Contacts of the strand formed by residues 237 - 243 (chain A) in PDB entry 2B25
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 LEU 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.9 28.7 - - + -
203A PHE* 5.2 6.3 - - + -
204A TYR* 3.9 26.0 - - + -
207A LEU* 4.4 11.2 - - + -
213A CYS* 4.8 3.4 - - + -
227A LEU* 6.2 0.2 - - - +
230A ILE* 3.7 38.1 - - + +
235A LEU* 2.9 14.7 + - + +
236A ALA* 1.3 70.9 - - - +
238A SER* 1.3 62.3 + - - +
239A CYS* 3.7 2.3 + - - +
326A LEU* 4.1 25.8 - - + -
327A ARG 3.5 4.3 - - - +
328A LYS* 3.8 28.5 - - + +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 3.8 1.2 + - - -
237A LEU* 1.3 72.5 - - - +
239A CYS* 1.3 67.9 + - - +
240A GLU* 3.3 13.0 + - - +
326A LEU* 3.4 3.1 - - - -
327A ARG* 2.9 37.3 + - - -
329A VAL* 4.4 22.2 - - - -
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Residues in contact with CYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 3.7 30.7 - - + -
237A LEU 3.7 3.6 + - - -
238A SER* 1.3 72.7 + - - +
240A GLU* 1.3 61.3 + - - +
241A LYS 4.2 4.7 - - - -
242A ILE* 3.7 38.6 - - - -
324A VAL* 4.1 12.6 - - - -
326A LEU* 3.7 9.6 - - + +
702A UNX 4.5 5.6 - - - -
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Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A SER* 3.8 18.3 + - - +
239A CYS* 1.3 74.0 - - - +
241A LYS* 1.3 61.1 + - + +
325A LYS* 2.8 39.8 + - + +
327A ARG* 2.7 55.2 + - + +
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MET* 5.8 4.5 - - - -
98A MET* 4.4 11.4 - - + -
239A CYS* 3.7 2.0 - - - -
240A GLU* 1.3 82.3 - - + +
242A ILE* 1.3 73.9 + - - +
243A SER* 3.4 21.5 - - - +
323A LEU 3.8 1.2 - - - +
324A VAL* 3.6 1.2 - - - +
325A LYS* 2.9 50.2 + - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE* 4.8 6.5 - - + -
223A VAL* 4.0 23.1 - - + -
227A LEU* 4.5 9.2 - - + -
239A CYS* 3.7 24.2 - - - -
241A LYS* 1.3 80.8 - - - +
243A SER* 1.3 63.7 + - - +
322A PHE* 4.3 22.7 - - + -
323A LEU 3.5 2.7 - - - -
324A VAL* 4.3 22.0 - - + -
702A UNX 4.1 13.5 - - - -
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MET* 5.2 6.1 - - - +
98A MET* 4.2 8.3 - - - +
241A LYS* 3.4 27.2 - - - +
242A ILE* 1.3 78.3 + - - +
244A GLU* 1.3 68.5 + - - +
245A VAL* 5.0 5.8 - - - -
322A PHE* 3.5 8.5 - - - -
323A LEU* 3.0 41.9 + - - +
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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