Contacts of the helix formed by residues 847 - 867 (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 847 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A ALA* 3.9 9.6 - - + +
846A LEU* 1.3 76.3 - - - +
848A MET* 1.3 65.7 + - - +
849A GLY* 3.6 5.3 + - - -
850A ASP* 3.0 39.4 + - - +
851A LEU* 3.2 19.2 + - - +
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Residues in contact with MET 848 (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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847A THR* 1.3 74.3 - - - +
849A GLY* 1.3 63.6 + - - +
851A LEU* 3.0 15.9 + - + +
852A ILE* 3.0 39.2 + - + +
975A ASN 6.1 1.6 - - - +
977A SER* 4.9 21.8 - - - +
980A MET* 6.4 0.4 - - + -
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Residues in contact with GLY 849 (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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847A THR* 3.3 6.7 + - - -
848A MET* 1.3 78.4 - - - +
850A ASP* 1.3 59.1 + - - +
852A ILE* 3.6 10.8 + - - +
853A SER* 3.0 28.1 + - - -
1009A MET* 6.1 3.4 - - - +
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Residues in contact with ASP 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A ALA 3.8 3.5 - - - +
846A LEU* 3.5 11.5 - - + -
847A THR* 3.0 37.9 + - - +
848A MET 3.1 0.2 - - - -
849A GLY* 1.3 78.7 - - - +
851A LEU* 1.3 57.3 + - - +
853A SER* 3.1 9.2 + - - -
854A PHE* 3.0 46.9 + - + -
886A ARG* 3.2 26.3 + - - -
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Residues in contact with LEU 851 (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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816A LEU* 4.0 12.6 - - + -
846A LEU* 4.6 12.3 - - + +
847A THR 3.3 14.8 - - - +
848A MET* 3.0 15.6 + - + +
850A ASP* 1.3 76.9 - - - +
852A ILE* 1.3 62.7 + - + +
854A PHE* 3.3 12.6 + - + +
855A ALA* 3.1 22.3 + - - +
944A ILE* 3.7 39.5 - - + +
945A VAL* 4.6 15.7 - - + +
947A LEU* 4.0 26.7 - - + -
975A ASN 6.1 0.7 - - - +
980A MET* 6.1 0.4 - - - -
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Residues in contact with ILE 852 (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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848A MET* 3.0 39.5 + - + +
849A GLY* 3.9 8.1 - - - +
851A LEU* 1.3 74.1 - - + +
853A SER* 1.3 66.2 + - - +
855A ALA* 3.8 6.0 - - - +
856A TRP* 3.0 23.2 + - - +
980A MET* 3.8 25.1 - - + -
1005A LEU* 3.7 32.4 - - + +
1008A MET* 4.3 25.6 - - + +
1009A MET* 4.5 17.5 - - + +
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Residues in contact with SER 853 (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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849A GLY 3.0 15.4 + - - -
850A ASP* 3.1 13.9 + - - -
852A ILE* 1.3 76.9 - - - +
854A PHE* 1.3 58.0 + - - +
856A TRP* 3.4 8.5 + - - +
857A GLN* 3.0 52.9 + - - +
1009A MET* 5.4 7.8 - - - -
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Residues in contact with PHE 854 (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* 4.2 13.9 - - + -
815A PHE* 4.3 11.9 - + - -
816A LEU* 4.8 3.4 - - + -
846A LEU* 4.2 22.0 - - + -
850A ASP* 3.0 29.5 + - + -
851A LEU* 3.6 21.8 - - + +
852A ILE 3.3 0.4 - - - -
853A SER* 1.3 75.3 - - - +
855A ALA* 1.3 64.4 - - - +
857A GLN* 3.2 13.6 + - - +
858A ILE* 3.0 28.9 + - - +
886A ARG* 3.8 37.0 - - + -
888A MET* 3.2 41.8 - - + +
944A ILE* 4.7 10.5 - - + -
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Residues in contact with ALA 855 (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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851A LEU 3.1 13.0 + - - +
852A ILE* 3.8 5.8 - - - +
854A PHE* 1.3 79.0 - - - +
856A TRP* 1.3 52.9 + - - +
858A ILE* 3.3 6.5 + - - +
859A SER* 2.8 34.7 + - - -
937A PHE* 3.7 7.6 - - + -
941A LEU* 3.8 29.4 - - + -
944A ILE* 4.2 14.3 - - + +
980A MET* 5.8 0.7 - - + -
1005A LEU* 3.7 14.1 - - + -
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Residues in contact with TRP 856 (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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786A HIS* 4.9 6.3 - - - -
852A ILE 3.0 17.8 + - - +
853A SER* 3.7 7.4 - - - +
854A PHE 3.2 0.2 - - - -
855A ALA* 1.3 74.0 - - - +
857A GLN* 1.3 79.2 + - + +
859A SER* 3.1 2.2 + - - -
860A GLN* 2.9 63.4 + - + +
1002A SER* 3.6 17.5 - - - -
1005A LEU* 3.6 16.1 - - + +
1006A GLU* 2.8 45.0 + - + +
1009A MET* 3.9 17.5 - - + -
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Residues in contact with GLN 857 (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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786A HIS* 3.3 49.3 - - + +
853A SER* 3.0 39.8 + - - +
854A PHE* 3.2 11.6 + - - +
856A TRP* 1.3 89.9 - - + +
858A ILE* 1.3 61.1 + - - +
860A GLN* 3.5 1.0 + - - -
861A GLY 3.4 9.2 + - - -
886A ARG 3.6 13.5 + - - -
887A LYS* 3.4 14.1 - - - +
888A MET* 2.7 43.0 + - + +
