Contacts of the strand formed by residues 924 - 932 (chain A) in PDB entry 3PT6
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 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A GLU* 4.7 1.2 - - - +
921A VAL 2.7 29.0 + - - +
922A ASP* 4.1 6.7 - - + +
923A GLY* 1.3 81.6 + - - +
925A VAL* 1.3 64.9 + - - +
926A TYR* 3.1 24.6 - - + +
1004A HIS* 2.9 47.9 + - + -
1005A CYS 3.0 16.0 - - - -
1006A GLY* 3.4 13.3 - - - +
1016A ASP* 2.9 36.4 + - - -
1018A LYS* 4.0 21.6 - - - +
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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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917A GLN* 3.3 30.5 - - + +
919A GLU 3.6 10.3 - - - +
920A GLU* 4.0 29.2 - - + +
923A GLY 4.2 0.6 - - - -
924A ARG* 1.3 70.3 - - - +
926A TYR* 1.3 73.6 + - - +
927A CYS* 4.3 6.5 - - - -
1004A HIS* 3.1 3.3 - - - -
1005A CYS* 2.7 39.8 + - - +
1006A GLY 5.1 3.3 + - - +
1007A LYS* 5.7 5.6 - - + -
1012A VAL* 4.0 27.8 - - + -
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Residues in contact with TYR 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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917A GLN* 3.5 4.5 - - - -
918A ILE* 2.6 35.9 + - + -
919A GLU* 2.7 24.5 + - + +
921A VAL* 4.5 21.4 - - + +
924A ARG* 3.1 27.1 - - + +
925A VAL* 1.3 73.7 - - - +
927A CYS* 1.3 57.1 + - - +
1002A GLU* 3.7 30.8 + - + -
1003A ILE 3.4 9.6 - - - -
1004A HIS* 3.5 32.0 + + + -
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Residues in contact with CYS 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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914A VAL* 3.5 30.3 - - + -
916A GLU 3.3 10.8 - - - +
917A GLN* 4.3 6.1 - - - -
918A ILE* 4.0 6.1 - - - +
925A VAL* 4.3 15.5 - - - -
926A TYR* 1.3 80.4 - - - +
928A SER* 1.3 61.3 + - - +
929A SER 4.3 0.4 - - - +
930A ILE* 4.3 7.2 - - + -
939A LEU* 3.7 13.7 - - - +
1003A ILE* 2.7 42.3 + - + +
1005A CYS* 5.0 12.6 - - - -
1012A VAL* 5.5 1.6 - - - -
1017A ILE* 6.3 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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916A GLU* 3.0 37.2 + - - +
917A GLN 5.2 0.5 - - - -
918A ILE* 4.6 9.4 + - - +
927A CYS* 1.3 74.5 - - - +
929A SER* 1.3 59.7 + - - +
938A ARG* 3.3 5.2 - - - +
939A LEU* 3.0 46.9 + - - +
1003A ILE* 4.1 5.6 - - - +
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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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914A VAL* 3.7 2.6 - - - +
915A LEU* 2.7 47.6 + - - +
916A GLU* 3.0 38.9 + - - -
927A CYS* 3.8 1.2 - - - +
928A SER* 1.3 80.3 + - - +
930A ILE* 1.3 56.1 + - - +
936A VAL* 4.2 5.4 - - - +
937A TYR 3.4 5.6 + - - -
938A ARG* 3.8 18.7 - - - +
1003A ILE* 4.4 0.4 - - - +
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Residues in contact with ILE 930 (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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913A LYS 3.8 7.2 - - - +
914A VAL* 3.7 28.3 - - + +
915A LEU* 3.2 10.6 - - - +
927A CYS* 4.3 5.2 - - + -
929A SER* 1.3 76.5 - - - +
931A THR* 1.3 59.4 + - - +
936A VAL* 3.9 0.2 - - - +
937A TYR* 2.8 37.2 + - + +
1003A ILE* 3.7 30.7 - - + -
1017A ILE* 3.7 28.9 - - + -
1019A LEU* 4.4 4.5 - - + -
1056A PHE* 3.6 38.8 - - + -
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Residues in contact with THR 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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911A MET 5.8 0.9 - - - +
912A PRO* 3.6 1.2 - - - +
913A LYS* 3.2 39.6 + - + +
915A LEU* 3.3 30.7 - - + +
930A ILE* 1.3 76.6 - - - +
932A LYS* 1.3 63.8 + - - +
934A GLY* 4.4 7.3 + - - -
935A VAL 2.8 22.5 + - - -
936A VAL* 3.8 11.1 - - - +
937A TYR* 4.7 0.4 - - - -
1056A PHE* 3.9 4.5 - - - -
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Residues in contact with LYS 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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909A LYS 4.6 0.9 - - - -
910A GLU 4.0 12.6 - - - +
911A MET 4.7 1.1 - - - -
912A PRO* 4.4 17.9 - - + -
931A THR* 1.3 76.6 + - - +
933A ASN* 1.3 82.1 + - + +
934A GLY 3.1 3.9 + - - -
935A VAL* 3.0 23.8 + - - +
937A TYR* 4.2 10.3 + - + -
1056A PHE* 2.7 55.4 + - + +
1057A SER* 3.6 14.6 + - - +
1059A VAL* 2.9 31.5 + - - +
1060A GLN 6.2 0.2 - - - -
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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