Contacts of the helix formed by residues 158 - 163 (chain O) in PDB entry 5XS0
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 PHE 158 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N ASN* 3.6 15.1 + - - +
81N TYR* 3.6 27.3 - + - +
43O LEU* 3.2 27.1 - - + +
79O PHE* 4.3 4.9 - + + -
113O VAL* 3.8 28.7 - - + -
115O LEU* 3.5 39.9 - - + -
119O SER* 3.9 9.0 - - - -
120O TYR 4.6 1.3 - - - -
121O HIS* 3.3 38.6 - + + -
154O ALA 4.5 0.2 - - - -
155O LEU* 3.3 24.2 + - + +
156O ARG 3.1 2.2 + - - -
157O SER* 1.3 78.6 - - - +
159O GLY* 1.3 56.6 + - - +
162O LEU* 3.8 20.6 - - + -
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Residues in contact with GLY 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ASN* 4.4 4.5 - - - -
76N ASN* 3.7 11.0 - - - +
43O LEU* 3.9 10.5 - - - +
155O LEU 4.5 0.4 + - - -
156O ARG 3.4 6.2 + - - +
157O SER 3.5 1.0 - - - -
158O PHE* 1.3 81.1 - - - +
160O ASN* 1.3 67.0 + - - -
161O ALA 3.3 2.7 - - - -
162O LEU* 3.3 10.2 + - - +
163O GLY 3.5 0.5 + - - -
164O ASN* 3.1 22.1 + - - +
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Residues in contact with ASN 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N HIS* 5.9 0.3 - - - -
73N ASN* 3.4 33.4 + - - +
43O LEU 3.0 4.2 + - - -
44O ARG* 3.3 28.2 + - - +
45O GLN 3.5 15.5 - - - +
46O ARG* 4.4 9.6 + - - +
47O LEU* 3.1 12.8 - - - +
159O GLY* 1.3 73.1 - - - -
161O ALA* 1.3 58.3 + - - +
163O GLY 2.9 17.3 + - - -
164O ASN* 3.7 1.3 - - - -
165O CYS* 3.5 41.2 + - + +
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Residues in contact with ALA 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N LYS* 4.5 14.4 - - + -
42O ALA 3.5 25.1 - - - +
43O LEU* 2.9 22.4 + - + +
45O GLN 3.2 11.5 + - - +
47O LEU* 3.5 19.4 - - - +
74O LEU* 3.5 20.4 - - - +
78O MET* 4.6 8.7 - - + -
159O GLY 3.3 0.6 - - - -
160O ASN* 1.3 75.0 - - - +
162O LEU* 1.3 58.3 + - - +
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Residues in contact with LEU 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O LEU* 4.1 11.8 - - + +
66O ILE* 4.8 4.5 - - - +
71O VAL* 4.3 18.1 - - + +
74O LEU* 3.8 18.8 - - + +
75O ALA* 3.7 33.9 - - + +
78O MET* 4.7 4.3 - - + -
79O PHE* 3.5 35.4 - - + -
152O LYS 4.8 1.2 - - - +
155O LEU* 3.4 42.0 - - + +
156O ARG* 4.1 2.6 + - - +
158O PHE* 3.8 18.2 - - + -
159O GLY 3.3 7.1 + - - +
160O ASN 3.1 0.8 - - - -
161O ALA* 1.3 78.2 - - - +
163O GLY* 1.3 57.8 + - - +
164O ASN 3.8 0.4 - - - -
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Residues in contact with GLY 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O LEU* 4.7 0.7 - - - -
66O ILE* 3.8 23.5 - - - +
156O ARG* 3.6 16.8 - - - +
160O ASN 2.9 7.3 + - - -
161O ALA 3.4 1.0 - - - -
162O LEU* 1.3 79.4 - - - +
164O ASN* 1.3 66.3 + - - +
165O CYS 3.3 2.5 - - - -
166O ILE* 3.1 25.9 - - - +
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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