Contacts of the strand formed by residues 2152 - 2156 (chain B) in PDB entry 3O2X
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 ASN2152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2116B MET* 2.8 9.1 + - - +
2117B ASN* 3.1 31.6 + - - +
2118B LEU* 2.9 27.8 + - - +
2146B SER* 4.9 2.1 - - - -
2150B PRO 3.6 14.1 + - - +
2151B LEU* 1.3 78.8 - - - +
2153B PHE* 1.3 68.4 + - - +
2154B THR* 5.6 1.1 - - - +
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Residues in contact with PHE2153 (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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2118B LEU* 3.4 32.1 - - + -
2119B THR 5.3 0.4 - - - -
2120B TYR* 4.1 19.2 - + + -
2142B PHE* 3.5 62.4 - + + -
2145B TRP* 4.6 1.3 - - + -
2146B SER* 4.1 16.8 - - - -
2151B LEU* 4.0 22.9 - - + -
2152B ASN* 1.3 77.6 - - - +
2154B THR* 1.3 65.1 + - - +
2163B ILE* 4.2 5.2 - - + -
2228B LEU* 3.8 30.3 - - + -
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Residues in contact with THR2154 (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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2118B LEU 3.1 10.5 + - - -
2119B THR* 3.2 12.9 - - + -
2120B TYR* 3.0 27.2 + - - -
2152B ASN* 5.6 0.7 - - - +
2153B PHE* 1.3 76.2 + - - +
2155B ARG* 1.3 72.7 + - - +
2156B LEU* 4.8 10.1 - - + -
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Residues in contact with ARG2155 (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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4B SO4 2.7 45.1 + - - +
2120B TYR* 3.3 41.1 - - + +
2122B ILE* 3.7 19.1 - - + +
2125B TYR* 3.7 18.8 + - - -
2135B GLU* 3.7 21.7 + - - +
2154B THR* 1.3 81.9 - - - +
2156B LEU* 1.3 74.8 + - - +
2157B HIS* 3.4 48.6 + - - +
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Residues in contact with LEU2156 (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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1247A THR* 3.5 42.0 - - + +
1248A GLY* 5.0 4.5 - - - +
1249A LYS 5.9 2.2 - - - +
2119B THR* 3.6 38.6 - - + +
2120B TYR 2.7 12.5 + - - +
2121B ARG* 3.5 23.2 - - + +
2122B ILE 4.3 1.7 + - - +
2154B THR* 4.8 7.0 - - + -
2155B ARG* 1.3 86.5 + - - +
2157B HIS* 1.3 64.5 + - - +
2158B ASP 4.1 12.6 - - - +
2160B ILE 3.7 13.5 - - - +
2161B ALA* 3.8 7.6 - - + -
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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