Contacts of the helix formed by residues 895 - 911 (chain A) in PDB entry 3H2U
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 ASN 895 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894A ILE* 1.3 73.2 - - - +
896A GLN* 1.3 58.5 + - - +
897A PRO* 3.1 17.3 - - - +
898A MET* 2.8 43.1 - - + +
899A MET* 3.1 19.8 + - - +
934A SER* 2.7 16.6 + - - +
937A VAL* 3.7 24.2 - - + +
938A ARG* 3.9 5.4 - - + +
1020A THR* 4.1 10.9 - - - +
1024A VAL* 3.2 24.6 - - - +
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Residues in contact with GLN 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A GLN* 3.9 37.4 + - + +
892A GLU 5.7 0.3 - - - +
894A ILE* 3.7 13.4 + - + +
895A ASN* 1.3 69.6 - - - +
897A PRO* 1.3 69.8 - - + +
899A MET* 3.1 7.1 + - + +
900A MET* 2.8 31.2 + - - +
938A ARG* 5.2 2.6 + - - -
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Residues in contact with PRO 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ASN* 3.1 12.3 - - - +
896A GLN* 1.3 95.9 - - + +
898A MET* 1.3 55.7 + - - +
900A MET* 3.4 7.5 - - + +
901A ALA* 3.0 27.5 + - - +
1024A VAL* 3.6 24.9 - - + -
1028A GLN* 3.6 19.4 + - - +
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Residues in contact with MET 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ASN* 2.8 29.3 - - - +
897A PRO* 1.3 74.5 - - - +
899A MET* 1.3 60.6 + - - +
900A MET 3.1 1.1 - - - -
901A ALA* 3.3 6.2 + - - +
902A ALA* 2.9 28.2 + - - +
930A MET* 3.9 11.8 - - - +
933A MET* 3.5 35.2 - - + +
934A SER* 3.6 22.2 - - - -
937A VAL* 4.3 11.9 - - + -
1023A LEU* 3.8 24.0 - - + +
1024A VAL* 4.3 12.1 - - - +
1027A ALA* 3.7 29.8 - - + -
1028A GLN* 5.8 0.7 - - - -
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Residues in contact with MET 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A PHE* 3.7 10.8 - - + -
888A GLN* 6.1 1.6 - - + -
894A ILE* 4.2 24.2 - - + -
895A ASN 3.1 13.0 + - - +
896A GLN* 3.1 4.7 + - + +
898A MET* 1.3 76.2 - - - +
900A MET* 1.3 57.3 + - - +
902A ALA* 3.4 3.8 + - - +
903A ARG* 2.8 49.0 + - - +
931A ALA* 3.5 25.8 - - + +
934A SER* 2.9 35.1 - - - +
935A ARG* 4.4 10.3 - - - +
92B TYR* 3.4 39.0 - - + +
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Residues in contact with MET 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A GLN 2.8 17.1 + - - +
897A PRO* 3.4 10.3 - - + +
899A MET* 1.3 74.8 - - - +
901A ALA* 1.3 55.6 + - - +
903A ARG* 3.0 30.8 + - + +
904A GLN* 2.8 76.8 + - - +
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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
----------------------------------------------------------
897A PRO 3.0 16.8 + - - +
898A MET* 3.5 8.1 - - - +
900A MET* 1.3 74.4 - - - +
902A ALA* 1.3 65.4 + - - +
904A GLN* 3.2 12.5 + - - +
905A LEU* 3.1 17.0 + - - +
930A MET* 4.9 0.9 - - + -
1027A ALA 4.6 1.3 - - - +
1028A GLN* 4.3 20.6 - - + +
1031A MET* 3.6 34.4 - - + +
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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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885A PHE* 4.3 8.5 - - + -
898A MET 2.9 14.7 + - - +
899A MET* 3.4 11.9 - - - +
901A ALA* 1.3 75.9 - - - +
903A ARG* 1.3 57.7 + - - +
905A LEU* 3.1 5.4 + - - +
906A HIS* 2.8 27.5 + - - +
927A ALA* 3.7 24.7 - - - +
930A MET* 3.8 15.5 - - + -
931A ALA* 3.8 11.0 - - - +
1031A MET* 4.1 7.0 - - - +
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Residues in contact with ARG 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A GLU* 5.0 3.6 - - - -
885A PHE* 3.2 40.3 + - + +
886A PRO 2.4 33.3 + - - -
887A GLU* 3.7 12.0 - - - +
888A GLN* 4.7 10.7 - - - +
899A MET* 2.8 41.4 + - - +
900A MET* 3.5 28.2 - - + +
902A ALA* 1.3 73.7 - - - +
