Contacts of the helix formed by residues 1016 - 1020 (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 ASN1016 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663D VAL* 3.5 3.4 - - - +
667D HIS* 2.6 29.9 + - - +
689D ALA* 3.1 25.1 + - - +
692D ASP* 3.5 13.4 + - + +
693D ALA* 3.1 22.4 - - - +
696D THR* 4.7 4.9 - - + -
1014F GLY 3.6 0.4 + - - -
1015F PRO* 1.3 87.7 + - - +
1017F LEU* 1.3 62.6 + - - +
1018F ASN* 3.1 12.0 - - - +
1019F LEU* 3.0 15.6 + - - +
1057F ASN* 2.8 14.3 + - - -
1160F CA2 3.3 30.8 - - + -
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Residues in contact with LEU1017 (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* 3.8 12.1 - - + +
1014F GLY 3.6 31.7 + - - +
1015F PRO 3.1 4.6 + - - +
1016F ASN* 1.3 72.2 - - - +
1018F ASN* 1.3 55.9 + - - +
1019F LEU 3.0 5.6 - - - -
1020F LEU* 2.9 36.5 + - + +
1028F TYR* 6.0 0.2 - - + -
1033F LEU* 3.7 20.0 - - + +
1055F GLN* 4.3 4.9 - - + -
1079F ASN* 3.7 36.6 - - - +
1081F ALA* 4.1 4.0 - - + -
1107F ILE* 4.2 15.9 - - + -
1138F TYR* 4.7 1.3 - - - +
1160F CA2 3.8 30.5 - - + +
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Residues in contact with ASN1018 (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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667D HIS* 3.3 33.2 + - - +
1016F ASN* 3.2 16.5 - - - -
1017F LEU* 1.3 78.1 - - - +
1019F LEU* 1.3 79.1 + - - +
1020F LEU 3.3 2.7 + - - +
1022F GLN* 4.3 4.2 - - - +
1033F LEU* 4.2 16.7 + - + +
1055F GLN* 3.5 27.8 + - + +
1057F ASN* 3.7 4.0 - - - +
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Residues in contact with LEU1019 (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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667D HIS* 3.7 25.4 - - + +
670D ARG* 3.9 26.2 - - - +
671D LEU* 6.5 0.7 - - + -
696D THR* 3.7 29.4 - - + +
1016F ASN 3.0 8.6 + - - +
1017F LEU 3.0 1.2 - - - -
1018F ASN* 1.3 97.5 - - - +
1020F LEU* 1.3 67.4 + - - +
1021F GLY 3.3 0.2 + - - -
1022F GLN* 3.1 40.7 + - + +
1023F ARG* 6.1 0.4 - - + -
1160F CA2 3.3 17.2 - - + -
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Residues in contact with LEU1020 (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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1017F LEU* 2.9 21.7 + - + +
1018F ASN 3.3 2.4 - - - +
1019F LEU* 1.3 80.3 - - - +
1021F GLY* 1.3 61.3 + - - +
1022F GLN* 3.4 5.4 + - - +
1028F TYR* 4.0 17.3 - - + +
1029F GLY 5.6 0.2 - - - +
1031F ASP 3.5 12.6 - - - +
1032F THR* 3.4 21.6 - - - +
1033F LEU* 3.9 17.9 + - + +
1036F VAL* 3.8 29.2 - - + -
1107F ILE* 3.8 29.8 - - + -
1135F VAL* 4.6 2.9 - - + -
1138F TYR* 5.7 0.2 - - - +
1160F CA2 3.8 28.9 - - + -
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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