.9 - + - -
891A ILE* 3.9 20.9 - - + -
922A ILE* 3.2 28.0 + - + +
923A ALA* 3.2 30.7 - - + +
925A ASN* 1.3 77.5 - - - +
927A MET* 1.3 109.2 + - + +
929A GLU* 3.0 12.4 + - - +
930A VAL* 2.9 27.4 + - + +
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Residues in contact with MET 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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856A ILE* 3.6 28.0 - - + -
889A TYR* 3.5 46.0 - - + -
923A ALA 3.0 14.0 + - - +
924A GLU* 3.6 16.6 - - - +
926A TRP* 1.3 96.2 - - + +
928A SER* 1.3 60.3 + - - +
930A VAL* 3.2 14.2 + - - +
931A ALA* 3.2 13.0 + - - +
941A VAL* 3.8 25.4 - - + +
942A ARG* 3.8 25.6 - - + +
945A ASN* 3.9 5.4 - - + -
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Residues in contact with SER 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 GLU 2.9 14.1 + - - -
925A ASN* 2.6 24.4 + - - -
927A MET* 1.3 77.0 - - - +
929A GLU* 1.3 56.7 + - - +
931A ALA* 3.5 7.4 + - - +
932A VAL* 3.1 32.7 + - - +
938A ALA* 6.0 1.1 - - - -
942A ARG* 4.1 14.8 - - - +
1272A PHE* 4.0 13.6 - - - -
1275A LYS* 3.8 19.8 + - - -
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Residues in contact with GLU 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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730A VAL* 3.8 13.4 - - + +
846A TYR* 2.6 41.8 + - - -
848A VAL* 6.3 0.7 - - + -
850A PHE* 4.9 1.1 - - - -
925A ASN* 3.3 20.3 + - - +
926A TRP* 3.0 8.6 + - - +
928A SER* 1.3 78.5 - - - +
930A VAL* 1.3 60.9 + - + +
932A VAL* 3.9 1.3 - - - -
933A THR* 2.9 34.8 + - - -
1275A LYS* 4.5 10.6 + - - +
1293A LEU* 3.8 41.6 - - + +
1294A PHE 4.7 6.4 - - - +
1295A ARG* 5.4 2.8 - - - -
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Residues in contact with VAL 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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730A VAL* 6.2 0.2 - - + -
848A VAL* 4.1 14.4 - - + -
850A PHE* 3.5 47.1 - - + -
854A GLY* 3.5 28.3 - - - +
856A ILE* 4.6 5.2 - - + -
926A TRP* 2.9 28.9 + - + +
927A MET* 3.2 9.8 + - - +
929A GLU* 1.3 78.8 - - - +
931A ALA* 1.3 64.0 + - - +
933A THR* 3.8 0.9 - - - -
934A CYS* 3.0 24.3 + - - -
941A VAL* 4.1 9.4 - - + -
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Residues in contact with ALA 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 MET 3.2 9.0 + - - +
928A SER* 3.7 9.6 - - - +
930A VAL* 1.3 79.9 - - - +
932A VAL* 1.3 59.0 + - + +
934A CYS* 3.3 1.6 + - - -
935A GLY* 2.8 24.4 + - - -
936A LEU 3.1 25.4 + - - +
938A ALA* 3.9 20.4 - - + -
941A VAL* 3.9 25.1 - - + +
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Residues in contact with VAL 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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928A SER* 3.1 17.8 + - - +
929A GLU* 4.0 0.4 - - - +
931A ALA* 1.3 77.7 - - + +
933A THR* 1.3 63.5 + - - +
935A GLY* 3.0 15.6 + - - -
1279A ARG* 3.6 44.4 + - - +
1291A LYS* 3.7 19.1 - - - +
1292A GLU 3.7 12.1 - - - +
1293A LEU* 3.4 28.5 - - + -
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Residues in contact with THR 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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728A ASN* 4.4 15.0 + - + +
730A VAL* 3.9 8.3 - - + +
850A PHE* 3.8 24.5 - - + -
929A GLU 2.9 22.0 + - - -
930A VAL 3.8 3.1 - - - -
932A VAL* 1.3 78.3 - - - +
934A CYS* 1.3 61.5 + - - +
1291A LYS* 3.2 32.6 + - + +
1293A LEU* 3.5 22.0 - - - +
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Residues in contact with CYS 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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728A ASN* 4.6 2.5 - - - +
850A PHE* 3.7 17.3 - - - -
851A MET 3.5 24.5 - - - -
852A LYS* 3.6 26.9 - - - +
854A GLY* 3.7 13.0 - - - -
930A VAL 3.0 21.3 + - - +
931A ALA* 3.8 3.6 - - - +
933A THR* 1.3 76.5 - - - +
935A GLY* 1.3 65.1 + - - +
936A LEU* 3.7 20.2 - - + +
1291A LYS* 4.2 7.3 + - - +
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Residues in contact with GLY 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 ALA 2.8 5.6 + - - -
932A VAL* 3.0 14.7 + - - -
933A THR 3.2 0.4 - - - -
934A CYS* 1.3 81.0 - - - +
936A LEU* 1.3 65.1 - - - +
937A PRO* 4.8 0.5 - - - +
1279A ARG* 6.3 0.4 - - - -
1290A THR* 6.5 0.4 - - - -
1291A LYS* 4.3 11.9 - - - -
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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