Contacts of the helix formed by residues 920 - 930 (chain A) in PDB entry 6DMY
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 TYR 920 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812A TYR* 3.8 14.9 + - - +
813A PRO* 3.4 37.9 - - + +
918A ALA 2.7 27.4 + - - +
919A PHE* 1.3 79.4 - + - +
921A ILE* 1.3 65.2 + - + +
922A TYR 3.2 0.9 - - - -
923A LEU* 3.4 7.2 - - + +
924A THR* 2.9 36.2 + - + +
945A ARG* 5.3 5.6 - - - -
966A ALA* 5.2 11.9 - - + +
967A GLU 4.5 10.3 - - - -
968A PRO* 4.1 23.1 - - + +
969A ILE* 3.6 33.2 - - + -
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Residues in contact with ILE 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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886A LEU* 4.0 11.7 - - + -
889A GLN* 3.7 32.1 - - + +
891A GLY* 5.0 7.0 - - - +
892A SER 6.0 1.3 - - - +
918A ALA* 4.6 14.3 + - + -
919A PHE 4.6 0.2 - - - +
920A TYR* 1.3 77.3 - - + +
922A TYR* 1.3 67.8 + - + +
924A THR* 3.2 6.1 + - + +
925A ALA* 3.0 24.8 + - - +
963A ILE* 3.6 50.0 - - + +
964A PRO 4.7 6.5 - - - +
965A ALA* 5.3 5.4 - - - -
966A ALA 5.8 0.7 - - - +
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Residues in contact with TYR 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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848A PHE* 3.2 25.4 - - + -
851A TRP* 4.0 3.3 - - - -
852A LEU* 3.8 21.5 - - + -
886A LEU* 3.5 45.9 + - + -
889A GLN* 4.5 5.7 + - + -
905A GLN* 2.7 30.3 + - - -
907A LEU* 3.3 22.1 - - + +
915A ASN* 4.6 2.9 - - + -
916A PRO* 3.6 33.8 + - + +
918A ALA* 4.7 7.3 - - + +
919A PHE* 3.9 22.4 - - - +
921A ILE* 1.3 81.3 - - + +
923A LEU* 1.3 56.7 + - - +
925A ALA* 3.7 6.2 + - - +
926A TRP* 3.0 21.7 + - - +
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Residues in contact with LEU 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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844A TRP* 4.1 12.8 - - + -
848A PHE* 3.7 10.1 - - + -
919A PHE* 3.2 38.4 + - + +
920A TYR* 3.2 10.2 + - + +
921A ILE 3.2 0.8 - - - -
922A TYR* 1.3 75.7 - - - +
924A THR* 1.3 59.6 + - - +
926A TRP* 3.0 15.3 + - + +
927A VAL* 2.9 33.3 + - + +
941A ILE* 3.9 21.5 - - + -
945A ARG* 3.8 27.8 - - + -
969A ILE* 3.7 28.5 - - + -
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Residues in contact with THR 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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920A TYR 2.9 20.4 + - - +
921A ILE* 3.2 9.3 + - + -
923A LEU* 1.3 72.2 - - - +
925A ALA* 1.3 63.0 + - - +
927A VAL* 3.5 8.8 - - - +
928A SER* 3.0 33.4 + - - -
945A ARG* 3.7 18.4 - - + -
946A PRO* 4.1 15.9 - - + +
948A TRP* 4.9 3.4 + - - +
963A ILE* 3.3 21.8 - - - +
964A PRO* 4.7 6.3 - - - +
966A ALA* 3.7 28.9 - - + -
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Residues in contact with ALA 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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851A TRP* 3.8 12.3 - - + -
882A LEU* 4.4 5.8 - - + -
886A LEU* 4.1 19.7 - - + -
921A ILE 3.0 14.4 + - - +
922A TYR 3.9 3.8 - - - +
924A THR* 1.3 83.6 + - - +
926A TRP* 1.3 56.3 + - - +
929A ASN* 2.9 46.9 + - - +
948A TRP* 4.6 13.0 - - + -
963A ILE* 5.0 2.2 - - + +
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Residues in contact with TRP 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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844A TRP* 4.1 34.5 - + + -
847A TYR* 4.2 21.4 + - + -
848A PHE* 3.5 32.1 - + + -
851A TRP* 3.7 29.1 - + + -
922A TYR 3.0 18.8 + - - +
923A LEU* 3.0 13.4 + - + +
925A ALA* 1.3 75.4 - - - +
927A VAL* 1.3 67.2 + - + +
930A ASP* 2.9 56.1 + - + +
933A ALA* 4.0 21.3 - - - +
934A TYR* 3.6 36.8 - + + -
937A SER* 5.0 2.0 - - - -
939A ALA* 5.7 0.4 - - + -
941A ILE* 4.8 5.6 - - + -
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Residues in contact with VAL 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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923A LEU* 2.9 24.4 + - + +
924A THR* 3.5 6.7 - - - +
926A TRP* 1.3 80.9 - - + +
928A SER* 1.3 63.6 + - - +
930A ASP 4.6 6.2 + - - +
931A PRO* 4.8 4.5 - - - +
934A TYR* 3.6 55.4 - - + +
941A ILE* 5.8 0.7 - - + -
945A ARG* 3.7 35.9 - - + +
946A PRO 5.5 0.4 - - - +
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Residues in contact with SER 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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924A THR 3.0 19.9 + - - -
927A VAL* 1.3 80.6 - - - +
929A ASN* 1.3 59.9 + - - +
930A ASP 3.7 0.4 - - - -
931A PRO* 4.3 10.5 - - - +
946A PRO 4.8 0.4 - - - -
947A GLU* 3.7 12.6 - - - +
948A TRP 2.9 44.4 + - - -
949A VAL* 3.3 19.9 + - - +
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Residues in contact with ASN 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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851A TRP* 4.5 14.1 + - + -
882A LEU* 4.6 7.7 - - + +
925A ALA* 2.9 34.1 + - - +
928A SER* 1.3 75.8 + - - +
930A ASP* 1.3 59.8 + - - +
931A PRO* 3.5 10.2 - - - +
948A TRP* 3.1 23.8 + - - +
949A VAL* 3.8 6.3 - - - +
950A HIS* 3.1 41.2 + - - +
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Residues in contact with ASP 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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284A LYS* 6.2 0.3 - - - +
847A TYR 5.0 0.2 - - - +
851A TRP* 3.3 33.8 - - + +
926A TRP* 2.9 34.3 + - + +
927A VAL 4.8 0.9 - - - -
929A ASN* 1.3 79.5 - - - +
931A PRO* 1.3 62.2 - - - +
932A VAL* 3.9 10.6 - - - +
933A ALA* 3.3 29.4 + - - +
934A TYR* 3.3 17.8 + - - +
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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