Contacts of the strand formed by residues 1049 - 1057 (chain A) in PDB entry 1OBO
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 TYR1049 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003A LYS* 3.5 46.1 + - + +
1004A ILE* 3.5 14.7 - - + -
1005A GLY 3.0 22.6 + - - -
1047A TYR* 3.3 7.6 - - - +
1048A GLN* 1.3 101.3 - - + +
1050A LEU* 1.3 61.4 + - - +
1082A LEU* 3.5 18.4 - - + -
1167A PHE* 3.4 55.5 + + + -
1168A GLY 5.2 1.0 + - - -
1169A LEU* 4.0 13.5 - - + +
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Residues in contact with LEU1050 (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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1004A ILE* 4.6 0.2 - - - -
1005A GLY 3.3 13.5 - - - +
1007A PHE* 3.7 24.2 - - + -
1044A LEU* 4.0 18.8 - - + +
1047A TYR* 3.8 23.6 - - + +
1049A TYR* 1.3 74.7 - - - +
1051A ILE* 1.3 67.8 + - - +
1052A ILE* 4.2 7.2 - - + -
1078A PHE* 3.7 36.6 - - + -
1081A LYS* 4.1 13.9 - - + -
1082A LEU 3.0 9.0 + - - +
1083A VAL* 3.3 20.3 - - + -
1084A ALA 2.8 24.6 + - - -
1167A PHE* 3.8 2.6 - - - -
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Residues in contact with ILE1051 (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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1004A ILE* 3.7 21.1 - - + -
1005A GLY 2.9 7.0 + - - +
1006A LEU* 3.2 17.5 - - + +
1007A PHE 2.9 27.2 + - - +
1022A ILE* 4.2 9.6 - - + -
1026A PHE* 3.7 31.4 - - + -
1031A VAL* 5.1 1.3 - - + -
1050A LEU* 1.3 78.8 - - - +
1052A ILE* 1.3 65.9 + - - +
1084A ALA* 3.2 8.1 - - + +
1086A PHE* 3.6 31.0 - - + -
1159A TRP* 4.1 13.2 - - + -
1163A LEU* 4.1 10.1 - - + -
1167A PHE* 4.3 9.2 - - + -
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Residues in contact with ILE1052 (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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1007A PHE* 3.5 8.5 - - + -
1044A LEU* 4.6 8.7 - - + -
1050A LEU* 4.6 11.2 - - + -
1051A ILE* 1.3 78.7 - - - +
1053A GLY* 1.3 59.5 + - - +
1054A CYS 4.3 0.2 + - - -
1066A TRP* 3.6 36.8 - - + -
1083A VAL* 3.6 26.0 - - + -
1084A ALA 2.7 8.5 + - - -
1085A TYR* 3.3 26.9 - - + +
1086A PHE* 2.9 28.3 + - - +
1102A ILE* 4.5 1.3 - - + +
1105A LEU* 3.7 25.4 - - + -
1109A ILE* 3.9 12.3 - - + -
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Residues in contact with GLY1053 (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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1007A PHE 2.9 13.4 + - - -
1008A TYR* 3.2 12.7 - - - -
1009A GLY 3.3 2.1 + - - -
1015A THR* 4.0 6.5 - - - -
1051A ILE 4.0 0.2 + - - -
1052A ILE* 1.3 74.7 - - - +
1054A CYS* 1.3 61.9 + - - -
1066A TRP* 2.9 19.7 + - - -
1086A PHE* 3.1 33.7 - - - -
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Residues in contact with CYS1054 (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 THR* 3.9 3.4 - - - +
1052A ILE 4.3 0.2 + - - -
1053A GLY* 1.3 77.0 - - - +
1055A PRO* 1.3 86.8 - - - +
1056A THR 3.9 0.2 + - - -
1062A LEU* 4.5 1.6 - - - -
1063A GLN* 3.7 19.7 - - - -
1066A TRP* 3.5 29.2 - - + -
1086A PHE 3.1 7.3 + - - -
1087A GLY* 3.3 20.6 - - - -
1088A THR* 3.5 4.3 + - - +
1099A GLN* 4.8 0.5 - - - +
1101A ALA* 3.9 16.2 - - + +
1102A ILE* 4.1 6.8 - - + +
1105A LEU* 3.6 17.7 - - + -
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Residues in contact with PRO1055 (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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1009A GLY 3.2 20.0 - - - +
1010A THR* 4.6 0.2 - - - -
1015A THR* 3.3 10.1 - - - +
1054A CYS* 1.3 102.3 - - - +
1056A THR* 1.3 62.3 + - - +
1057A LEU* 3.7 15.7 + - + -
1063A GLN* 3.8 23.8 + - + +
1088A THR* 3.0 24.0 - - - +
1101A ALA* 3.6 2.5 - - - +
1170A FMN 3.5 30.3 - - - +
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Residues in contact with THR1056 (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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1054A CYS 3.9 0.5 + - - -
1055A PRO* 1.3 72.6 - - - +
1057A LEU* 1.3 60.4 + - - +
1060A GLY* 3.6 21.3 - - - -
1061A GLU 3.5 7.0 - - - +
1088A THR 3.3 7.7 + - - -
1097A ASN 3.7 6.3 - - - +
1099A GLN* 3.3 8.5 + - - -
1100A ASP* 3.1 15.3 + - + -
1101A ALA* 2.9 24.5 + - - +
1170A FMN 2.8 68.4 + - + +
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Residues in contact with LEU1057 (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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1011A GLN* 3.4 34.3 - - + -
1055A PRO* 3.9 16.8 - - + +
1056A THR* 1.3 83.1 - - - +
1058A ASN* 1.3 80.4 - - - +
1059A ILE 3.0 4.2 + - - -
1061A GLU* 2.8 36.0 + - - +
1062A LEU 4.9 3.6 - - - +
1063A GLN* 3.9 23.8 - - + -
1064A SER 5.3 0.2 - - - +
1170A FMN 3.7 44.6 - - + +
2135B ASN* 4.5 8.1 - - - +
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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