Contacts of the helix formed by residues 1032 - 1046 (chain F) in PDB entry 2BT4
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 THR1032 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020F LEU* 3.4 19.3 - - - +
1021F GLY* 4.8 3.6 - - - -
1022F GLN* 5.9 3.4 - - + -
1030F SER 4.4 6.1 - - - +
1031F ASP* 1.3 78.0 - - - +
1033F LEU* 1.3 64.9 + - - +
1034F ALA* 3.5 9.8 + - - +
1035F ASP* 2.9 28.6 + - - +
1036F VAL* 3.0 22.5 + - - +
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Residues in contact with LEU1033 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013F ASN* 4.1 13.5 - - + +
1017F LEU* 3.7 29.4 - - + +
1018F ASN* 4.2 12.5 + - + +
1020F LEU* 3.9 20.3 + - + +
1032F THR* 1.3 76.3 - - - +
1034F ALA* 1.3 56.2 + - - +
1036F VAL* 3.2 8.6 + - + +
1037F GLU* 2.9 26.3 + - - +
1053F PHE* 3.8 26.5 - - + -
1055F GLN* 3.6 37.0 - - + -
1138F TYR* 4.8 2.5 - - - +
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Residues in contact with ALA1034 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032F THR* 3.2 9.9 + - - +
1033F LEU* 1.3 72.9 - - - +
1035F ASP* 1.3 62.6 + - - +
1037F GLU* 3.3 14.9 + - - +
1038F ALA* 2.9 27.7 + - - +
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Residues in contact with ASP1035 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030F SER 4.5 1.0 - - - +
1031F ASP* 3.4 31.0 - - + +
1032F THR* 2.9 35.9 + - - +
1034F ALA* 1.3 80.2 - - - +
1036F VAL* 1.3 62.1 + - - +
1038F ALA* 3.2 7.9 + - - +
1039F LEU* 3.0 25.8 + - - +
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Residues in contact with VAL1036 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020F LEU* 3.8 14.8 - - + -
1031F ASP* 4.8 2.5 - - + -
1032F THR 3.0 18.7 + - - +
1033F LEU* 3.5 10.3 - - + +
1035F ASP* 1.3 74.9 - - - +
1037F GLU* 1.3 64.5 + - - +
1039F LEU* 3.1 9.5 + - + +
1040F CYS* 2.9 22.1 + - - -
1053F PHE* 4.0 9.0 - - + -
1135F VAL* 3.6 33.9 - - + +
1138F TYR* 3.7 46.2 - - + -
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Residues in contact with GLU1037 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033F LEU 2.9 12.9 + - - +
1034F ALA* 3.3 17.0 + - - +
1036F VAL* 1.3 73.8 - - - +
1038F ALA* 1.3 58.5 + - - +
1040F CYS* 3.1 3.3 + - - +
1041F VAL* 2.9 43.9 + - + +
1051F VAL* 5.4 0.4 - - + +
1053F PHE* 3.6 51.3 + - + +
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Residues in contact with ALA1038 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034F ALA 2.9 13.1 + - - +
1035F ASP* 3.5 11.9 - - - +
1036F VAL 3.2 0.4 - - - -
1037F GLU* 1.3 75.3 - - - +
1039F LEU* 1.3 57.2 + - - +
1041F VAL* 3.4 9.2 + - - +
1042F LYS* 3.0 30.0 + - - +
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Residues in contact with LEU1039 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031F ASP* 4.6 8.1 - - - +
1035F ASP 3.0 14.8 + - - +
1036F VAL* 3.1 12.8 + - + +
1038F ALA* 1.3 76.8 - - - +
1040F CYS* 1.3 59.0 + - - +
1042F LYS* 3.7 18.1 - - + +
1043F ALA* 3.0 29.6 + - - +
1135F VAL* 3.4 47.8 - - + +
1136F GLN* 4.6 1.6 - - - +
1138F TYR* 5.8 0.7 - - + -
1139F VAL* 4.3 22.6 - - + +
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Residues in contact with CYS1040 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011F ILE* 3.6 32.1 - - + -
1036F VAL 2.9 17.2 + - - +
1037F GLU 3.5 7.9 - - - +
1039F LEU* 1.3 76.5 - - - +
1041F VAL* 1.3 64.6 + - - +
1043F ALA* 4.0 1.6 - - - +
1044F ALA* 3.0 26.5 + - - +
1051F VAL* 3.6 7.2 - - + +
1053F PHE* 4.1 12.6 - - + -
1138F TYR* 3.8 37.5 - - - -
1139F VAL* 5.8 0.7 - - - -
1142F VAL* 4.4 10.8 - - - +
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Residues in contact with VAL1041 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037F GLU* 2.9 30.7 + - + +
1038F ALA* 3.6 10.8 - - - +
1040F CYS* 1.3 75.1 - - - +
1042F LYS* 1.3 64.3 + - - +
1044F ALA* 3.9 1.9 - - - +
1045F ALA* 3.0 27.3 + - + +
1049F GLY 5.0 0.3 - - - +
1050F THR* 5.9 0.4 - - - +
1051F VAL* 3.8 22.9 - - + +
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Residues in contact with LYS1042 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038F ALA 3.0 17.3 + - - +
1039F LEU* 3.7 18.7 - - + +
1041F VAL* 1.3 78.4 - - - +
1043F ALA* 1.3 65.7 + - + +
1045F ALA* 3.3 6.3 + - - +
1046F ALA* 3.0 23.9 + - + +
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Residues in contact with ALA1043 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039F LEU 3.0 18.4 + - - +
1040F CYS* 4.0 2.5 - - - +
1042F LYS* 1.3 79.9 - - - +
1044F ALA* 1.3 60.8 + - - +
1046F ALA* 3.3 8.1 + - - +
1047F HIS* 2.9 30.2 - - + -
1139F VAL* 4.0 30.1 - - + +
1142F VAL* 3.9 19.5 - - + -
1143F GLU* 5.5 1.1 - - + -
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Residues in contact with ALA1044 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004F LEU* 5.3 0.7 - - - -
1009F ILE* 4.4 6.1 - - + -
1040F CYS 3.0 18.1 + - - +
1041F VAL 3.9 2.9 - - - +
1043F ALA* 1.3 77.7 - - - +
1045F ALA* 1.3 58.7 + - - +
1047F HIS* 2.9 17.6 + - - +
1048F GLY 3.1 0.3 + - - -
1049F GLY* 2.8 39.7 + - - +
1050F THR* 3.9 3.8 - - - +
1051F VAL* 3.7 20.4 - - + +
1142F VAL* 3.7 13.6 - - + +
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Residues in contact with ALA1045 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041F VAL* 3.0 21.2 + - + +
1042F LYS* 3.5 7.0 - - - +
1044F ALA* 1.3 78.1 - - - +
1046F ALA* 1.3 61.0 + - - +
1047F HIS 3.1 1.0 + - - -
1048F GLY* 3.1 11.0 + - - +
1049F GLY 3.4 11.5 + - - +
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Residues in contact with ALA1046 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042F LYS* 3.0 14.5 + - + +
1043F ALA* 3.6 12.1 - - - +
1044F ALA 3.2 0.4 - - - -
1045F ALA* 1.3 77.7 - - - +
1047F HIS* 1.4 68.1 + - + +
1048F GLY 3.5 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