Contacts of the strand formed by residues 1023 - 1028 (chain A) in PDB entry 3SQD
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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975A ALA 3.4 10.2 + - - +
976A LYS* 2.9 33.2 + - + +
977A TYR* 2.8 27.2 + - - +
1015A HIS* 5.3 2.7 - - - -
1021A LEU 3.7 1.4 + - - -
1022A SER* 1.3 72.9 - - - +
1024A ILE* 1.3 69.4 + - - +
1025A ILE* 3.5 9.5 - - + +
1063A TYR* 2.6 37.5 + - - -
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Residues in contact with ILE1024 (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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977A TYR* 3.3 14.6 - - + +
979A TYR 4.8 0.7 - - - +
1003A LEU* 3.9 25.8 - - + -
1007A PRO* 4.5 0.9 - - + -
1011A LYS* 4.0 13.7 - - + +
1012A LEU* 3.7 31.3 - - + +
1015A HIS* 3.6 48.6 - - + +
1016A LYS* 6.4 0.4 - - - +
1022A SER 3.6 0.4 + - - -
1023A GLU* 1.3 83.0 - - - +
1025A ILE* 1.3 69.1 + - - +
1026A LEU* 4.0 17.0 + - + +
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Residues in contact with ILE1025 (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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976A LYS* 3.7 28.9 - - + -
977A TYR 2.7 10.0 + - - +
978A PHE* 3.2 33.3 - - + +
979A TYR 2.9 23.9 + - - +
1023A GLU* 3.5 25.1 - - + +
1024A ILE* 1.3 77.4 - - - +
1026A LEU* 1.3 66.0 + - - +
1027A ILE* 3.9 22.2 + - + -
1047A HIS* 4.0 17.7 - - + +
1051A PHE* 3.9 22.0 - - + -
1063A TYR* 4.4 3.8 - - + -
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Residues in contact with LEU1026 (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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979A TYR* 3.5 31.9 - - + +
1007A PRO* 3.8 19.1 - - + -
1012A LEU* 4.4 6.1 - - + -
1024A ILE* 4.0 11.0 - - + +
1025A ILE* 1.3 78.4 - - - +
1027A ILE* 1.3 65.9 + - - +
1036A CYS* 6.4 0.7 - - - -
1039A TYR* 4.3 17.9 - - + -
1044A ILE* 3.6 31.4 - - + -
1045A ASP 3.7 14.5 + - - +
1046A VAL* 3.6 16.2 - - + -
1047A HIS* 2.8 28.7 + - - -
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Residues in contact with ILE1027 (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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978A PHE* 3.9 21.8 - - + -
979A TYR 2.8 8.8 + - - +
980A ILE* 3.4 21.2 - - + +
981A THR* 3.2 25.6 + - - +
984A ILE* 4.1 11.7 - - + -
991A MET* 4.3 9.4 - - + -
1025A ILE* 3.9 16.8 - - + -
1026A LEU* 1.3 84.5 - - - +
1028A SER* 1.3 64.9 + - - +
1046A VAL* 4.2 0.7 - - - -
1047A HIS* 3.2 19.7 - - + +
1049A ALA* 4.0 24.7 - - - +
1051A PHE* 4.2 15.9 - - + -
1052A VAL* 4.4 7.0 - - + -
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Residues in contact with SER1028 (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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981A THR* 2.9 30.1 + - - +
984A ILE* 3.5 13.7 - - - +
1027A ILE* 1.3 76.3 - - - +
1029A CYS* 1.3 68.9 + - - +
1032A ASP* 3.5 10.0 - - - +
1033A LEU* 3.9 11.8 - - - +
1036A CYS* 3.8 7.1 - - - -
1046A VAL* 3.5 19.9 - - - +
1047A HIS 2.7 10.3 + - - -
1048A ASN* 3.5 21.3 - - - +
1049A ALA 3.9 1.0 + - - -
1068A PHE* 3.8 3.8 - - - -
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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