Contacts of the strand formed by residues 1008 - 1015 (chain A) in PDB entry 3K72
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 CYS1008 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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953A TRP* 3.4 9.6 - - + -
954A VAL 3.3 26.5 - - - -
955A PRO* 3.8 2.2 - - - -
956A VAL* 5.4 0.9 - - - +
983A LYS* 3.8 7.1 - - - +
984A ILE* 3.3 38.5 + - + -
986A PRO* 4.7 0.2 - - - +
1003A CYS* 2.0 56.9 + - + +
1006A ALA 2.7 5.0 + - - +
1007A GLY* 1.3 77.0 - - - +
1009A LEU* 1.3 71.9 + - - +
1010A ARG 4.4 0.2 - - - -
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Residues in contact with LEU1009 (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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953A TRP* 3.5 5.0 - - - -
954A VAL 3.0 35.4 + - - +
956A VAL* 4.2 20.2 - - + -
967A VAL* 5.1 6.7 - - + +
981A SER* 4.1 9.4 - - - -
982A GLU 3.6 19.7 - - - +
983A LYS* 4.5 20.2 - - + -
1008A CYS* 1.3 81.0 - - - +
1010A ARG* 1.3 77.0 + - - +
1011A PHE* 3.5 37.6 - - + -
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Residues in contact with ARG1010 (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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951A ASN* 4.1 22.4 - - - +
952A PHE 3.2 13.0 - - - +
953A TRP* 3.4 38.8 - - + -
980A SER 3.5 1.0 - - - +
981A SER* 3.4 7.1 - - - -
982A GLU* 2.9 66.1 + - + +
984A ILE* 4.6 21.1 - - + +
1008A CYS 4.4 0.2 - - - -
1009A LEU* 1.3 73.5 - - - +
1011A PHE* 1.3 64.1 + - - +
1012A ARG* 4.1 9.6 + - - +
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Residues in contact with PHE1011 (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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950A ILE 3.2 4.5 - - - +
951A ASN* 3.2 7.9 - - - -
952A PHE* 3.1 49.6 + + + +
954A VAL* 4.3 17.3 - - + -
967A VAL* 3.6 31.0 - - + -
968A GLU* 4.6 10.3 - - + -
969A VAL* 4.4 18.4 - - + -
979A CYS* 5.2 3.4 - - + -
980A SER 3.1 14.6 - - - +
981A SER* 4.8 6.5 - - - -
1009A LEU* 3.5 47.6 - - + -
1010A ARG* 1.3 72.9 - - - +
1012A ARG* 1.3 61.1 + - - +
1013A CYS* 3.6 7.2 - - - -
1028A LEU* 5.9 2.5 - - + -
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Residues in contact with ARG1012 (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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949A SER* 3.4 19.3 + - - +
951A ASN* 3.5 20.9 - - - +
978A ARG 4.1 0.3 - - - +
979A CYS* 3.6 1.6 - - - -
980A SER* 3.1 52.1 + - - -
982A GLU* 5.6 3.6 + - - -
1010A ARG* 4.1 9.7 - - - +
1011A PHE* 1.3 71.2 - - - +
1013A CYS* 1.3 56.9 + - - +
1014A ASP* 2.8 44.7 + - - +
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Residues in contact with CYS1013 (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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949A SER* 3.5 0.8 - - - -
950A ILE* 2.9 47.8 + - + +
952A PHE* 4.6 9.4 - - - -
969A VAL* 4.1 16.4 - - - -
977A LEU* 6.3 0.9 - - + -
979A CYS* 2.0 48.9 - - - -
1011A PHE* 4.5 11.9 - - - -
1012A ARG* 1.3 70.8 - - - +
1014A ASP* 1.3 66.4 + - - +
1015A VAL* 3.8 5.5 - - + +
1026A PHE* 4.8 11.4 - - + -
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Residues in contact with ASP1014 (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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948A VAL 3.9 1.8 - - - +
949A SER* 2.7 30.9 + - - -
977A LEU* 4.0 15.4 - - - +
978A ARG* 3.6 16.2 + - + +
1012A ARG* 2.8 39.8 + - - +
1013A CYS* 1.3 78.0 - - - +
1015A VAL* 1.3 63.5 + - - +
1016A PRO* 4.6 0.4 - - - +
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Residues in contact with VAL1015 (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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947A PRO* 3.8 3.3 - - - +
948A VAL* 2.9 47.0 + - + +
949A SER* 4.9 0.4 - - - +
950A ILE* 4.9 10.8 - - + -
977A LEU* 4.6 8.7 - - + -
1013A CYS* 3.8 10.1 - - + +
1014A ASP* 1.3 83.8 - - - +
1016A PRO* 1.3 80.9 - - + +
1017A SER 3.9 2.5 - - - +
1018A PHE* 3.9 26.7 - - + +
1024A LEU* 4.5 21.8 - - + -
1026A PHE* 5.7 2.2 - - + -
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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