Contacts of the strand formed by residues 243 - 246 (chain A) in PDB entry 2BDX
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 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LYS 3.2 2.5 + - - +
169A ILE* 3.4 25.0 - - + -
170A PHE* 2.8 27.9 + - - +
236A LEU* 3.7 9.8 - - - +
241A LEU* 4.7 0.2 - - - +
242A ASP* 1.3 82.0 - - + +
244A ILE* 1.3 68.2 + - - +
245A CYS* 3.9 0.4 - - + -
257A PHE* 4.5 7.6 - - + -
261A ARG 3.8 11.9 - - - +
262A GLN* 3.5 25.8 - - - +
263A LEU 4.0 3.4 - - - +
264A VAL* 4.0 18.8 - - + +
283A MET* 4.0 28.9 - - + -
291A CYS* 4.9 6.1 - - - -
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Residues in contact with ILE 244 (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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170A PHE* 3.3 18.4 - - + +
172A CYS* 5.1 5.6 - - - -
175A GLY* 5.6 3.1 - - - -
176A LEU* 3.8 35.0 - - + -
232A VAL* 3.8 21.5 - - + -
235A PHE* 3.9 19.5 - - + -
236A LEU* 3.8 13.5 - - + -
243A LEU* 1.3 77.0 - - - +
245A CYS* 1.3 68.2 + - - +
246A ARG* 4.2 7.6 - - + -
262A GLN 3.0 11.3 + - - +
263A LEU* 3.3 23.4 - - + -
264A VAL 3.0 26.9 + - - +
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Residues in contact with CYS 245 (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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61A ILE* 3.9 17.0 - - - -
90A LEU* 4.0 4.2 - - - +
169A ILE* 3.7 12.1 - - + +
170A PHE 2.8 8.6 + - - +
171A CYS* 3.2 40.1 - - - +
172A CYS 3.2 5.9 + - - +
243A LEU* 3.9 1.8 - - + -
244A ILE* 1.3 72.6 - - - +
246A ARG* 1.3 62.6 + - - +
264A VAL* 3.7 9.0 - - + -
266A LEU* 3.6 33.4 - - - -
283A MET* 3.9 17.5 - - + -
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Residues in contact with ARG 246 (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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90A LEU* 3.7 9.8 - - - +
172A CYS* 3.2 18.6 - - - +
173A HIS 3.7 0.2 - - - +
174A GLY 2.6 23.3 + - - +
175A GLY* 5.1 0.9 - - - -
207A SER 3.0 19.0 + - - -
208A ASP* 2.8 25.1 + - - -
209A PRO* 3.3 15.2 - - - +
244A ILE* 4.2 8.1 - - + -
245A CYS* 1.3 74.8 - - - +
247A ALA* 1.3 76.0 + - - +
248A HIS* 3.5 10.5 - - - +
249A GLN* 2.9 22.2 + - - +
263A LEU* 3.8 26.7 - - + -
264A VAL 2.9 14.6 + - - +
265A THR* 3.1 30.5 + - - +
266A LEU* 2.8 23.6 + - - +
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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