Contacts of the helix formed by residues 1001 - 1009 (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 CYS1001 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000F ALA* 1.3 68.8 - - - +
1002F THR* 1.3 60.1 + - - +
1003F LYS 3.1 6.3 - - - -
1004F TYR* 3.1 24.8 + - - +
1005F LEU* 3.8 2.1 + - - +
1309F LEU* 3.9 29.2 - - + -
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Residues in contact with THR1002 (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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1000F ALA* 3.1 7.2 - - - +
1001F CYS* 1.3 75.1 - - - +
1003F LYS* 1.3 59.5 + - - +
1004F TYR 3.2 0.4 - - - -
1005F LEU* 3.1 13.9 + - - +
1006F SER* 2.9 26.9 + - - -
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Residues in contact with LYS1003 (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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1000F ALA* 3.5 16.5 + - + +
1001F CYS 3.1 0.8 - - - -
1002F THR* 1.3 75.8 - - - +
1004F TYR* 1.3 59.0 + - - +
1006F SER* 3.4 7.5 + - - +
1007F SER* 2.9 29.3 + - - -
1312F VAL* 5.6 5.4 - - + -
1316F HIS* 3.8 33.9 - - + +
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Residues in contact with TYR1004 (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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1001F CYS* 3.1 14.3 + - - +
1003F LYS* 1.3 78.8 - - - +
1005F LEU* 1.3 56.1 + - - +
1007F SER* 3.3 8.1 + - - -
1008F ALA* 2.9 27.4 + - - +
1093F VAL* 5.2 4.3 - - + +
1140F LEU* 6.5 0.4 - - + -
1309F LEU* 5.4 9.9 - - + -
1312F VAL* 4.6 22.5 - - + +
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Residues in contact with LEU1005 (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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1001F CYS 3.8 1.7 + - - +
1002F THR* 3.1 21.2 + - - +
1004F TYR* 1.3 76.5 - - - +
1006F SER* 1.3 59.8 + - - +
1008F ALA* 2.9 22.5 + - - +
1009F GLY* 3.0 17.2 + - - +
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Residues in contact with SER1006 (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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1002F THR 2.9 14.9 + - - -
1003F LYS* 3.7 9.0 - - - -
1004F TYR 3.3 0.2 - - - -
1005F LEU* 1.3 76.1 - - - +
1007F SER* 1.3 60.1 + - - +
1008F ALA 3.4 0.3 + - - -
1009F GLY* 3.8 7.9 + - - +
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Residues in contact with SER1007 (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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1003F LYS 2.9 16.8 + - - -
1004F TYR* 3.6 8.3 - - - -
1005F LEU 3.2 0.2 - - - -
1006F SER* 1.3 77.0 - - - +
1008F ALA* 1.3 59.9 + - - +
1092F LYS* 4.8 2.4 - - - +
1093F VAL* 4.2 27.9 + - - -
1096F ARG* 4.5 14.9 - - - +
1097F LEU* 5.6 7.4 - - - -
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Residues in contact with ALA1008 (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 TYR 2.9 12.5 + - - +
1005F LEU* 2.9 14.2 + - - +
1007F SER* 1.3 80.8 - - - +
1009F GLY* 1.3 65.9 + - - +
1012F LEU* 4.7 11.5 - - + +
1013F LEU* 5.9 3.6 - - + +
1089F THR* 5.4 16.3 - - - +
1092F LYS* 5.0 9.3 - - - +
1093F VAL* 5.1 9.2 - - + +
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Residues in contact with GLY1009 (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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1005F LEU 3.0 12.0 + - - +
1006F SER 3.8 6.6 + - - -
1007F SER 3.5 1.8 - - - -
1008F ALA* 1.3 85.2 - - - +
1010F ILE* 1.3 64.7 + - - -
1011F LEU* 3.3 2.9 + - - -
1012F LEU 4.0 1.9 + - - -
1013F LEU* 3.6 17.7 + - - +
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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