Contacts of the helix formed by residues 923 - 932 (chain A) in PDB entry 5M64
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 ASN 923 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A ASP* 6.0 2.0 - - - -
913A PRO* 5.8 2.2 - - - +
916A THR* 4.8 3.8 - - - +
918A LYS* 3.0 38.1 + - + +
919A LYS* 3.1 24.1 + - - +
920A PHE* 3.2 16.7 - - - +
921A PRO* 3.4 4.5 - - - +
922A CYS* 1.3 69.0 - - - +
924A SER* 1.3 60.8 + - - +
925A MET 3.5 0.4 - - - -
926A GLN* 3.2 41.3 - - - +
927A ALA* 3.0 26.9 + - - +
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Residues in contact with SER 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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679A TRP* 4.9 4.7 - - - -
826A PHE* 3.4 35.4 - - - -
827A THR 2.9 28.5 + - - -
828A CYS* 3.3 15.6 - - - +
829A GLY 4.6 0.3 + - - -
831A ASP* 5.6 1.0 + - - -
832A ASP* 5.4 3.1 - - - +
918A LYS* 5.0 0.8 - - - +
922A CYS 3.4 6.8 + - - -
923A ASN* 1.3 72.0 - - - +
925A MET* 1.3 68.4 + - - +
927A ALA* 3.9 2.8 - - - +
928A MET* 3.0 18.7 + - - +
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Residues in contact with MET 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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826A PHE* 5.2 1.6 - - - -
828A CYS* 3.9 17.5 - - - -
832A ASP* 3.4 39.9 - - - +
923A ASN 3.5 0.2 - - - -
924A SER* 1.3 81.3 + - - +
926A GLN* 1.3 65.9 + - - +
928A MET* 3.4 6.8 + - - +
929A ALA* 3.0 34.0 + - + +
939A ASN* 5.3 1.3 - - + +
940A VAL* 4.6 8.3 - - + +
943A ILE* 3.8 31.6 - - + -
951B PRO 6.0 0.4 - - - +
954B PHE* 4.7 7.0 - - + +
955B PRO* 3.8 45.0 - - + +
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Residues in contact with GLN 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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832A ASP* 2.6 39.0 + - - +
912A VAL* 5.5 9.6 - - + -
916A THR* 4.1 11.0 + - + +
918A LYS 4.8 0.4 + - - -
920A PHE* 5.1 2.2 - - + -
923A ASN* 3.2 41.2 + - - +
924A SER 3.4 0.4 + - - -
925A MET* 1.3 83.7 + - - +
927A ALA* 1.3 56.4 + - - +
929A ALA* 4.3 2.6 - - - +
930A LEU* 2.8 36.0 + - + +
940A VAL* 5.5 6.7 - - + -
944A MET* 3.1 33.9 - - + +
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Residues in contact with ALA 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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678A VAL* 5.4 10.0 - - + +
679A TRP* 4.9 10.5 - - + +
826A PHE* 5.9 0.2 - - + -
920A PHE* 3.8 27.2 - - + -
921A PRO* 3.8 15.3 - - + +
923A ASN* 3.0 21.2 + - - +
924A SER* 3.9 4.0 - - - +
926A GLN* 1.3 77.4 - - - +
928A MET* 1.3 57.5 + - - +
930A LEU* 4.2 0.5 - - - +
931A SER* 3.1 29.1 + - - -
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Residues in contact with MET 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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671A GLN* 4.1 6.1 - - + -
675A SER* 3.7 24.4 + - - +
826A PHE* 4.3 6.9 - - + -
924A SER 3.0 17.1 + - - +
925A MET* 3.7 5.2 - - - +
926A GLN 3.2 0.2 - - - -
927A ALA* 1.3 77.4 - - - +
929A ALA* 1.3 64.0 + - - +
931A SER* 2.4 22.5 + - - -
932A GLY 3.3 5.0 + - - -
933A ALA* 3.5 10.7 + - + -
934A LYS* 3.6 26.5 - - + +
951B PRO 4.6 2.2 - - - +
952B HIS* 3.6 59.0 - - + +
955B PRO* 3.8 19.3 - - + -
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Residues in contact with ALA 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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754A LYS* 4.5 2.4 + - - -
925A MET* 3.0 26.4 + - + +
926A GLN 4.3 0.9 - - - +
928A MET* 1.3 77.0 - - - +
930A LEU* 1.3 63.3 + - - +
932A GLY* 3.3 8.7 + - - -
934A LYS 3.7 20.0 - - - +
935A GLY* 3.5 18.3 - - - +
936A SER* 3.9 8.9 - - - +
937A ASN 5.0 0.2 + - - -
939A ASN* 6.1 0.7 - - + -
940A VAL* 3.6 28.3 - - + -
955B PRO* 4.6 3.6 - - + -
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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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754A LYS* 3.5 38.9 + - - +
755A ILE* 4.5 5.4 - - - +
756A LYS* 4.4 24.0 - - + +
759A TYR* 4.2 33.2 - - + +
920A PHE* 4.3 19.7 - - + -
926A GLN* 2.8 22.1 + - + +
927A ALA* 4.2 4.0 - - - +
929A ALA* 1.3 76.3 - - - +
931A SER* 1.3 64.1 + - - +
932A GLY 3.4 0.7 + - - -
937A ASN* 4.0 23.1 - - - +
940A VAL* 5.3 0.8 - - - +
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Residues in contact with SER 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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674A ILE* 5.0 2.2 - - - +
675A SER* 5.3 1.9 - - - -
678A VAL* 4.3 17.8 - - - +
754A LYS* 4.6 7.9 - - - +
782A ASP* 2.7 45.8 - - - +
783A LYS* 4.3 5.0 - - - +
927A ALA 3.1 16.8 + - - -
928A MET* 2.4 26.0 + - - -
930A LEU* 1.3 79.0 - - - +
932A GLY* 1.3 57.9 + - - +
933A ALA* 3.5 9.4 + - - +
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Residues in contact with GLY 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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754A LYS* 4.9 9.6 - - - -
783A LYS* 3.6 18.5 - - - +
928A MET 3.3 0.8 + - - -
929A ALA 3.3 11.0 + - - -
930A LEU 3.2 5.8 - - - -
931A SER* 1.3 79.4 - - - +
933A ALA* 1.3 66.7 + - - +
934A LYS* 3.5 1.9 - - - -
935A GLY 4.1 9.5 - - - +
936A SER* 5.2 1.8 - - - -
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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