Contacts of the helix formed by residues 920 - 929 (chain A) in PDB entry 3B7B
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 ARG 920 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A SO4 3.9 14.1 + - - +
853A LYS* 5.1 5.7 - - - +
883A ALA 3.6 16.4 - - - +
884A PHE* 3.6 13.3 + - - +
885A SER 2.9 20.3 + - - -
886A GLY* 3.4 20.1 - - - +
915A ALA* 2.9 15.4 + - - +
918A GLU* 3.1 38.5 + - + +
919A ASN* 1.3 71.4 + - - +
921A TYR* 1.3 66.0 + - - +
922A ASP* 3.6 1.8 - - - -
923A CYS* 3.0 23.6 + - + -
924A VAL* 3.0 14.2 + - - +
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Residues in contact with TYR 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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5A SO4 3.2 15.3 + - - +
919A ASN* 3.3 7.7 + - - +
920A ARG* 1.3 70.5 - - - +
922A ASP* 1.3 80.5 + - - +
923A CYS 2.8 1.9 + - - -
924A VAL* 2.9 23.4 + - + +
925A VAL* 3.0 27.9 + - + +
953A GLN* 3.4 60.8 - - + -
954A VAL* 3.4 8.1 - - + +
957A ALA* 4.0 16.2 - - + +
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Residues in contact with ASP 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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5A SO4 3.2 27.9 + - - +
886A GLY 5.2 0.9 - - - +
888A VAL* 3.3 29.5 - - + +
920A ARG 3.6 0.4 - - - -
921A TYR* 1.3 91.0 - - - +
923A CYS* 1.3 57.2 + - - +
925A VAL* 3.3 7.2 + - - +
926A LEU* 3.0 24.6 + - - +
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Residues in contact with CYS 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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882A ALA 4.1 10.3 - - - -
883A ALA* 4.4 6.1 - - - -
886A GLY* 3.5 38.8 + - - -
888A VAL* 3.9 13.9 - - - -
891A ALA* 4.4 12.6 - - - -
915A ALA* 3.9 15.0 - - + -
920A ARG* 3.0 14.1 + - + +
921A TYR 2.8 3.4 + - - -
922A ASP* 1.3 71.3 - - - +
924A VAL* 1.3 66.2 + - - +
925A VAL 2.9 1.9 + - - -
926A LEU* 3.0 5.9 + - - +
927A PHE* 2.9 34.0 + - + -
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Residues in contact with VAL 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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912A LEU* 3.8 18.6 - - + -
915A ALA* 3.9 10.2 - - + +
920A ARG 3.0 12.5 + - - +
921A TYR* 2.9 27.1 - - + +
923A CYS* 1.3 73.2 - - - +
925A VAL* 1.3 55.3 + - + +
927A PHE* 3.9 0.7 - - - +
928A LEU* 2.9 35.3 + - + +
954A VAL* 3.5 24.7 - - + -
957A ALA* 4.8 7.4 - - + -
958A LEU* 3.7 35.7 - - + -
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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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921A TYR* 3.0 48.6 + - + +
922A ASP* 3.3 10.5 - - - +
923A CYS 2.9 0.8 - - - -
924A VAL* 1.3 76.7 - - + +
926A LEU* 1.3 67.9 + - - +
928A LEU* 3.3 6.5 + - + +
929A SER* 2.9 26.3 + - - -
957A ALA* 5.1 8.3 - - + -
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Residues in contact with LEU 926 (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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888A VAL* 4.4 11.4 - - + +
891A ALA* 4.0 13.2 - - + -
892A GLU* 3.9 29.4 - - + +
895A LEU* 3.6 23.3 - - + -
922A ASP 3.0 14.3 + - - +
923A CYS* 3.0 6.3 + - - +
925A VAL* 1.3 76.3 - - - +
927A PHE* 1.3 71.6 + - + +
929A SER* 3.0 18.7 + - - -
930A ARG* 3.2 51.4 + - + +
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Residues in contact with PHE 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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879A LEU* 3.9 19.7 - - + -
883A ALA* 4.0 11.2 - - + -
891A ALA* 4.4 8.1 - - + -
895A LEU* 4.0 17.9 - - + -
901A LEU* 3.8 22.6 - - + +
911A PRO* 3.5 34.1 - - + -
912A LEU* 3.7 30.7 - - + -
915A ALA* 3.9 14.6 - - + -
923A CYS* 2.9 23.1 + - + +
924A VAL 3.9 3.8 - - - +
926A LEU* 1.3 92.1 - - + +
928A LEU* 1.3 61.5 + - - +
930A ARG* 2.9 13.9 + - - +
931A ASP 3.5 0.2 + - - -
932A SER* 3.3 22.0 + - - -
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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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912A LEU* 3.9 19.1 - - + -
924A VAL* 2.9 42.2 + - + +
925A VAL* 3.8 6.7 - - + +
927A PHE* 1.3 75.3 - - - +
929A SER* 1.3 57.5 + - - +
930A ARG 3.0 5.4 + - - -
931A ASP* 3.0 16.3 + - - +
932A SER 4.3 5.8 - - - +
934A VAL* 3.7 30.3 - - + -
957A ALA* 4.2 12.8 - - + +
958A LEU* 3.9 10.1 - - + -
961A SER* 4.0 20.4 - - - +
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Residues in contact with SER 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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925A VAL* 2.9 17.8 + - - -
926A LEU* 3.0 14.8 + - - -
928A LEU* 1.3 76.8 - - - +
930A ARG* 1.3 69.1 + - - +
931A ASP* 3.5 4.1 - - - +
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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