Contacts of the helix formed by residues 897 - 913 (chain A) in PDB entry 5HG1
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 897 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A ASP* 3.3 10.2 + - - -
601A THR* 3.3 18.5 + - - +
657A ASP 3.7 13.2 - - - -
660A GLY* 3.7 12.7 - - - -
661A THR* 3.6 20.6 + - - +
896A GLY* 1.3 70.0 - - - -
898A GLY* 1.3 63.9 + - - +
899A LYS 3.3 0.2 - - - -
900A GLY* 3.1 11.8 + - - -
901A ALA 3.1 9.4 + - - -
1003A BG6 1.3 52.4 + - - -
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Residues in contact with GLY 898 (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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530A ALA* 3.4 7.3 - - - +
531A LEU 4.5 4.9 - - - -
532A ASP* 4.2 9.2 + - - -
541A LEU* 3.2 27.1 - - - +
601A THR* 3.9 9.4 + - - -
896A GLY 3.2 2.0 - - - -
897A SER* 1.3 79.4 + - - +
899A LYS* 1.3 63.3 + - - +
901A ALA* 2.9 16.9 + - - +
902A ALA 3.0 10.0 + - - -
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Residues in contact with LYS 899 (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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541A LEU* 3.3 10.7 - - - +
543A VAL* 4.3 11.1 - - + +
553A VAL* 3.8 28.8 - - + +
555A MET* 3.9 23.8 - - + -
664A THR* 3.8 16.8 + - + +
667A PHE* 3.6 27.1 - - - -
668A GLU* 4.6 10.7 + - - +
895A ASP* 3.3 34.0 + - + +
896A GLY 3.4 12.3 + - - +
897A SER 3.3 1.0 - - - -
898A GLY* 1.3 75.2 - - - +
900A GLY* 1.3 56.0 + - - +
902A ALA* 3.6 3.2 + - - +
903A LEU* 3.1 38.5 + - + +
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Residues in contact with GLY 900 (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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660A GLY 3.4 19.3 - - - -
663A MET* 3.9 4.9 - - - -
664A THR* 3.0 20.8 + - - -
897A SER 3.1 1.4 + - - -
898A GLY 3.0 1.2 - - - -
899A LYS* 1.3 73.4 - - - +
901A ALA* 1.3 60.5 + - - +
902A ALA 3.2 1.1 - - - -
903A LEU* 3.7 3.7 - - - +
904A ILE* 2.8 42.0 + - - +
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Residues in contact with ALA 901 (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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530A ALA* 3.9 5.4 - - + -
599A GLY* 3.8 7.0 - - - -
600A PHE 3.8 23.6 - - - +
601A THR* 3.2 26.0 + - - +
653A ALA* 5.3 1.3 - - - +
655A VAL* 4.2 12.1 - - + -
660A GLY* 4.4 1.8 - - - -
897A SER 3.1 5.7 + - - -
898A GLY* 2.9 9.1 + - - +
900A GLY* 1.3 76.2 - - - +
902A ALA* 1.3 61.4 + - - +
904A ILE* 3.3 4.6 + - - +
905A THR* 3.0 26.0 + - - -
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Residues in contact with ALA 902 (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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528A PHE* 4.1 13.4 - - + +
529A LEU 4.8 1.8 - - - -
530A ALA* 3.9 16.8 - - + +
543A VAL* 2.9 43.5 - - + -
898A GLY 3.0 6.0 + - - +
899A LYS 3.8 6.5 - - - +
901A ALA* 1.3 76.2 - - - +
903A LEU* 1.3 57.8 + - - +
905A THR* 3.4 8.5 + - - -
906A ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 903 (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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520A PRO* 4.8 11.7 - - + -
543A VAL* 5.8 4.9 - - + -
545A VAL* 5.1 10.5 - - + -
553A VAL* 4.6 13.7 - - + -
663A MET* 4.0 23.6 - - + +
664A THR* 4.6 1.1 - - - -
667A PHE* 3.9 41.1 - - + -
899A LYS* 3.1 35.5 + - + +
900A GLY* 3.2 6.7 + - - +
902A ALA* 1.3 75.9 - - + +
904A ILE* 1.3 65.2 + - - +
906A ALA* 3.2 8.7 + - + +
907A VAL* 2.9 31.0 + - + +
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Residues in contact with ILE 904 (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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516A VAL* 4.0 25.6 - - + -
518A ALA 6.0 0.4 - - - +
611A LEU* 4.3 15.7 - - + -
653A ALA* 4.3 5.6 - - + -
655A VAL* 3.7 32.3 - - + -
659A VAL* 3.8 18.2 - - + +
663A MET* 3.2 38.4 - - + -
900A GLY 2.8 26.2 + - - +
901A ALA 3.7 3.6 - - - +
903A LEU* 1.3 71.2 - - - +
905A THR* 1.3 61.7 + - - +
907A VAL* 3.6 6.3 + - - +
