Contacts of the helix formed by residues 834 - 852 (chain A) in PDB entry 5I4E
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 834 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A GLY 3.3 9.4 + - - -
833A ASP* 1.3 80.2 + - - +
835A ILE* 1.4 57.6 + - - +
836A GLU* 4.2 5.8 - - - -
837A SER* 2.8 34.6 + - - -
838A VAL* 3.0 16.1 + - - +
918A GLN* 3.6 6.0 + - - -
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Residues in contact with ILE 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A SER* 1.4 71.0 - - - +
836A GLU* 1.3 57.8 + - + +
838A VAL* 3.4 3.8 + - - +
839A GLN* 2.9 41.5 + - - +
915A LEU* 4.4 6.5 - - + +
918A GLN* 3.4 41.0 + - + +
919A LYS* 3.9 38.1 - - + -
922A ALA* 3.5 24.0 - - + -
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Residues in contact with GLU 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A SER* 3.2 5.5 - - - -
835A ILE* 1.3 76.1 - - + +
837A SER* 1.4 59.2 + - - +
839A GLN* 3.5 19.8 - - - +
840A SER* 3.1 25.1 + - - -
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Residues in contact with SER 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A PHE 2.7 27.2 + - - -
832A GLY* 3.6 5.3 - - - -
834A SER* 2.8 36.5 + - - -
836A GLU* 1.4 75.6 - - - +
838A VAL* 1.4 59.4 + - - +
840A SER* 3.1 8.2 + - - -
841A PHE* 3.1 37.4 + - - -
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Residues in contact with VAL 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A PHE* 4.1 10.8 - - + -
833A ASP 5.3 0.4 - - - +
834A SER 3.0 17.1 + - - +
835A ILE 3.9 4.0 - - - +
837A SER* 1.4 83.8 + - - +
839A GLN* 1.4 59.5 + - - +
841A PHE* 4.1 3.6 - - - -
842A MET* 3.5 10.0 + - - +
911A LEU* 3.4 35.2 - - + +
914A GLU* 3.4 38.6 - - + +
915A LEU* 3.8 29.6 - - + +
918A GLN* 3.7 14.8 - - + -
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Residues in contact with GLN 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ILE* 2.9 27.8 + - - +
836A GLU* 3.5 29.5 + - - +
837A SER 3.2 0.2 - - - -
838A VAL* 1.4 76.8 - - - +
840A SER* 1.4 53.3 + - - +
842A MET* 3.1 7.7 + - - +
843A ASN* 2.9 43.7 + - - +
915A LEU* 4.5 13.0 - - + +
919A LYS* 4.8 11.1 - - - +
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Residues in contact with SER 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A GLU 3.1 14.4 + - - -
837A SER* 3.1 12.5 + - - -
839A GLN* 1.4 75.0 - - - +
841A PHE* 1.3 58.8 + - - +
843A ASN* 3.3 8.6 + - - +
844A ALA* 3.0 30.1 + - - +
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Residues in contact with PHE 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A SER 5.8 2.9 - - - -
828A SER* 5.5 5.2 - - - -
830A ASP 3.8 19.5 - - - -
831A PHE* 3.2 43.1 - + + -
837A SER* 3.1 29.7 + - - +
838A VAL 4.2 0.4 - - - +
839A GLN 3.4 0.2 - - - -
840A SER* 1.3 77.1 - - - +
842A MET* 1.4 57.6 + - - +
844A ALA* 4.1 5.4 - - + +
845A HIS* 3.3 27.5 + - - +
907A HIS* 4.7 14.4 + + - -
911A LEU* 3.7 26.2 - - + +
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Residues in contact with MET 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A VAL 3.5 8.5 + - - +
839A GLN* 3.1 11.3 + - - +
841A PHE* 1.4 77.2 - - - +
843A ASN* 1.3 64.2 + - - +
845A HIS* 4.3 1.8 - - - +
846A LYS* 3.2 59.0 + - + +
908A ALA 6.0 0.9 - - - +
911A LEU* 3.8 39.7 - - + +
912A ARG* 5.0 21.3 - - + +
915A LEU* 4.3 24.5 - - + -
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Residues in contact with ASN 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A GLN* 2.9 23.0 + - - +
840A SER* 3.3 8.4 + - - +
842A MET* 1.3 78.4 - - - +
844A ALA* 1.4 61.5 + - - +
846A LYS* 3.8 4.3 + - - +
