Contacts of the strand formed by residues 1024 - 1030 (chain A) in PDB entry 3BU6
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 GLU1024 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997A THR* 5.6 0.5 + - - -
1014A ASN* 3.5 37.6 + - - +
1015A ALA 3.3 14.4 - - - +
1016A ARG* 3.7 24.1 - - + +
1022A GLU* 3.1 8.9 - - - +
1023A ALA* 1.3 83.1 - - + +
1025A THR* 1.3 65.8 + - - +
1026A ARG 4.4 0.5 + - - -
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Residues in contact with THR1025 (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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1014A ASN* 3.6 5.3 - - - -
1015A ALA* 2.7 40.6 + - - -
1018A ILE* 3.8 18.5 - - - +
1019A ILE* 4.0 20.2 + - + +
1022A GLU* 2.7 34.9 + - - +
1024A GLU* 1.3 74.8 - - - +
1026A ARG* 1.3 76.5 + - - +
1027A VAL* 3.6 9.4 + - + +
1063A LEU* 5.0 1.3 - - + -
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Residues in contact with ARG1026 (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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999A LEU* 3.5 25.5 - - - +
1000A ARG* 5.9 3.2 - - - +
1012A GLU* 2.7 35.4 + - + +
1013A GLY 3.4 10.8 - - - +
1014A ASN* 3.6 20.9 + - - +
1024A GLU 4.4 0.4 + - - -
1025A THR* 1.3 85.3 - - - +
1027A VAL* 1.3 56.9 + - - +
1063A LEU* 5.6 0.2 - - - +
1078A LEU* 3.7 26.2 + - + +
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Residues in contact with VAL1027 (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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996A ILE* 5.4 1.1 - - + -
1012A GLU* 3.4 8.5 - - - +
1013A GLY 2.8 48.6 + - - +
1014A ASN 4.3 0.9 - - - +
1015A ALA* 3.8 23.6 - - + +
1018A ILE* 4.6 0.7 - - + -
1025A THR* 3.7 15.3 - - + +
1026A ARG* 1.3 78.8 - - - +
1028A ALA* 1.3 57.9 + - - +
1029A VAL* 3.8 13.5 - - + -
1063A LEU* 3.7 25.8 - - + -
1075A VAL* 3.8 20.2 - - + -
1076A MET 3.6 7.9 - - - +
1078A LEU* 3.8 8.5 - - - +
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Residues in contact with ALA1028 (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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1002A LEU* 4.1 7.9 - - + -
1010A VAL* 4.3 4.7 - - + -
1011A TYR 3.4 4.5 - - - -
1027A VAL* 1.3 74.3 - - - +
1029A VAL* 1.3 62.7 + - - +
1030A LYS 4.2 0.7 - - - -
1074A VAL 3.7 0.2 - - - +
1075A VAL* 3.5 3.6 - - - -
1076A MET* 2.8 48.3 + - + +
1077A GLU 4.2 4.0 - - - +
1078A LEU* 3.9 4.5 - - + +
621B TYR* 3.7 35.7 - - + +
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Residues in contact with VAL1029 (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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996A ILE* 4.1 10.3 - - + -
998A LEU* 3.9 26.7 - - + -
1009A MET 3.8 1.4 - - - +
1010A VAL* 3.4 3.4 - - - +
1011A TYR* 2.7 42.8 + - + +
1013A GLY* 4.6 4.5 - - - -
1027A VAL* 3.8 20.9 - - + -
1028A ALA* 1.3 79.8 - - - +
1030A LYS* 1.3 64.8 + - - +
1031A THR* 4.5 2.5 - - + -
1073A LEU* 3.7 42.8 - - + -
1074A VAL 3.4 6.3 - - - +
1075A VAL* 4.5 6.3 - - + -
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Residues in contact with LYS1030 (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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1005A GLY* 5.2 4.7 - - - -
1006A SER* 4.9 8.8 + - - +
1007A PHE* 5.8 2.2 - - - +
1009A MET 4.1 3.6 - - - -
1010A VAL* 3.8 29.4 - - + -
1029A VAL* 1.3 74.0 - - - +
1031A THR* 1.3 64.1 + - - +
1044A PHE* 3.6 21.6 - - + -
1047A GLU* 3.6 30.2 + - - +
1051A MET* 5.1 3.4 - - + +
1073A LEU* 3.7 2.1 - - - -
1074A VAL* 2.8 43.9 + - + +
1076A MET* 3.7 33.7 - - + -
1149A GLY 5.5 2.0 + - - -
1150A ASP* 4.2 16.6 + - - +
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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