Contacts of the strand formed by residues 1024 - 1033 (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 CYS1024 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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810A ARG* 3.3 17.0 + - - +
1017A LYS* 4.3 28.0 - - + -
1018A ALA 3.3 5.2 - - - +
1019A CYS* 2.1 43.1 - - - -
1022A ALA 5.9 0.2 - - - -
1023A MET* 1.3 96.6 - - - +
1025A TYR* 1.3 61.9 - - - +
1026A GLY 3.5 3.5 + - - +
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Residues in contact with TYR1025 (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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725A GLU* 3.6 23.1 + - + -
946A SER* 4.9 1.7 + - - -
998A PHE* 4.2 4.7 - - + -
1018A ALA 2.7 16.2 + - - +
1020A ASP* 3.0 33.9 + - - -
1022A ALA* 5.4 1.4 - - - +
1023A MET* 3.4 33.5 - - + +
1024A CYS* 1.3 71.9 - - - +
1026A GLY* 1.3 53.7 + - - +
1042A VAL 4.1 0.2 - - - +
1043A GLY* 3.3 7.8 - - - -
1044A LYS* 2.9 54.9 + - - +
1045A GLY* 3.8 1.1 - - - -
1046A GLY* 3.3 35.7 - - - -
1047A HIS* 5.2 2.8 + - - -
1050A SER* 4.5 0.5 + - - -
1052A PHE* 3.6 26.0 - + - -
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Residues in contact with GLY1026 (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* 3.4 3.6 - - - +
1018A ALA* 2.9 25.2 + - - +
1024A CYS* 3.5 4.9 - - - +
1025A TYR* 1.3 78.7 + - - +
1027A SER* 1.3 64.5 + - - -
1041A ILE* 4.0 7.4 - - - -
1042A VAL 3.7 11.9 - - - -
1043A GLY* 4.5 0.7 - - - -
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Residues in contact with SER1027 (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* 3.7 18.9 + - - -
1016A ILE 3.3 6.7 - - - -
1017A LYS* 3.7 18.2 - - - -
1026A GLY* 1.3 75.7 - - - -
1028A THR* 1.3 62.9 + - - +
1041A ILE* 4.0 3.8 - - - +
1042A VAL 4.3 1.6 + - - -
1201A SO4 5.4 0.7 - - - -
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Residues in contact with THR1028 (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* 3.4 5.3 - - - -
1016A ILE* 3.0 32.4 + - - +
1027A SER* 1.3 74.1 - - - +
1029A THR* 1.3 77.3 + - - +
1030A ALA 3.4 1.2 + - - -
1039A ILE* 4.5 10.5 - - + -
1040A HIS 2.9 27.6 + - - +
1041A ILE* 3.3 20.4 - - - +
1042A VAL 4.3 2.1 + - - -
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Residues in contact with THR1029 (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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670A THR* 5.9 2.1 - - - +
1013A LEU* 3.4 39.0 - - + +
1014A THR 3.6 4.9 - - - -
1015A SER* 4.7 3.2 + - - +
1027A SER 4.4 0.2 + - - -
1028A THR* 1.3 82.6 - - - +
1030A ALA* 1.3 60.2 + - - +
1031A ASN* 3.8 15.3 + - - +
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Residues in contact with ALA1030 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A PHE 3.4 2.9 - - - +
1013A LEU* 3.3 5.7 - - - +
1014A THR* 2.7 39.8 + - + +
1016A ILE* 3.7 21.1 - - + -
1028A THR 3.4 1.4 + - - -
1029A THR* 1.3 72.6 - - - +
1031A ASN* 1.3 62.4 + - - +
1032A LEU* 3.6 14.0 + - + +
1039A ILE* 3.7 31.2 - - + -
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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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1012A PHE 4.0 2.5 - - - -
1013A LEU* 4.2 21.9 - - - +
1029A THR* 3.8 17.2 + - - +
1030A ALA* 1.3 71.9 - - - +
1032A LEU* 1.3 64.4 + - - +
1033A VAL* 4.0 5.0 + - - +
1037A ASN* 4.3 3.1 - - - +
1039A ILE* 4.9 4.9 - - - +
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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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981A ILE* 4.1 13.7 - - + -
1004A VAL* 3.7 25.8 - - + -
1006A LEU* 4.0 14.8 - - + -
1011A ALA* 3.2 7.6 - - - +
1012A PHE* 2.8 43.3 + - + +
1014A THR* 3.7 25.8 - - + -
1030A ALA* 3.7 24.0 - - + -
1031A ASN* 1.3 74.2 - - - +
1033A VAL* 1.3 64.5 + - - +
1037A ASN* 3.5 32.8 - - + +
1039A ILE* 3.7 11.7 - - + -
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Residues in contact with VAL1033 (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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1006A LEU* 3.6 6.4 - - - +
1010A SER 3.4 10.1 - - - +
1011A ALA* 4.9 6.5 - - + -
1031A ASN 4.0 4.9 + - - +
1032A LEU* 1.3 77.1 - - - +
1034A ARG* 1.3 74.9 + - - +
1035A GLY 3.4 0.5 + - - +
1036A GLN 5.2 3.4 - - - +
1037A ASN* 3.0 32.6 + - - +
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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