847A GLU* 3.4 21.1 + - - +
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Residues in contact with ALA 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A SER* 3.0 17.8 + - - +
841A PHE* 4.2 6.5 - - + +
843A ASN* 1.4 74.1 - - - +
845A HIS* 1.4 53.6 + - - +
847A GLU* 3.1 8.2 + - - +
848A TYR* 2.9 35.6 + - - +
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Residues in contact with HIS 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A LEU* 3.9 10.9 - - + +
841A PHE 3.3 17.8 + - - +
842A MET* 4.3 3.1 - - - +
844A ALA* 1.4 77.0 - - - +
846A LYS* 1.4 73.5 + - + +
848A TYR* 3.8 17.0 - + - +
849A LYS* 3.0 39.5 + - + +
904A GLU* 3.6 39.6 + - + +
907A HIS* 3.4 30.9 - + + +
908A ALA* 4.2 10.5 - - + +
911A LEU* 4.7 5.2 - - + -
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Residues in contact with LYS 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A MET* 3.2 47.8 + - + +
843A ASN* 4.2 5.4 - - - +
844A ALA 3.3 0.8 - - - -
845A HIS* 1.4 92.9 + - - +
847A GLU* 1.3 65.1 + - - +
849A LYS* 3.7 10.4 - - + +
850A LYS* 3.6 20.1 + - - +
908A ALA* 4.6 13.5 - - - +
911A LEU* 5.7 1.0 - - - +
912A ARG* 5.5 7.7 - - - +
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Residues in contact with GLU 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ASN 3.4 11.4 + - - +
844A ALA* 3.1 9.5 + - - +
846A LYS* 1.3 76.2 - - - +
848A TYR* 1.4 53.2 + - - +
850A LYS* 2.9 10.2 + - - +
851A THR* 2.7 66.2 + - + +
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Residues in contact with TYR 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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818A TRP* 3.8 28.1 - + - -
822A LYS* 3.7 47.4 - - + +
826A LEU* 4.5 11.8 - - + +
844A ALA 2.9 16.5 + - - +
845A HIS* 3.8 20.4 - + - +
847A GLU* 1.4 75.4 - - - +
849A LYS* 1.3 59.4 + - + +
851A THR* 4.9 0.9 - - - -
852A GLU* 3.4 30.3 + - + +
853A LYS* 3.0 34.0 + - + +
900A LEU* 4.1 8.3 - - - +
904A GLU* 3.0 35.6 + - + -
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Residues in contact with LYS 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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845A HIS* 3.0 32.0 + - + +
846A LYS* 3.7 13.0 - - + +
847A GLU 3.2 0.2 - - - -
848A TYR* 1.3 79.2 - - + +
850A LYS* 1.4 89.4 + - + +
853A LYS* 3.6 45.9 - - + +
854A PRO* 4.3 2.6 - - - +
901A GLU* 5.0 2.2 + - - -
904A GLU* 5.2 4.0 + - + +
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Residues in contact with LYS 850 (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 LYS 3.6 14.3 + - - +
847A GLU* 2.9 7.4 + - - +
849A LYS* 1.4 114.1 - - + +
851A THR* 1.4 61.9 + - - +
854A PRO* 4.1 11.8 - - - +
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Residues in contact with THR 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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847A GLU* 2.7 51.5 + - + +
848A TYR* 3.7 1.1 + - - -
850A LYS* 1.4 74.6 + - - +
852A GLU* 1.3 66.1 + - + +
854A PRO* 3.5 7.2 - - - +
855A PRO* 3.4 17.2 - - - +
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Residues in contact with GLU 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A TRP* 4.1 25.0 + - + -
822A LYS* 4.3 13.4 + - - +
848A TYR* 3.4 35.6 + - + +
851A THR* 1.3 81.6 - - + +
853A LYS* 1.3 61.9 + - - +
855A PRO* 3.0 21.9 - - - +
856A LYS* 3.2 17.2 - - - +
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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
------------------------------------------------------------
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