Contacts of the strand formed by residues 1033 - 1040 (chain A) in PDB entry 2BOA
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 ALA1033 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025A ILE* 4.1 7.4 - - + +
1026A ALA* 3.6 25.0 - - - +
1029A PHE 3.1 17.4 + - - +
1030A PRO* 3.8 9.5 + - - +
1032A LEU* 1.3 79.5 - - - +
1034A ARG* 1.3 63.3 + - - +
1050A LEU* 4.0 8.1 - - + -
1051A LYS 3.3 4.3 - - - -
1052A PHE* 3.7 25.8 - - + -
1087A VAL* 4.1 5.4 - - + -
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Residues in contact with ARG1034 (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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1026A ALA* 3.8 7.6 - - + -
1030A PRO 5.7 0.9 - - - +
1033A ALA* 1.3 76.0 - - - +
1035A ARG* 1.3 63.2 + - - +
1036A VAL* 3.6 36.6 + - + +
1050A LEU* 3.5 6.1 - - - -
1051A LYS* 2.9 57.4 + - + +
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Residues in contact with ARG1035 (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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1019A TYR* 2.5 40.1 + - - +
1020A HIS* 4.4 1.0 - - - +
1022A MET* 3.7 23.6 - - + +
1023A ASP* 2.5 54.8 + - - +
1026A ALA* 4.1 5.5 - - + +
1034A ARG* 1.3 74.1 + - - +
1036A VAL* 1.3 63.6 + - - +
1037A LYS 4.0 0.9 + - - -
1048A TYR* 4.2 35.5 + - + -
1049A VAL 3.3 13.2 - - - +
1050A LEU* 3.9 5.6 - - + +
1016B GLU* 3.6 21.2 + - - -
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Residues in contact with VAL1036 (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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1034A ARG* 3.6 52.7 - - + +
1035A ARG* 1.3 76.1 - - - +
1037A LYS* 1.3 70.8 + - - +
1038A ILE* 3.7 10.6 + - + -
1048A TYR* 3.7 3.4 - - - -
1049A VAL* 2.9 41.7 + - + +
1051A LYS* 4.0 15.9 - - + -
1106A PHE* 5.4 0.9 - - + -
1182A PHE* 4.5 14.8 - - + -
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Residues in contact with LYS1037 (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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1035A ARG 4.0 2.0 + - - -
1036A VAL* 1.3 79.3 - - - +
1038A ILE* 1.3 61.0 + - - +
1039A GLY* 3.7 21.3 - - - +
1040A HIS* 3.8 28.6 + - + +
1046A PRO* 3.9 20.2 - - + -
1047A MET 3.4 8.3 - - - +
1048A TYR* 3.8 17.2 - - + -
97B GLU* 5.4 5.5 + - - -
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Residues in contact with ILE1038 (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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1036A VAL* 4.1 6.1 - - + +
1037A LYS* 1.3 75.5 - - - +
1039A GLY* 1.3 59.5 + - - +
1047A MET* 2.9 30.3 + - + +
1049A VAL* 4.1 28.9 - - + -
1063A TRP* 3.9 15.0 - - + -
1108A LEU* 4.5 5.2 - - + -
1178A SER* 4.0 25.5 + - - +
1179A VAL* 3.9 28.9 - - + -
1181A ASP* 6.1 0.2 - - - +
1182A PHE* 3.6 37.7 - - + +
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Residues in contact with GLY1039 (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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1037A LYS* 3.6 10.0 - - - +
1038A ILE* 1.3 84.0 - - - +
1040A HIS* 1.3 74.1 + - - -
1046A PRO* 3.7 1.4 - - - +
1047A MET* 3.0 23.2 + - - -
1178A SER* 3.4 13.7 - - - -
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Residues in contact with HIS1040 (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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1037A LYS* 3.8 33.0 + - + -
1039A GLY* 1.3 77.2 + - - -
1041A SER* 1.3 70.9 + - - +
1044A ASN* 3.5 23.8 - - - +
1045A ARG 3.3 20.9 - - - -
1046A PRO* 3.8 4.0 - - + +
1047A MET* 3.7 7.0 - - - +
1174A VAL* 3.2 24.3 - - - +
1178A SER* 3.8 3.4 + - - -
1121B THR* 4.0 25.9 - - + +
1122B GLN* 5.8 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