Contacts of the helix formed by residues 1065 - 1078 (chain F) in PDB entry 6BAA
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 ALA1065 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064F TYR* 1.3 80.5 - - - +
1066F MET* 1.3 57.7 + - - +
1068F PHE* 5.0 0.7 - - - -
1069F THR* 2.8 38.2 + - - +
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Residues in contact with MET1066 (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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1064F TYR 3.3 5.3 - - - +
1065F ALA* 1.3 78.1 - - - +
1067F VAL* 1.3 61.2 + - + +
1069F THR* 3.7 3.4 - - - -
1070F LEU* 2.9 25.2 + - - +
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Residues in contact with VAL1067 (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 TRP* 5.1 12.1 - - + +
1036F LYS 5.9 0.9 - - - +
1037F TRP* 5.1 19.1 - - + +
1064F TYR* 4.5 2.0 + - - +
1066F MET* 1.3 79.7 - - + +
1068F PHE* 1.3 58.1 + - - +
1070F LEU* 3.3 11.0 + - + +
1071F LEU* 2.8 27.4 + - - +
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Residues in contact with PHE1068 (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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560F VAL* 5.9 8.7 - - + -
563F VAL* 6.3 3.1 - - + -
1064F TYR 3.3 21.2 + - - +
1065F ALA* 4.3 1.3 - - - +
1066F MET 3.3 0.4 - - - -
1067F VAL* 1.3 76.3 - - - +
1069F THR* 1.3 59.0 + - - +
1071F LEU* 3.1 8.6 + - - +
1072F CYS* 2.9 27.9 + - - +
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Residues in contact with THR1069 (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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1065F ALA* 2.8 24.6 + - - -
1066F MET* 3.7 3.8 - - - -
1068F PHE* 1.3 74.5 - - - +
1070F LEU* 1.3 57.3 + - - +
1072F CYS* 3.4 6.7 + - - +
1073F SER* 2.9 30.1 + - - -
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Residues in contact with LEU1070 (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 TRP* 5.8 7.0 - - + -
1066F MET 2.9 14.6 + - - +
1067F VAL* 3.3 14.8 - - + +
1069F THR* 1.3 76.8 - - - +
1071F LEU* 1.3 56.3 + - - +
1073F SER* 3.4 7.0 + - - -
1074F LEU* 2.8 28.9 + - - +
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Residues in contact with LEU1071 (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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556F LEU* 5.4 4.3 - - - +
1030F ILE* 5.7 9.5 - - + +
1033F TRP* 5.9 7.6 - - + -
1034F LEU* 6.1 3.6 - - + +
1067F VAL 2.8 16.8 + - - +
1068F PHE* 3.1 11.6 + - - +
1070F LEU* 1.3 70.2 - - - +
1072F CYS* 1.3 61.1 + - - +
1074F LEU* 3.2 8.3 + - - +
1075F GLY* 2.9 25.3 + - - -
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Residues in contact with CYS1072 (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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556F LEU* 5.3 10.1 - - + -
1068F PHE 2.9 15.6 + - - +
1069F THR* 3.8 7.4 - - - +
1071F LEU* 1.3 75.1 - - - +
1073F SER* 1.3 62.9 + - - +
1075F GLY* 3.1 2.1 + - - -
1076F ILE* 3.1 24.1 + - - +
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Residues in contact with SER1073 (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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1069F THR 2.9 18.1 + - - -
1070F LEU* 3.6 7.4 - - - -
1072F CYS* 1.3 77.3 - - - +
1074F LEU* 1.3 62.6 + - - +
1076F ILE* 3.8 12.4 + - - +
1077F VAL* 4.0 8.7 + - - +
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Residues in contact with LEU1074 (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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1026F VAL* 4.8 13.2 - - + +
1029F ALA* 5.6 4.3 - - + -
1030F ILE* 4.9 20.6 - - + +
1070F LEU 2.8 17.9 + - - +
1071F LEU* 3.5 9.0 - - - +
1073F SER* 1.3 78.8 - - - +
1075F GLY* 1.3 57.1 + - - +
1077F VAL* 3.1 27.5 + - - +
1078F LEU* 4.1 2.3 + - - +
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Residues in contact with GLY1075 (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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552F ILE* 3.3 34.3 - - - +
556F LEU* 5.5 5.8 - - - -
1030F ILE* 5.9 4.0 - - - -
1071F LEU 2.9 14.6 + - - -
1072F CYS* 3.1 4.4 + - - -
1074F LEU* 1.3 74.4 - - - +
1076F ILE* 1.3 64.9 + - - +
1077F VAL 3.2 0.2 - - - -
1078F LEU* 4.0 8.6 + - - +
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Residues in contact with ILE1076 (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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1072F CYS 3.1 14.5 + - - +
1073F SER* 4.0 8.3 - - - +
1074F LEU 3.2 0.4 - - - -
1075F GLY* 1.3 78.4 - - - +
1077F VAL* 1.3 63.0 + - - +
1078F LEU 3.2 10.6 + - - +
1079F CYS* 5.0 1.6 - - - +
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Residues in contact with VAL1077 (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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1023F LYS* 5.6 1.0 - - - +
1026F VAL* 4.7 11.9 - - + -
1073F SER 4.0 5.5 + - - +
1074F LEU* 3.1 18.5 + - - +
1076F ILE* 1.3 78.3 - - - +
1078F LEU* 1.3 62.4 + - - +
1079F CYS* 3.3 12.1 + - - +
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Residues in contact with LEU1078 (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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545F PHE* 4.5 7.5 - - - -
548F THR 6.4 0.2 - - - -
549F ALA* 4.9 8.4 - - + +
552F ILE* 4.3 26.7 - - + -
1023F LYS* 4.6 24.0 - - + +
1026F VAL* 5.2 4.8 - - + +
1027F LEU* 6.2 0.4 - - + +
1074F LEU 4.1 2.9 + - - +
1075F GLY 4.0 8.3 + - - +
1076F ILE 3.2 12.8 + - - +
1077F VAL* 1.3 75.9 - - - +
1079F CYS* 1.3 58.4 + - - +
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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