Contacts of the helix formed by residues 926 - 937 (chain A) in PDB entry 3SQD
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 926 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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904A ILE* 3.9 1.2 - - - +
905A ALA 3.4 10.1 - - - +
906A SER* 4.7 4.7 - - - +
925A VAL* 1.3 76.9 - - - +
927A PRO* 1.3 68.2 - - + +
928A GLU* 3.3 28.6 + - - +
929A TRP* 3.0 25.1 + - - +
930A LEU 4.2 0.3 + - - -
945A TYR* 3.0 24.9 + - - +
946A ILE 4.7 2.5 - - - +
947A LEU* 4.2 21.8 - - + -
948A ARG 5.4 0.7 - - - +
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Residues in contact with PRO 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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874A PHE* 3.8 20.9 - - + -
882A TYR* 3.4 34.0 - - + +
904A ILE* 3.5 22.2 - - + -
905A ALA 3.9 9.4 - - - +
906A SER* 4.1 11.0 - - - -
926A THR* 1.3 84.8 - - - +
928A GLU* 1.3 77.3 + - - +
929A TRP 3.0 0.4 - - - -
930A LEU* 3.0 18.9 + - + +
931A GLU* 3.0 15.8 + - + +
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Residues in contact with GLU 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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906A SER* 5.5 1.4 - - - -
926A THR* 3.1 25.7 - - - +
927A PRO* 1.3 88.8 - - - +
929A TRP* 1.3 61.6 + - - +
931A GLU* 3.7 10.5 - - + +
932A GLU* 3.0 25.3 + - - +
945A TYR* 3.8 15.6 - - + -
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Residues in contact with TRP 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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867A PRO* 4.4 7.2 - - + -
869A VAL* 4.6 9.0 - - + -
886A LEU* 5.6 0.2 - - + -
902A HIS* 3.6 23.6 - + - -
904A ILE* 3.7 24.2 - - + -
925A VAL* 3.8 10.5 - - + -
926A THR 3.0 14.7 + - - +
928A GLU* 1.3 78.0 - - - +
930A LEU* 1.3 77.3 + - + +
932A GLU* 3.3 2.6 + - - +
933A CYS* 2.9 47.6 + - - -
939A PHE* 3.7 29.6 - + + -
940A ILE* 3.0 23.9 + - + -
941A ASP 3.8 8.4 + - - -
942A GLU* 3.7 30.4 - - + +
945A TYR* 3.5 41.5 - + + -
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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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869A VAL* 6.0 0.7 - - + -
871A PHE* 3.9 17.9 - - + -
882A TYR* 3.6 49.1 - - + +
885A LYS* 4.7 7.4 - - + -
886A LEU* 4.3 24.5 - - + +
889A LEU* 3.9 23.1 - - + -
904A ILE* 5.0 3.4 - - + -
926A THR 4.2 0.4 + - - -
927A PRO* 3.0 13.0 + - + +
929A TRP* 1.3 95.9 - - + +
931A GLU* 1.3 57.3 + - - +
933A CYS* 3.3 3.9 + - + +
934A PHE* 2.9 26.9 + - - +
939A PHE* 4.8 3.6 - - + -
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Residues in contact with GLU 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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882A TYR* 3.6 27.2 + - + +
885A LYS* 3.4 31.9 + - - -
927A PRO 3.0 19.3 + - - +
928A GLU* 3.7 12.1 - - + +
930A LEU* 1.3 72.8 - - - +
932A GLU* 1.3 60.7 + - - +
934A PHE* 3.4 4.9 + - - +
935A ARG* 3.0 27.2 + - - +
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Residues in contact with GLU 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 GLU 3.0 16.3 + - - +
929A TRP 3.7 2.7 - - - +
931A GLU* 1.3 74.8 - - - +
933A CYS* 1.3 65.5 + - - +
935A ARG* 2.8 41.9 + - - -
936A CYS* 3.0 43.9 + - - -
940A ILE* 3.3 23.6 - - + -
945A TYR* 3.3 21.8 - - + +
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Residues in contact with CYS 933 (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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889A LEU* 3.6 16.4 - - + +
929A TRP* 2.9 51.0 + - - -
930A LEU* 3.5 11.0 - - + +
932A GLU* 1.3 76.2 - - - +
934A PHE* 1.3 58.6 + - - +
936A CYS 3.3 0.3 + - - -
937A GLN* 2.9 22.7 + - - -
938A LYS 3.0 22.1 + - - +
939A PHE* 3.6 8.5 - - + -
940A ILE* 3.3 31.2 - - - -
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Residues in contact with PHE 934 (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 LYS* 3.5 68.9 - - + -
888A ILE* 4.0 27.1 - - + -
889A LEU* 3.8 10.7 - - + +
930A LEU 2.9 17.0 + - - +
931A GLU* 3.8 4.7 - - - +
932A GLU 3.2 0.2 - - - -
933A CYS* 1.3 74.2 - - - +
935A ARG* 1.3 69.9 + - - +
937A GLN* 2.7 39.3 + - - +
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Residues in contact with ARG 935 (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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931A GLU 3.0 18.0 + - - +
932A GLU* 2.8 42.3 + - - +
934A PHE* 1.3 82.8 - - - +
936A CYS* 1.3 63.9 + - - +
937A GLN* 3.5 4.2 + - - +
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Residues in contact with CYS 936 (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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932A GLU* 3.0 44.3 + - - +
933A CYS 3.9 3.1 - - - +
935A ARG* 1.3 83.7 - - - +
937A GLN* 1.3 69.0 + - - +
938A LYS* 3.1 27.5 + - + +
940A ILE* 4.4 12.8 - - + -
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Residues in contact with GLN 937 (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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859A MET* 5.4 7.9 - - - +
888A ILE* 4.0 22.8 + - - +
889A LEU* 3.6 13.3 - - - +
933A CYS 2.9 6.9 + - - -
934A PHE* 2.7 43.9 + - - +
935A ARG 4.5 4.0 - - - +
936A CYS* 1.3 80.0 - - - +
938A LYS* 1.3 59.9 + - - +
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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