Contacts of the helix formed by residues 920 - 932 (chain A) in PDB entry 1SIW
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 THR 920 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906A MET* 3.4 40.7 + - + +
910A GLY* 4.9 0.6 - - - -
911A ASN* 4.1 20.1 - - + +
918A TRP* 3.8 16.1 + - - -
919A ASN* 1.3 76.4 + - - +
921A GLN* 1.3 63.8 + - - +
922A SER 3.4 2.0 - - - -
923A GLU* 2.8 33.1 + - - +
924A MET* 3.2 17.7 + - + +
958A LEU* 3.6 13.0 + - + +
966A VAL* 4.7 1.2 - - - +
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Residues in contact with GLN 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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906A MET 5.2 0.6 + - - -
907A GLU* 3.0 50.5 + - - +
919A ASN* 3.0 19.9 + - - +
920A THR* 1.3 74.1 - - - +
922A SER* 1.3 67.6 + - - +
924A MET* 3.1 5.5 + - - +
925A ASP* 3.0 53.4 + - - +
928A ARG* 4.3 1.0 - - - +
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Residues in contact with SER 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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919A ASN* 4.7 0.8 + - - -
921A GLN* 1.3 77.1 - - - +
923A GLU* 1.3 84.9 + - - +
925A ASP* 3.2 11.6 + - - +
926A LEU* 3.0 22.2 + - - +
965A GLN* 3.3 18.9 + - - -
969A LYS* 3.1 15.2 + - - +
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Residues in contact with GLU 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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920A THR* 2.8 34.4 + - - +
921A GLN 3.2 0.4 - - - -
922A SER* 1.3 90.6 + - - +
924A MET* 1.3 57.6 + - - +
926A LEU* 3.2 7.4 + - - +
927A LEU* 2.9 31.7 + - - +
957A THR* 3.2 35.4 - - + +
958A LEU* 3.9 9.9 - - + -
963A ASN* 3.8 9.4 + - - +
965A GLN* 3.8 12.8 + - - +
966A VAL* 3.2 24.5 - - + +
969A LYS* 2.8 25.2 + - - -
993A LYS* 5.8 0.2 - - - -
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Residues in contact with MET 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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902A ILE* 3.3 37.2 - - + +
903A GLY 3.7 13.5 - - - +
906A MET* 4.0 17.5 - - + -
907A GLU* 3.7 41.5 - - + +
920A THR* 3.2 13.6 + - + +
921A GLN 3.1 8.1 + - - +
923A GLU* 1.3 74.4 - - - +
925A ASP* 1.3 66.5 + - - +
927A LEU* 3.2 18.1 + - - +
928A ARG* 3.1 30.4 + - - +
943A PRO* 3.9 23.2 - - + +
958A LEU* 4.8 4.7 - - + -
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Residues in contact with ASP 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 GLN* 3.0 45.4 + - - +
922A SER* 3.6 10.6 - - - +
924A MET* 1.3 76.2 - - - +
926A LEU* 1.3 63.3 + - - +
928A ARG* 3.3 26.6 + - - +
929A LYS* 3.5 25.3 + - - +
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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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922A SER 3.0 12.3 + - - +
923A GLU* 3.2 11.0 + - - +
925A ASP* 1.3 78.7 - - - +
927A LEU* 1.3 61.8 + - - +
929A LYS* 3.0 26.5 + - + +
930A LEU* 3.1 35.1 + - + -
957A THR* 4.0 9.4 - - + -
963A ASN* 5.1 0.2 - - - +
993A LYS* 3.6 32.8 - - + -
995A ARG* 3.8 17.5 - - - +
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Residues in contact with LEU 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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902A ILE* 4.9 4.3 - - + -
923A GLU 2.9 19.5 + - - +
924A MET* 3.6 24.2 - - - +
925A ASP 3.2 0.2 - - - -
926A LEU* 1.3 76.3 - - - +
928A ARG* 1.3 59.1 + - - +
930A LEU* 4.3 7.4 - - + +
931A ASN* 2.9 51.6 + - - +
943A PRO* 3.9 13.9 - - + +
953A GLU 3.8 9.9 - - - +
954A MET* 3.7 40.2 - - + +
957A THR* 3.9 13.2 - - - +
958A LEU* 4.3 18.8 - - + -
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Residues in contact with ARG 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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907A GLU* 2.9 35.3 + - - -
921A GLN* 4.3 0.2 - - - +
924A MET* 3.1 19.8 + - - +
925A ASP* 3.6 28.4 + - - +
926A LEU 3.2 0.4 - - - -
927A LEU* 1.3 76.8 - - - +
929A LYS* 1.3 59.9 + - + +
932A TYR* 3.0 29.7 + - - -
933A THR* 3.6 18.8 - - + +
941A GLY 2.7 21.0 + - - -
942A GLN* 2.9 32.7 + - - +
943A PRO* 3.4 22.2 - - + +
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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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925A ASP* 3.5 24.1 - - - +
926A LEU* 3.0 17.2 + - + +
928A ARG* 1.3 80.8 - - + +
930A LEU* 1.3 63.0 + - + +
932A TYR* 4.2 16.6 + - - -
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Residues in contact with LEU 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 LEU* 3.1 42.0 + - + +
927A LEU* 4.1 10.1 - - + +
929A LYS* 1.3 81.0 - - + +
931A ASN* 1.3 70.5 + - - +
932A TYR* 3.5 9.9 - - - -
950A ASP* 4.8 2.3 - - - +
953A GLU* 4.8 11.0 - - + +
957A THR* 4.0 6.3 - - - +
995A ARG* 3.7 39.7 - - - +
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Residues in contact with ASN 931 (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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902A ILE* 4.2 10.7 - - - +
927A LEU* 2.9 24.8 + - - +
930A LEU* 1.3 87.3 - - - +
932A TYR* 1.3 83.1 + - - +
943A PRO* 4.7 0.4 - - + -
944A MET* 3.0 42.1 + - - +
950A ASP* 3.1 46.2 + - - +
953A GLU* 4.1 13.7 - - - +
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Residues in contact with TYR 932 (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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928A ARG 3.0 17.0 + - - +
929A LYS* 4.4 14.1 - - - -
930A LEU 3.5 8.8 - - - -
931A ASN* 1.3 92.4 - - - +
933A THR* 1.3 71.3 + - - +
943A PRO* 3.3 3.5 - - - +
944A MET* 3.0 21.1 + - + -
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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