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Residues in contact with ILE 858 (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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786A HIS* 5.3 0.4 - - - -
812A LEU* 4.2 14.8 - - + -
854A PHE 3.0 18.2 + - - +
855A ALA* 3.6 6.5 - - - +
857A GLN* 1.3 74.3 - - - +
859A SER* 1.3 65.0 + - - +
861A GLY* 3.2 2.5 + - - +
862A MET* 3.1 23.1 + - + +
875A LEU* 4.4 7.4 - - + -
880A ILE* 3.9 23.3 - - + -
888A MET* 3.8 17.3 - - + -
890A ILE* 3.9 22.9 - - + +
937A PHE* 4.1 11.4 - - + -
940A LEU* 3.8 33.2 - - + -
944A ILE* 4.5 6.1 - - + -
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Residues in contact with SER 859 (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 2.8 20.8 + - - -
856A TRP* 3.1 6.0 + - - -
858A ILE* 1.3 73.4 - - - +
860A GLN* 1.3 56.9 + - - +
862A MET* 3.4 6.2 + - - +
863A GLN* 3.0 28.8 + - - +
937A PHE* 4.0 7.4 - - - -
998A PHE* 3.3 11.2 + - - +
1001A ILE* 3.4 18.9 - - - +
1002A SER* 2.7 36.0 + - - -
1005A LEU* 4.0 6.3 - - - -
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Residues in contact with GLN 860 (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 HIS* 3.9 11.2 + - + -
786A HIS* 4.2 11.4 - - + -
856A TRP* 2.9 63.6 + - + +
857A GLN 3.6 9.6 - - - +
858A ILE 3.2 0.2 - - - -
859A SER* 1.3 77.8 - - - +
861A GLY* 1.3 60.8 + - - +
863A GLN* 3.4 18.5 + - - +
864A TYR* 3.2 20.3 + - - +
1002A SER* 3.8 12.5 + - - +
1006A GLU* 3.9 6.5 + - - -
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Residues in contact with GLY 861 (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 HIS* 3.9 19.5 - - - -
786A HIS* 4.3 5.8 - - - -
787A VAL* 4.5 1.9 - - - +
857A GLN 3.4 7.4 + - - -
858A ILE 3.2 7.1 + - - -
860A GLN* 1.3 77.6 - - - +
862A MET* 1.3 58.0 + - - +
864A TYR* 3.3 7.2 + - - +
865A LEU* 3.1 28.9 + - - +
890A ILE* 3.9 15.7 - - - -
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Residues in contact with MET 862 (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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858A ILE* 3.1 20.1 + - + +
859A SER* 3.8 0.4 - - - +
861A GLY* 1.3 71.6 - - - +
863A GLN* 1.3 60.1 + - - +
864A TYR 3.1 2.0 - - - -
865A LEU* 3.8 18.2 - - + +
866A ALA* 2.8 35.6 + - + +
870A LEU 5.3 1.1 - - - +
872A HIS* 4.4 9.9 - - + +
875A LEU* 4.0 24.0 - - + -
890A ILE* 3.7 20.2 - - + -
930A THR* 6.2 0.2 - - + -
933A ASP* 3.7 27.4 - - + +
937A PHE* 5.1 0.2 - - + -
998A PHE* 3.5 50.2 - - + -
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Residues in contact with GLN 863 (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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859A SER 3.0 15.0 + - - +
860A GLN* 3.5 21.2 + - - +
862A MET* 1.3 76.6 - - - +
864A TYR* 1.3 59.6 + - - +
866A ALA* 4.4 1.4 - - - +
867A GLU* 3.3 23.6 + - - +
998A PHE* 4.0 10.2 - - + +
999A ALA* 3.5 28.1 - - - +
1002A SER* 3.1 26.4 + - - -
2015A FMT 4.0 16.8 - - - +
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Residues in contact with TYR 864 (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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781A GLN 4.1 1.7 + - - -
782A VAL* 3.5 29.0 - - + -
783A ASN 3.1 34.0 + - - -
784A HIS* 3.3 48.2 - + + +
787A VAL* 4.3 2.7 - - + -
860A GLN 3.2 5.1 + - - +
861A GLY 3.3 9.4 - - - +
862A MET 3.1 0.4 - - - -
863A GLN* 1.3 76.0 - - - +
865A LEU* 1.3 77.8 + - + +
867A GLU* 3.4 7.0 + - + +
868A MET* 3.4 46.9 + - + +
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Residues in contact with LEU 865 (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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782A VAL* 4.0 19.1 - - + -
787A VAL* 4.5 5.4 - - + -
861A GLY 3.1 16.1 + - - +
862A MET* 3.2 30.9 + - + +
864A TYR* 1.3 84.2 - - + +
866A ALA* 1.3 59.1 + - - +
868A MET* 2.8 22.4 + - - +
870A LEU* 3.1 54.7 + - + +
872A HIS* 4.7 8.5 - - + -
890A ILE* 4.4 7.0 - - + -
893A PHE* 3.7 29.2 - - + -
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Residues in contact with ALA 866 (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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862A MET* 2.8 22.8 + - + +
863A GLN 4.4 2.0 - - - +
865A LEU* 1.3 73.7 - - - +
867A GLU* 1.3 56.7 + - - +
869A LYS* 2.8 24.4 + - - +
870A LEU 4.1 8.0 + - - +
930A THR* 3.5 27.4 + - + -
998A PHE* 4.4 2.7 - - + -
2015A FMT 3.4 26.2 - - - +
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Residues in contact with GLU 867 (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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863A GLN 3.3 19.6 + - - +
864A TYR* 3.6 7.4 - - - +
865A LEU 3.1 0.4 - - - -
866A ALA* 1.3 78.4 - - - +
868A MET* 1.3 60.8 + - + +
869A LYS* 3.3 3.9 + - - +
2015A FMT 6.0 0.4 - - - -
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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