904A GLN* 1.3 56.1 + - - +
906A HIS* 3.2 2.9 + - - +
907A ASP* 2.8 48.8 + - - +
92B TYR* 4.8 2.2 + - - -
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Residues in contact with GLN 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A MET* 2.8 60.1 + - - +
901A ALA* 3.4 14.1 + - - +
903A ARG* 1.3 74.8 - - - +
905A LEU* 1.3 64.3 + - - +
907A ASP* 3.6 8.0 + - - +
908A GLU* 3.4 12.3 + - - +
1031A MET* 5.7 2.5 - - + +
1032A GLN* 5.4 4.0 - - - +
1035A LYS* 3.7 33.7 + - + +
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Residues in contact with LEU 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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901A ALA 3.1 7.4 + - - +
902A ALA 3.1 8.2 + - - +
904A GLN* 1.3 76.2 - - - +
906A HIS* 1.3 68.9 + - - +
908A GLU* 3.0 13.6 + - + +
909A ALA* 3.1 13.0 + - + +
923A ALA* 3.6 34.3 - - + +
926A MET* 4.1 7.6 - - + -
927A ALA* 4.1 3.6 - - + +
1031A MET* 3.7 37.7 + - + +
1034A VAL* 3.8 34.3 - - + +
1035A LYS* 4.0 25.1 - - + +
1038A VAL* 4.8 4.0 - - + -
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Residues in contact with HIS 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ASP 4.4 10.5 + - - -
883A GLU* 2.8 44.3 + - - -
884A GLU* 4.0 2.5 - - - -
885A PHE* 3.2 47.5 - + + +
902A ALA 2.8 12.9 + - - +
903A ARG 3.4 7.9 - - - +
905A LEU* 1.3 77.2 - - - +
907A ASP* 1.3 57.6 + - - +
909A ALA* 3.8 3.6 - - + +
910A ARG* 2.9 51.5 + - + +
924A LYS* 5.3 9.0 - - + +
927A ALA* 3.8 12.5 - - + +
928A LEU* 4.5 11.9 - - + -
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Residues in contact with ASP 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A GLU* 3.3 10.5 - - - +
900A MET* 5.9 0.2 - - - +
903A ARG* 2.8 37.9 + - - +
904A GLN* 4.0 8.7 + - - +
906A HIS* 1.3 79.9 + - - +
908A GLU* 1.3 63.2 + - - +
910A ARG* 2.4 51.8 + - - +
911A LYS* 3.6 16.5 - - - +
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Residues in contact with GLU 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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904A GLN 3.4 4.0 + - - +
905A LEU* 3.0 9.4 + - + +
907A ASP* 1.3 75.5 - - - +
909A ALA* 1.3 63.6 + - - +
911A LYS* 2.7 62.8 + - - +
912A TRP* 3.3 19.8 + - - -
1035A LYS* 3.9 33.0 + - + +
1038A VAL* 3.9 22.5 - - + +
1039A ARG* 3.3 34.1 + - + +
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Residues in contact with ALA 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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905A LEU* 3.1 13.9 + - + +
906A HIS* 4.0 4.0 - - - +
908A GLU* 1.3 78.4 - - - +
910A ARG* 1.3 66.4 + - - +
912A TRP* 3.0 23.4 + - - +
920A ILE* 3.9 16.7 - - + +
923A ALA* 4.0 23.1 - - + -
924A LYS* 3.5 30.1 - - + +
1038A VAL* 5.0 1.3 - - + -
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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
----------------------------------------------------------
882A ASP 3.7 27.7 + - - +
884A GLU* 2.9 44.1 + - - +
906A HIS* 2.9 34.9 + - + +
907A ASP* 2.4 48.1 + - - +
908A GLU 3.1 0.8 - - - -
909A ALA* 1.3 78.3 - - - +
911A LYS* 1.3 61.0 + - + +
912A TRP 2.7 17.2 + - - +
924A LYS* 4.5 8.1 - - - +
1061A LYS* 3.9 16.9 - - - +
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Residues in contact with LYS 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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907A ASP 3.6 14.1 - - - +
908A GLU* 2.7 54.7 + - - +
910A ARG* 1.3 82.8 - - + +
912A TRP* 1.3 67.9 + - + +
1039A ARG* 5.3 1.4 - - - +
1060A ARG* 2.8 65.8 - - - +
1061A LYS* 2.9 16.2 + - - +
1062A THR* 5.1 2.7 - - + -
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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