Contacts of the strand formed by residues 1023 - 1033 (chain A) in PDB entry 5ES4
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 GLU1023 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A TRP* 5.4 10.9 + - - +
483A ARG* 6.1 0.2 - - - -
935A ARG* 5.6 0.5 + - - -
937A GLN* 2.9 33.8 + - + +
938A VAL 3.5 5.2 - - - +
939A ASN* 3.1 24.2 - - - +
973A GLN* 6.0 0.9 - - - +
974A ASN* 4.7 3.6 + - - -
1021A GLN 3.5 3.2 + - - +
1022A GLU* 1.3 78.2 - - - +
1024A LEU* 1.3 76.0 + - - +
1025A ASP* 3.5 20.8 - - - +
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Residues in contact with LEU1024 (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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936A TYR 4.2 0.3 - - - +
937A GLN* 3.9 0.7 - - - -
938A VAL* 3.1 44.8 + - + +
950A ILE* 6.1 0.2 - - + -
971A HIS* 3.6 21.8 - - + +
973A GLN 4.5 0.4 - - - +
974A ASN* 4.0 15.9 - - + +
1015A VAL* 3.8 33.9 - - + -
1018A PHE* 4.0 24.2 - - + -
1022A GLU* 3.8 13.9 - - - +
1023A GLU* 1.3 83.0 - - - +
1025A ASP* 1.3 71.4 + - - +
1026A PHE* 3.6 19.1 - - + -
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Residues in contact with ASP1025 (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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935A ARG* 2.8 37.9 + - - +
936A TYR 3.8 2.7 - - - -
937A GLN* 4.0 10.4 - - - +
971A HIS* 3.0 22.3 + - - -
972A PRO* 3.4 23.9 - - + +
973A GLN* 6.3 2.4 - - + +
1023A GLU* 3.5 23.6 - - - +
1024A LEU* 1.3 82.7 - - - +
1026A PHE* 1.3 61.5 + - - +
1027A THR* 5.3 2.0 - - + -
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Residues in contact with PHE1026 (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 VAL* 6.4 0.7 - - + -
935A ARG* 3.7 0.5 - - - +
936A TYR* 2.9 39.2 + - + +
938A VAL* 3.9 16.6 - - + -
950A ILE* 4.0 19.7 - - + -
952A PHE* 3.5 35.7 - + + -
969A VAL* 4.3 12.1 - - + -
970A SER 3.9 2.0 - - - -
971A HIS* 3.2 45.3 - + + -
979A CYS* 5.2 0.2 - - - -
1013A CYS* 4.3 17.0 - - + -
1015A VAL* 4.6 6.5 - - + -
1024A LEU* 3.6 33.7 - - + -
1025A ASP* 1.3 72.8 - - - +
1027A THR* 1.3 65.6 + - - +
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Residues in contact with THR1027 (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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933A MET* 5.3 16.6 - - + -
934A HIS 3.3 6.5 - - - -
935A ARG* 3.6 31.0 - - + +
968A GLU 3.7 0.3 - - - +
969A VAL* 3.4 7.4 - - - +
970A SER* 3.0 58.3 + - - +
972A PRO* 5.0 4.9 - - + +
1025A ASP* 5.3 2.5 - - + -
1026A PHE* 1.3 81.6 - - - +
1028A LEU* 1.3 65.9 + - - +
1029A LYS* 5.4 3.8 + - - -
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Residues in contact with LEU1028 (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 ALA 3.6 1.1 - - - +
933A MET* 3.2 6.6 - - - +
934A HIS* 2.7 40.5 + - + +
936A TYR* 3.6 32.8 - - + -
952A PHE* 4.0 27.1 - - + -
954A VAL* 3.7 24.9 - - + -
964A TRP* 4.5 8.4 - - + -
967A VAL* 4.5 8.3 - - + -
968A GLU 3.7 2.9 - - - +
969A VAL* 3.7 28.0 - - + -
1011A PHE* 4.4 5.6 - - + -
1027A THR* 1.3 72.6 - - - +
1029A LYS* 1.3 61.5 + - - +
1049A SER* 3.6 14.4 - - - +
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Residues in contact with LYS1029 (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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931A VAL* 4.5 13.5 - - + -
932A ALA 3.3 3.8 - - - +
933A MET* 3.5 42.8 - - + +
964A TRP* 3.9 3.4 - - - -
966A ASP 3.7 2.6 - - - +
967A VAL* 3.3 4.9 - - - +
968A GLU* 3.2 33.8 + - + +
970A SER* 5.4 12.3 + - - -
1027A THR* 5.2 8.9 + - - +
1028A LEU* 1.3 75.7 - - - +
1030A GLY* 1.3 63.6 + - - +
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Residues in contact with GLY1030 (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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931A VAL* 4.3 1.3 - - - -
932A ALA* 3.0 25.3 + - - +
964A TRP* 2.6 26.3 + - - +
965A MET 3.5 11.7 - - - -
966A ASP* 4.3 2.9 - - - -
1029A LYS* 1.3 80.2 - - - +
1031A ASN* 1.3 65.5 + - - -
1032A LEU 3.1 0.9 + - - -
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Residues in contact with ASN1031 (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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929A SER* 3.0 37.5 + - - +
930A HIS 3.1 5.4 - - - +
931A VAL* 3.1 29.5 + - - +
964A TRP* 4.2 0.2 - - - -
965A MET* 3.2 37.0 + - + +
966A ASP* 5.9 0.4 - - - +
1030A GLY* 1.3 68.6 - - - -
1032A LEU* 1.3 63.0 + - - +
1033A SER 3.4 2.6 + - - -
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Residues in contact with LEU1032 (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 LEU* 3.6 31.2 - - + -
930A HIS 2.5 27.4 + - - +
932A ALA* 4.0 10.3 - - + -
963A VAL* 3.3 41.3 - - + +
964A TRP* 3.9 16.4 - - + +
1030A GLY 3.1 2.6 + - - -
1031A ASN* 1.3 69.5 - - - +
1033A SER* 1.3 72.7 + - - +
1034A PHE* 3.5 9.9 - - - -
1036A TRP* 4.0 3.4 - - + +
1047A VAL* 4.5 13.2 - - + -
1076A THR* 4.3 12.3 - - + -
1078A LEU* 4.0 23.6 - - + -
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Residues in contact with SER1033 (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 GLU 4.5 2.9 + - - -
927A LYS 5.2 2.4 + - - -
928A GLU 4.8 0.7 + - - -
929A SER* 4.0 10.8 - - - -
962A ALA* 3.5 19.3 + - - +
963A VAL 2.6 19.1 + - - -
965A MET* 4.0 20.4 - - - -
1031A ASN 3.4 2.8 + - - -
1032A LEU* 1.3 80.8 - - - +
1034A PHE* 1.3 65.4 + - - +
1035A GLY* 3.2 13.7 + - - -
1036A TRP* 2.9 21.8 + - - -
1078A LEU* 4.2 1.4 - - - +
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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