Contacts of the strand formed by residues 1046 - 1055 (chain A) in PDB entry 2OOQ
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 TYR1046 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1043A LEU* 2.8 71.0 + - + +
1044A ALA 3.6 0.6 - - - -
1045A GLU* 1.3 89.4 - - + +
1047A VAL* 1.3 58.7 + - - +
1048A ILE* 4.2 14.6 - - + -
1068A HIS 3.1 15.3 - - - +
1069A PHE* 3.7 4.0 - + + -
1070A THR* 3.8 6.0 + - - -
1083A GLY* 4.2 8.3 - - - -
1086A GLY* 4.1 5.7 + - - -
1087A PHE* 3.5 49.6 - + + -
1090A GLN* 2.8 41.4 + - + +
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Residues in contact with VAL1047 (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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1040A THR* 3.5 32.3 - - + -
1041A GLU 3.4 13.7 - - - +
1042A PRO* 4.0 9.2 - - + -
1046A TYR* 1.3 74.7 - - - +
1048A ILE* 1.3 68.5 + - - +
1049A ARG* 3.5 35.0 - - + +
1066A LEU 3.5 2.4 - - - +
1068A HIS* 2.9 46.4 + - + +
1070A THR* 4.5 7.2 - - + -
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Residues in contact with ILE1048 (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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301A B3P 3.9 22.1 + - - +
1039A GLU* 3.9 1.0 - - - +
1040A THR* 3.5 1.6 - - - -
1041A GLU* 2.7 58.6 + - + +
1046A TYR* 4.2 15.0 - - + -
1047A VAL* 1.3 75.2 - - - +
1049A ARG* 1.3 66.7 + - - +
1050A THR* 4.5 1.5 + - - +
1065A ARG* 4.3 16.2 - - + -
1066A LEU 3.4 7.9 - - - +
1067A PHE* 3.9 35.4 - - + -
1090A GLN* 3.9 31.6 - - - +
1094A LEU* 4.3 4.5 - - + -
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Residues in contact with ARG1049 (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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1023A TRP* 3.7 45.7 - - - +
1037A LEU* 4.0 9.9 - - + -
1039A GLU 3.3 5.8 - - - +
1040A THR* 4.0 22.1 + - + +
1047A VAL* 3.5 26.1 - - + +
1048A ILE* 1.3 78.1 - - - +
1050A THR* 1.3 63.2 + - - +
1051A PHE* 3.8 19.5 - - + -
1065A ARG* 3.3 2.9 - - - +
1066A LEU* 2.8 45.3 + - + +
1068A HIS* 3.5 30.5 + - - +
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Residues in contact with THR1050 (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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301A B3P 2.6 37.9 + - - +
1037A LEU* 3.6 4.2 - - - +
1038A ILE* 2.9 37.5 + - + -
1039A GLU* 2.9 21.3 + - + +
1048A ILE* 4.5 1.4 + - - +
1049A ARG* 1.3 77.5 - - - +
1051A PHE* 1.3 63.7 + - - +
1063A GLU* 3.7 35.9 - - + +
1064A LEU 3.4 5.8 - - - +
1065A ARG* 3.8 8.6 - - + +
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Residues in contact with PHE1051 (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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994A TRP* 5.3 1.8 - + - -
1023A TRP* 3.6 26.9 - + + -
1024A PRO* 3.6 21.8 - - + -
1035A VAL* 3.5 22.9 - - + -
1036A THR 3.1 7.6 - - - +
1037A LEU* 3.5 34.1 - - + -
1038A ILE* 4.2 5.4 - - - +
1049A ARG* 3.8 35.7 - - + -
1050A THR* 1.3 73.1 - - - +
1052A THR* 1.3 69.9 + - - +
1053A VAL* 4.5 5.2 - - + -
1063A GLU* 3.4 6.6 - - - +
1064A LEU* 2.8 49.8 + - + +
1066A LEU* 3.9 16.4 - - + -
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Residues in contact with THR1052 (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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1034A LYS 3.6 1.6 + - - +
1035A VAL* 3.3 5.0 - - - -
1036A THR* 2.9 51.7 + - - +
1038A ILE* 4.0 26.3 - - + +
1051A PHE* 1.3 76.5 - - - +
1053A VAL* 1.3 61.8 + - - +
1061A ILE* 3.8 23.5 - - + +
1062A ARG 3.2 6.3 - - - +
1063A GLU* 5.4 2.7 - - + -
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Residues in contact with VAL1053 (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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994A TRP* 4.2 20.0 - - + -
997A ILE* 5.2 5.2 - - + -
998A TRP* 3.5 22.3 - - + -
1033A ILE* 3.3 31.9 - - + -
1034A LYS 3.4 3.4 - - - -
1035A VAL* 4.3 4.9 - - + -
1051A PHE* 4.5 5.8 - - + -
1052A THR* 1.3 80.7 - - - +
1054A GLN* 1.3 61.6 + - - +
1061A ILE* 3.6 1.7 - - - -
1062A ARG* 2.8 39.6 + - + +
1064A LEU* 3.8 30.5 - - + -
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Residues in contact with GLN1054 (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 TRP* 3.8 7.6 - - - -
1033A ILE* 3.6 2.2 - - - -
1034A LYS* 2.8 60.6 + - + +
1053A VAL* 1.3 77.0 - - - +
1055A LYS* 1.3 72.6 + - - +
1056A LYS* 3.5 6.3 + - - +
1057A GLY 5.3 1.0 - - - +
1058A TYR 2.9 21.3 + - - +
1059A HIS* 4.4 5.7 + - - +
1060A GLU 3.5 13.9 - - - +
1061A ILE* 3.9 29.6 - - + +
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Residues in contact with LYS1055 (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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995A ARG* 5.7 7.5 - - - +
998A TRP* 3.7 48.3 - - + +
1032A ASP* 2.7 40.8 + - - +
1033A ILE* 3.8 12.9 - - + +
1054A GLN* 1.3 71.7 - - - +
1056A LYS* 1.3 69.8 + - - +
1058A TYR* 3.1 56.6 + - + +
1060A GLU 4.5 0.2 + - - -
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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