Contacts of the helix formed by residues 52 - 56 (chain B) in PDB entry 1XJB
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 ALA 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B SER* 1.3 92.0 + - - +
53B HIS* 1.3 67.6 + - - +
54B VAL 3.1 2.0 - - - +
55B TYR* 3.2 25.8 + - + +
56B ASN 4.0 1.2 + - - -
58B GLU* 3.8 11.4 - - - +
81B TYR* 4.3 1.0 + - - -
83B SER* 4.1 1.6 - - - -
84B LYS* 3.7 15.5 - - + +
117B HIS* 3.5 35.9 - - + +
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 1.3 73.2 - - - +
54B VAL* 1.3 60.0 + - - +
56B ASN* 3.0 22.5 + - - +
58B GLU* 3.4 15.4 + - - +
83B SER* 4.0 0.8 + - - -
84B LYS 3.6 18.1 + - - +
85B LEU* 5.9 0.2 - - - -
86B TRP* 4.3 17.1 - - + +
88B ASN* 5.2 7.4 + - - -
98B ALA* 5.6 4.9 - - + +
101B ARG* 3.3 44.0 + - + -
102B SER* 3.9 17.9 - - - +
105B ASN* 5.0 8.5 - - - -
114B TYR* 6.0 0.4 - - - +
126B GLU* 5.1 5.8 + - - -
128B VAL* 4.6 16.5 - - + +
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Residues in contact with VAL 54 (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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24B TYR* 5.5 2.3 - - - -
52B ALA* 3.1 1.4 - - + +
53B HIS* 1.3 84.8 - - - +
55B TYR* 1.4 70.2 + - + +
56B ASN* 3.1 5.4 + - - +
86B TRP* 4.0 37.6 - - + +
117B HIS* 3.3 34.5 + - + +
128B VAL* 4.0 29.7 - - + +
129B ILE* 6.1 1.3 - - + -
6002B ACT 4.9 4.7 - - + -
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Residues in contact with TYR 55 (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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23B THR* 3.9 7.9 - - - -
24B TYR* 3.6 36.7 - + + -
31B LYS* 3.2 15.8 - - - -
51B SER* 3.5 27.8 - - - -
52B ALA* 3.2 21.1 + - + +
53B HIS 3.2 1.6 + - - -
54B VAL* 1.4 82.2 - - + +
56B ASN* 1.3 71.0 + - - +
57B ASN* 3.1 18.5 + - - +
84B LYS* 3.1 21.4 + - - -
117B HIS* 3.8 9.1 + + - -
5001B NAP 3.1 31.1 - - - -
6002B ACT 2.6 37.8 + - - -
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Residues in contact with ASN 56 (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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31B LYS* 3.3 27.6 - - - +
52B ALA 4.0 0.4 + - - -
53B HIS 3.0 15.8 + - - +
54B VAL 3.1 5.3 - - - +
55B TYR* 1.3 79.5 - - - +
57B ASN* 1.3 56.8 + - - +
58B GLU 3.8 1.8 - - - +
60B GLN* 3.9 3.5 + - - -
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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