Contacts of the helix formed by residues 1034 - 1039 (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 GLU1034 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032B ASP* 2.8 13.0 + - - +
1033B LYS* 1.3 102.7 + - - +
1035B ARG* 1.3 64.9 + - - +
1036B PHE 3.4 2.2 - - - -
1037B ASN* 3.0 35.7 + - - +
1038B HIS* 2.9 48.5 + - + +
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Residues in contact with ARG1035 (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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539A SER* 3.8 8.3 + - - +
1025B LEU* 4.3 1.0 - - - +
1028B LEU* 3.8 26.1 + - - +
1029B PHE* 3.3 43.6 - - + +
1032B ASP* 3.0 30.0 + - + +
1033B LYS 3.4 1.2 - - - -
1034B GLU* 1.3 76.9 - - - +
1036B PHE* 1.3 62.9 + - - +
1038B HIS 3.1 0.9 + - - -
1039B PHE* 2.9 52.8 + - + +
1055B SER* 2.7 22.0 + - - -
1057B ASN 2.7 29.5 + - - -
1059B VAL* 3.0 30.1 + - - +
1060B THR* 5.0 1.6 - - - +
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Residues in contact with PHE1036 (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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539A SER* 3.2 37.8 + - - +
540A SER* 3.8 9.4 - - - +
543A GLY* 3.8 32.1 - - - -
544A LEU 4.5 0.4 - - - -
1034B GLU 3.4 0.4 - - - -
1035B ARG* 1.3 77.8 - - - +
1037B ASN* 1.3 71.3 + - - +
1039B PHE 3.6 0.2 - - - -
1040B SER* 2.5 56.1 + - - -
1051B LEU* 4.2 16.4 - - + -
1053B ASP* 3.5 39.9 - - + -
1055B SER* 4.0 8.5 - - - -
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Residues in contact with ASN1037 (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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1033B LYS 4.8 3.8 + - - -
1034B GLU* 3.0 38.6 + - - +
1036B PHE* 1.3 94.1 - - - +
1038B HIS* 1.3 66.1 + - + +
1039B PHE 3.6 0.3 + - - -
1040B SER* 4.0 13.8 + - - +
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Residues in contact with HIS1038 (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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1032B ASP* 4.4 8.9 + - - -
1034B GLU* 2.9 48.9 + - + +
1035B ARG 3.8 3.1 - - - +
1037B ASN* 1.3 80.8 - - + +
1039B PHE* 1.3 83.3 + - + +
1040B SER 3.8 0.9 - - - -
1054B TYR* 3.9 6.9 + - - -
1061B GLU* 3.4 32.7 + - + +
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Residues in contact with PHE1039 (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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1032B ASP* 4.7 5.8 - - - -
1035B ARG* 2.9 57.9 + - + +
1036B PHE 3.3 1.8 + - - -
1038B HIS* 1.3 91.3 - - + +
1040B SER* 1.3 58.4 + - - +
1053B ASP* 3.7 0.2 - - - +
1054B TYR* 3.0 56.3 + + + -
1055B SER* 3.0 22.3 + - - -
1059B VAL* 4.3 8.7 - - + -
1060B THR* 3.9 9.9 - - - -
1061B GLU* 3.7 42.0 - - + -
1064B MET* 3.6 25.1 - - + -
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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