Contacts of the helix formed by residues 1109 - 1116 (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 PRO1109 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107F LEU 3.7 2.3 - - - +
1108F ALA* 1.3 79.1 - - - +
1110F MET* 1.3 65.6 + - - +
1111F ARG* 3.2 14.5 + - + +
1112F PHE* 3.6 12.9 + - + +
1113F PHE* 3.8 8.1 + - - +
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Residues in contact with MET1110 (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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506F MET 6.1 0.2 - - - -
507F LYS* 5.1 14.4 - - + -
510F LYS* 4.8 19.2 - - + +
1109F PRO* 1.3 72.4 - - - +
1111F ARG* 1.3 58.6 + - - +
1113F PHE* 3.1 11.3 + - + +
1114F GLU* 2.9 28.6 + - - +
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Residues in contact with ARG1111 (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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1109F PRO* 3.2 7.9 - - + +
1110F MET* 1.3 79.2 - - - +
1112F PHE* 1.3 57.0 + - - +
1114F GLU* 3.7 7.7 - - - +
1115F THR* 2.9 30.5 + - - -
1354F TYR* 5.9 8.7 - - + -
1395F MET 6.0 2.0 - - - +
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Residues in contact with PHE1112 (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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1108F ALA* 4.6 7.2 - - + -
1109F PRO* 3.6 12.6 + - + +
1110F MET 3.3 1.0 - - - -
1111F ARG* 1.3 77.2 - - - +
1113F PHE* 1.3 62.4 + - - +
1115F THR* 4.5 3.5 - - - +
1116F THR* 3.2 26.7 + - - -
1121F ILE* 5.6 0.3 - - - +
1319F LEU* 3.8 36.9 - - + +
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Residues in contact with PHE1113 (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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503F LEU 5.9 0.2 - - - +
506F MET* 5.7 9.4 - - + -
1109F PRO 3.8 5.6 + - - +
1110F MET* 3.1 15.5 + - - +
1112F PHE* 1.3 80.4 - - - +
1114F GLU* 1.3 58.0 + - - +
1116F THR* 2.9 21.5 - - - +
1118F LEU* 4.6 21.3 - - + +
1121F ILE* 5.2 10.1 - - + -
1319F LEU* 5.2 1.5 - - - +
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Residues in contact with GLU1114 (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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1110F MET 2.9 16.5 + - - +
1111F ARG* 3.2 9.6 + - - +
1113F PHE* 1.3 78.5 - - - +
1115F THR* 1.3 63.7 + - - +
1116F THR 3.8 2.6 - - - +
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Residues in contact with THR1115 (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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1111F ARG 2.9 16.8 + - - -
1112F PHE* 4.5 4.3 - - - -
1114F GLU* 1.3 79.5 - - - +
1116F THR* 1.3 59.6 + - - +
1117F PRO* 4.0 4.0 - - - +
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Residues in contact with THR1116 (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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1112F PHE 3.2 18.4 + - - -
1113F PHE 2.9 19.4 - - - +
1114F GLU 3.8 3.3 - - - +
1115F THR* 1.3 80.4 - - - +
1117F PRO* 1.3 76.2 - - - +
1118F LEU* 3.8 0.7 + - - +
1120F SER* 5.6 2.2 - - - -
1121F ILE* 5.0 9.9 - - - -
1319F LEU* 5.7 8.3 - - - -
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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