Contacts of the helix formed by residues 1024 - 1031 (chain B) in PDB entry 1XTB
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 ASN1024 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1022B GLU 3.2 8.2 + - - +
1023B LEU* 1.3 74.6 - - - +
1025B LEU* 1.3 68.2 + - - +
1026B ARG* 3.3 13.8 + - - +
1027B HIS* 2.9 41.5 + - + +
1028B LEU* 2.9 26.7 + - - +
1468B GLU 5.3 3.2 + - - -
1470B ASN* 3.3 20.9 - - - +
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Residues in contact with LEU1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023B LEU 4.2 0.4 - - - -
1024B ASN* 1.3 70.4 - - - +
1026B ARG* 1.3 64.6 + - - +
1028B LEU* 3.0 7.4 + - + +
1029B PHE* 2.9 30.4 + - + -
1035B ARG* 4.3 6.7 - - - +
1055B SER 4.5 0.7 - - - +
1056B LYS* 3.6 25.4 - - - +
1057B ASN 3.2 34.3 - - - +
1058B LEU* 3.6 10.1 - - + +
1436B MET* 3.6 31.4 - - + +
1470B ASN* 2.8 27.1 + - - +
1471B ARG 3.8 27.1 - - - +
1472B PRO* 4.0 2.5 - - + -
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Residues in contact with ARG1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024B ASN* 3.3 11.0 + - - +
1025B LEU* 1.3 77.9 - - - +
1027B HIS* 1.3 58.3 + - - +
1029B PHE* 3.9 1.1 - - - +
1030B ASP* 3.0 50.9 + - - +
1436B MET* 3.8 26.5 + - + +
1437B LYS* 3.2 55.8 + - + +
1438B GLY 4.0 3.2 + - - -
1440B SER* 4.6 5.9 - - - +
1443B GLU* 2.9 41.9 + - - -
1470B ASN* 5.8 0.2 - - - +
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Residues in contact with HIS1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022B GLU 5.7 3.4 - - - -
1024B ASN* 2.9 29.8 + - + +
1026B ARG* 1.3 75.2 - - - +
1028B LEU* 1.3 71.8 + - + +
1030B ASP* 3.3 6.3 + - - +
1031B THR* 2.9 57.5 + - + +
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Residues in contact with LEU1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023B LEU* 4.3 21.3 - - + -
1024B ASN 2.9 27.1 + - - +
1025B LEU* 3.4 14.6 - - + +
1027B HIS* 1.3 85.7 - - + +
1029B PHE* 1.3 61.2 + - - +
1031B THR* 3.5 5.7 + - - +
1032B ASP* 3.1 28.8 + - - +
1035B ARG* 3.8 40.0 - - - +
1057B ASN 4.7 0.9 - - - +
1058B LEU* 5.1 0.2 - - - -
1059B VAL 3.9 9.6 - - - +
1060B THR* 4.4 16.8 - - + -
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Residues in contact with PHE1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ASP* 3.9 25.4 - - + -
539A SER* 3.4 28.2 + - - -
540A SER* 3.6 22.7 - - - -
1025B LEU* 2.9 31.3 + - + +
1026B ARG 4.0 3.1 - - - +
1028B LEU* 1.3 73.9 - - - +
1030B ASP* 1.3 68.8 + - - +
1031B THR 3.3 0.7 + - - -
1032B ASP 3.4 16.9 + - - +
1033B LYS* 4.4 2.1 + - - -
1035B ARG* 3.3 33.9 - - + +
1055B SER* 3.5 30.3 - - - -
1056B LYS* 4.0 14.8 - - + -
1436B MET* 4.0 18.8 - - + -
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Residues in contact with ASP1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B ARG* 3.0 42.3 + - - +
1027B HIS* 3.3 8.2 + - - +
1029B PHE* 1.3 78.7 - - - +
1031B THR* 1.3 63.9 + - + +
1032B ASP 3.5 0.6 + - - -
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Residues in contact with THR1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027B HIS* 2.9 48.6 + - + +
1028B LEU* 3.5 9.2 + - - +
1030B ASP* 1.3 82.4 - - + +
1032B ASP* 1.3 58.3 + - - +
1033B LYS 4.2 0.7 - - - -
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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