908A ALA* 3.0 22.3 + - - +
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Residues in contact with THR 905 (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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528A PHE* 3.7 23.1 - - + -
597A PRO* 4.1 8.3 - - + -
598A LEU 3.6 2.2 + - - +
599A GLY* 2.9 37.8 + - - +
652A VAL* 3.9 26.9 - - + +
653A ALA* 4.2 7.8 - - - +
901A ALA 3.0 6.0 + - - -
902A ALA* 3.5 9.6 - - - -
903A LEU 3.2 0.2 - - - -
904A ILE* 1.3 75.1 - - - +
906A ALA* 1.3 66.2 + - - +
908A ALA* 2.9 16.7 + - - +
909A CYS* 2.9 13.9 + - - -
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Residues in contact with ALA 906 (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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524A GLU* 4.2 21.2 - - + +
528A PHE* 3.4 39.7 - - + -
545A VAL* 4.9 2.9 - - + -
902A ALA 3.0 14.0 + - - +
903A LEU* 3.2 12.1 + - + +
905A THR* 1.3 75.2 - - - +
907A VAL* 1.3 64.2 + - + +
909A CYS* 3.1 12.1 + - - +
910A ARG* 3.2 14.4 + - - +
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Residues in contact with VAL 907 (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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518A ALA* 3.3 41.5 - - + +
519A THR 3.6 6.5 - - - +
520A PRO* 3.5 38.1 - - + -
524A GLU* 3.9 7.4 - - + +
663A MET* 4.9 0.7 - - + -
903A LEU* 2.9 21.2 + - + +
904A ILE* 3.9 7.0 - - - +
906A ALA* 1.3 75.9 - - + +
908A ALA* 1.3 61.4 + - - +
910A ARG* 3.2 28.7 - - - +
911A ILE* 3.4 10.6 + - + +
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Residues in contact with ALA 908 (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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611A LEU* 4.0 18.6 - - + -
652A VAL* 3.7 23.1 - - + -
904A ILE 3.0 16.7 + - - +
905A THR 2.9 6.7 + - - +
907A VAL* 1.3 77.8 - - - +
909A CYS* 1.3 63.9 + - - +
911A ILE* 3.8 9.2 + - - +
912A ARG* 3.6 20.0 + - - +
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Residues in contact with CYS 909 (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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528A PHE* 4.3 19.5 - - + -
597A PRO* 4.7 6.7 - - - -
652A VAL* 4.6 5.2 - - - -
905A THR* 2.9 24.5 + - - -
906A ALA* 3.1 8.7 + - - +
908A ALA* 1.3 73.6 - - - +
910A ARG* 1.3 68.1 + - - +
911A ILE 3.1 1.8 - - - -
912A ARG* 2.8 37.5 + - - +
913A GLU* 2.7 24.1 + - + +
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Residues in contact with ARG 910 (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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518A ALA* 4.7 3.0 - - - +
519A THR 3.9 4.8 + - - -
521A ASP* 2.4 44.5 + - - +
523A THR 4.3 8.6 + - - +
524A GLU* 3.4 34.1 - - + -
906A ALA 3.2 8.9 + - - +
907A VAL* 3.2 36.3 - - - +
909A CYS* 1.3 76.2 - - - +
911A ILE* 1.3 80.1 + - - +
913A GLU* 3.0 28.6 - - - +
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Residues in contact with ILE 911 (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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518A ALA* 3.7 30.1 - - + -
907A VAL* 3.4 16.5 + - + +
908A ALA* 4.0 8.3 - - - +
909A CYS 2.9 1.4 + - - -
910A ARG* 1.3 94.6 - - - +
912A ARG* 1.3 62.2 + - + +
913A GLU 4.1 2.4 - - - +
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Residues in contact with ARG 912 (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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597A PRO* 5.5 1.0 - - - +
650A ASP* 2.8 30.7 + - - -
652A VAL* 4.1 17.8 - - - +
908A ALA 3.6 10.2 + - - +
909A CYS* 2.8 51.9 + - - +
911A ILE* 1.3 77.0 - - + +
913A GLU* 1.3 62.0 + - + +
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Residues in contact with GLU 913 (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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909A CYS* 2.7 20.1 + - + +
910A ARG* 3.0 21.8 - - - +
911A ILE 4.1 3.1 - - - +
912A ARG* 1.3 79.3 - - + +
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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