Contacts of the helix formed by residues 919 - 930 (chain A) in PDB entry 3H44
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 ASP 919 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A TYR* 2.8 35.1 + - + -
917A ASN* 2.8 6.4 + - - +
918A PHE* 1.3 76.4 - - - +
920A ARG* 1.3 65.6 + - - +
921A ASP* 2.8 4.8 + - - -
922A ASN* 2.9 33.0 + - - +
923A THR* 3.5 17.2 + - - +
1011A HIS* 6.2 3.6 - - + -
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Residues in contact with ARG 920 (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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800A GLN* 5.5 1.4 + - - -
805A ASN* 3.6 11.1 + - - -
893A ARG* 3.6 9.9 - - - +
910A GLU* 2.7 39.8 + - - +
913A SER* 5.3 0.4 + - - -
915A GLN* 2.6 32.1 + - - +
917A ASN* 2.7 50.6 + - - +
918A PHE 3.3 1.8 + - - -
919A ASP* 1.3 70.7 - - - +
921A ASP* 1.3 56.1 + - - +
923A THR* 3.2 4.0 - - - -
924A GLU* 2.7 88.6 + - + +
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Residues in contact with ASP 921 (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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893A ARG* 3.0 50.8 + - - +
894A LEU* 4.2 11.4 - - + -
906A LYS* 2.3 36.8 + - - -
918A PHE 5.2 1.6 + - - +
919A ASP 2.8 5.6 + - - -
920A ARG* 1.3 76.3 - - - +
922A ASN* 1.3 60.9 + - - +
925A VAL* 3.0 37.4 + - + +
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Residues in contact with ASN 922 (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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547A TYR* 3.8 7.6 + - - -
894A LEU* 3.9 20.0 - - - +
919A ASP* 2.9 30.8 + - - +
921A ASP* 1.3 76.5 - - - +
923A THR* 1.3 53.9 + - - +
925A VAL* 3.9 1.0 - - - +
926A ALA* 2.8 39.3 + - - +
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Residues in contact with THR 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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802A THR* 3.7 24.7 - - + +
917A ASN* 4.8 9.1 + - - +
919A ASP* 3.5 22.1 + - - +
920A ARG* 3.2 14.1 - - - +
922A ASN* 1.3 76.5 - - - +
924A GLU* 1.3 62.3 + - + +
926A ALA* 3.2 6.3 + - - +
927A TYR* 3.0 28.6 + - - +
1011A HIS* 6.0 0.8 + - + -
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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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802A THR* 4.3 23.1 + - + +
805A ASN* 3.0 22.6 - - - +
806A MET* 3.3 31.0 - - - +
809A GLU* 4.6 2.9 - - - +
893A ARG* 2.7 40.4 + - - +
917A ASN* 4.8 1.3 + - - +
920A ARG* 2.7 58.5 + - + +
921A ASP 4.4 0.4 - - - +
923A THR* 1.3 77.1 - - + +
925A VAL* 1.3 55.9 + - - +
927A TYR* 3.7 4.5 + - - +
928A LEU* 3.0 20.6 + - - +
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Residues in contact with VAL 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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806A MET* 5.2 3.4 - - + -
890A ALA* 4.1 18.6 - - + +
893A ARG* 3.9 26.5 - - + -
894A LEU* 3.9 37.0 - - + -
921A ASP* 3.0 23.2 + - - +
922A ASN* 4.0 1.8 - - - +
924A GLU* 1.3 74.4 - - + +
926A ALA* 1.3 70.2 + - - +
928A LEU* 2.8 23.3 + - + +
929A LYS* 3.2 27.2 + - + +
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Residues in contact with ALA 926 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922A ASN 2.8 24.2 + - - +
923A THR* 3.3 7.0 - - - +
925A VAL* 1.3 73.4 - - - +
927A TYR* 1.3 64.1 + - - +
929A LYS* 3.6 17.6 + - - +
930A THR* 4.0 5.9 + - - -
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Residues in contact with TYR 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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802A THR* 3.7 25.4 - - + -
803A SER* 3.2 38.8 - - - -
806A MET* 4.1 17.0 - - + -
807A PHE* 3.8 15.5 - + - -
923A THR 3.0 12.7 + - - +
924A GLU 3.8 2.5 - - - +
926A ALA* 1.3 80.2 - - - +
928A LEU* 1.3 64.3 + - - +
930A THR* 3.0 30.9 - - + +
931A LEU* 3.2 26.0 - - + +
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Residues in contact with LEU 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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806A MET* 3.2 25.6 - - + -
810A LEU* 3.9 33.9 - - + -
886A ILE* 3.6 37.1 - - + +
889A LEU* 3.8 19.5 - - + -
890A ALA* 4.1 10.5 - - + +
924A GLU 3.0 12.9 + - - +
925A VAL* 2.8 16.0 + - + +
927A TYR* 1.3 78.8 - - - +
929A LYS* 1.3 54.0 + - + +
931A LEU* 2.8 41.2 + - + +
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Residues in contact with LYS 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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883A GLN* 4.8 7.8 + - - +
886A ILE* 4.1 27.4 - - + +
887A GLN* 4.9 11.1 + - - +
890A ALA* 4.9 8.8 - - + +
894A LEU* 5.5 3.2 - - - +
925A VAL* 3.3 34.4 - - + +
926A ALA* 3.8 10.1 - - - +
928A LEU* 1.3 73.7 - - + +
930A THR* 1.3 56.0 + - - +
931A LEU 3.1 11.1 + - - +
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Residues in contact with THR 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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926A ALA 4.0 5.3 + - - -
927A TYR* 3.0 30.5 + - + +
928A LEU 2.9 0.6 + - - -
929A LYS* 1.3 76.6 - - - +
931A LEU* 1.3 72.2 + - + +
932A THR* 4.0 3.1 + - - +
935A ASP* 4.1 5.0 - - - +
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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