Contacts of the strand formed by residues 1011 - 1019 (chain A) in PDB entry 5J9H
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 ALA1011 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666A GLY* 5.6 6.9 - - - -
667A TRP* 4.1 15.9 + - - +
979A CYS* 4.1 4.0 - - - -
1006A LEU* 3.9 2.7 - - - -
1009A CYS* 3.8 10.6 - - - +
1010A SER* 1.3 80.5 - - - +
1012A PHE* 1.3 63.7 + - - +
1032A LEU 3.2 13.2 - - - +
1033A VAL* 4.9 7.2 - - + -
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Residues in contact with PHE1012 (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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667A TRP 3.5 13.5 - - - -
668A THR 3.9 2.7 - - - -
669A ASP* 3.5 46.9 - - + -
977A THR* 3.6 21.8 - - + -
979A CYS* 3.4 26.9 - - + -
981A ILE* 3.7 28.9 - - + -
1006A LEU* 3.6 19.7 - - + -
1011A ALA* 1.3 77.4 - - - +
1013A LEU* 1.3 59.9 + - - +
1014A THR* 3.4 27.1 - - + -
1030A ALA 3.4 1.7 - - - +
1031A ASN* 4.9 0.7 - - - -
1032A LEU* 2.8 40.7 + - + +
1056A HIS* 4.4 4.7 - + - -
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Residues in contact with LEU1013 (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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667A TRP 3.0 8.9 + - - +
668A THR* 2.6 48.6 + - - +
669A ASP 3.5 2.1 + - - -
670A THR* 4.1 15.0 - - + +
1012A PHE* 1.3 70.3 - - - +
1014A THR* 1.3 66.2 + - - +
1029A THR* 3.4 32.5 - - + -
1030A ALA 3.3 5.8 - - - +
1031A ASN* 4.2 19.7 - - - +
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Residues in contact with THR1014 (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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669A ASP* 2.8 21.1 + - - -
670A THR* 3.9 7.4 - - - -
981A ILE* 4.8 1.1 - - + -
1012A PHE* 3.4 17.7 - - + -
1013A LEU* 1.3 77.9 - - - +
1015A SER* 1.3 62.4 + - - +
1016A ILE* 4.0 17.0 - - + -
1029A THR* 3.5 3.9 - - - -
1030A ALA* 2.7 39.4 + - - +
1032A LEU* 3.7 30.5 - - + -
1056A HIS* 2.9 22.5 + - + -
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Residues in contact with SER1015 (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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669A ASP* 4.4 0.2 + - - -
670A THR* 4.0 13.7 - - - +
1014A THR* 1.3 79.1 + - - +
1016A ILE* 1.3 61.1 + - - +
1017A LYS* 4.3 4.6 + - - +
1027A SER* 3.7 20.8 + - - -
1028A THR 3.4 8.7 + - - -
1029A THR* 4.7 3.3 + - - +
1055A CYS 4.3 0.5 - - - +
1056A HIS* 3.3 25.3 - - - +
1201A SO4 3.6 30.7 + - - -
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Residues in contact with ILE1016 (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 ILE* 4.7 1.3 - - + -
983A LEU* 4.0 14.1 - - + -
1002A CYS* 4.2 14.8 - - + -
1004A VAL* 4.3 25.8 - - + -
1014A THR* 4.0 16.8 - - + -
1015A SER* 1.3 81.0 - - - +
1017A LYS* 1.3 63.4 + - - +
1027A SER* 3.3 1.2 - - - -
1028A THR 3.0 31.5 + - - +
1030A ALA* 3.7 24.9 - - + -
1039A ILE* 4.5 9.6 - - + -
1041A ILE* 3.5 24.4 - - + +
1055A CYS 3.5 8.5 - - - +
1056A HIS* 4.3 15.7 - - + -
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Residues in contact with LYS1017 (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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1015A SER* 4.4 5.8 - - - +
1016A ILE* 1.3 78.1 - - - +
1018A ALA* 1.3 59.8 + - - +
1019A CYS* 3.9 12.3 - - - -
1024A CYS* 4.3 22.1 - - + -
1026A GLY 3.4 8.3 - - - +
1027A SER* 3.7 17.5 - - - -
1041A ILE* 3.8 4.9 - - - +
1053A MET 3.4 1.7 - - - +
1054A CYS* 3.6 3.5 - - - -
1055A CYS* 2.8 45.1 + - - +
1056A HIS* 4.8 0.9 - - - +
1057A ASP 2.9 34.3 + - - +
1201A SO4 2.8 38.7 + - - +
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Residues in contact with ALA1018 (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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998A PHE* 4.1 21.5 - - + -
1000A LEU* 3.9 20.2 - - + -
1017A LYS* 1.3 72.2 - - - +
1019A CYS* 1.3 57.5 + - - +
1024A CYS* 3.3 1.6 - - - -
1025A TYR* 2.7 35.2 + - - -
1026A GLY 2.9 8.8 + - - +
1041A ILE* 3.9 19.7 - - + +
1043A GLY* 4.7 5.2 - - - -
1052A PHE* 5.2 1.6 - - + -
1053A MET 3.5 5.2 - - - -
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Residues in contact with CYS1019 (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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1017A LYS* 3.9 6.5 - - - -
1018A ALA* 1.3 75.3 - - - +
1020A ASP* 1.3 66.6 + - - +
1023A MET 3.4 8.7 - - - +
1024A CYS* 2.1 46.0 - - - -
1025A TYR* 4.4 1.3 - - - -
1052A PHE* 4.2 6.2 - - - +
1053A MET* 2.7 42.2 + - - +
1055A CYS* 3.6 33.7 - - - -
1060A CYS* 4.6 2.0 - - - -
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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