Contacts of the strand formed by residues 180 - 183 (chain O) in PDB entry 2BDI
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 MET 180 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97O PRO* 6.5 0.2 - - + -
98O LEU 4.7 1.6 - - - +
99O LEU 4.4 1.6 - - - +
100O ALA* 4.0 24.9 - - + +
172O TYR* 6.4 0.4 - - - -
175O LEU 3.2 24.5 - - - +
176O TYR* 3.6 21.4 + - + -
177O HIS* 2.8 50.9 + - + +
178O PRO 3.0 5.8 + - - +
179O SER* 1.3 82.4 - - - +
181O PHE* 1.3 65.0 + - - +
214O SER* 6.1 0.7 - - - +
215O PHE* 3.6 33.4 - - + -
227O VAL* 3.4 16.8 - - + -
228O TYR 3.2 8.7 - - - +
229O THR* 5.0 0.7 - - - -
230O ASN* 3.8 8.3 + - - +
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Residues in contact with PHE 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129O PRO* 3.6 33.2 - - + -
162O VAL* 4.5 8.7 - - + -
163O VAL 5.9 0.9 - - - +
168O CYS* 4.0 10.1 - - - -
176O TYR* 4.8 0.2 - - - -
180O MET* 1.3 76.9 - - - +
182O CYS* 1.4 71.6 + - - +
183O ALA* 4.5 5.2 - - + -
199O LEU* 3.3 35.4 - - + -
210O GLN* 3.9 11.9 - - + -
211O GLY* 4.1 5.6 - - - -
227O VAL* 3.3 4.7 - - - -
228O TYR* 2.8 53.7 + + + -
229O THR 3.5 20.9 - - - -
230O ASN* 3.3 26.9 - - - +
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Residues in contact with CYS 182 (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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162O VAL* 3.8 2.6 - - - +
163O VAL* 2.9 34.0 + - + +
168O CYS* 2.1 53.9 - - + +
172O TYR* 3.9 23.8 - - - -
181O PHE* 1.4 81.5 - - - +
183O ALA* 1.3 63.0 + - - +
225O PRO* 3.7 23.1 - - + -
226O GLY 3.2 7.2 - - - +
227O VAL* 4.8 3.6 - - - -
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Residues in contact with ALA 183 (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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136O CYS* 6.2 0.2 - - - -
160O VAL* 4.0 17.1 - - + +
161O SER 3.2 15.5 - - - +
162O VAL* 4.2 4.3 - - + +
163O VAL* 3.9 1.1 - - - -
181O PHE* 4.5 2.5 - - + -
182O CYS* 1.3 76.9 - - - +
184O GLY* 1.3 61.4 + - - +
189O ASP* 4.5 2.6 - - - +
199O LEU* 4.4 10.1 - - + -
225O PRO* 4.1 1.3 - - - -
226O GLY 3.2 25.1 + - - +
228O TYR* 3.5 30.2 + - + -
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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