Contacts of the strand formed by residues 180 - 183 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98P LEU 4.7 1.8 - - - +
99P LEU 4.5 1.6 - - - +
100P ALA* 4.1 24.9 - - + +
172P TYR* 6.3 0.7 - - - -
175P LEU 3.1 25.1 - - - +
176P TYR* 3.6 27.4 + - + -
177P HIS* 2.9 45.3 - - + +
178P PRO 3.0 5.9 + - - +
179P SER* 1.3 82.2 - - - +
181P PHE* 1.4 63.8 + - - +
214P SER* 6.1 0.4 - - - +
215P PHE* 3.6 32.8 - - + -
227P VAL* 3.4 17.7 - - + -
228P TYR 3.2 9.0 - - - +
229P THR* 5.0 0.2 - - - -
230P ASN* 3.8 8.4 + - - +
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Residues in contact with PHE 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PRO* 3.6 33.7 - - + -
162P VAL* 4.4 7.6 - - + -
163P VAL 5.8 1.3 - - - +
168P CYS* 4.2 8.5 - - - -
176P TYR* 4.9 0.7 - - - -
180P MET* 1.4 74.6 - - - +
182P CYS* 1.4 72.2 - - - +
183P ALA* 4.5 4.5 - - + -
199P LEU* 3.3 34.5 - - + -
210P GLN* 3.8 15.7 - - + -
211P GLY* 4.0 5.2 - - - -
226P GLY 3.8 0.2 - - - +
227P VAL* 3.5 4.5 - - - -
228P TYR* 2.8 54.1 + + + +
229P THR 3.5 20.9 - - - -
230P ASN* 3.4 24.0 - - - +
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Residues in contact with CYS 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P VAL* 3.9 1.0 - - - +
163P VAL* 3.0 29.6 + - + +
168P CYS* 2.1 55.4 - - + -
171P LEU* 5.5 0.4 - - - -
172P TYR* 3.8 27.1 - - - -
181P PHE* 1.4 83.7 - - - +
183P ALA* 1.4 61.6 + - - +
225P PRO* 3.7 24.9 - - + -
226P GLY 3.1 7.9 - - - +
227P VAL* 4.7 3.1 - - - +
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Residues in contact with ALA 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P CYS* 6.2 0.4 - - + -
160P VAL* 4.0 16.7 - - + +
161P SER 3.1 16.2 - - - +
162P VAL* 4.2 4.5 - - + -
163P VAL* 3.9 2.5 - - - -
181P PHE* 4.5 2.9 - - + -
182P CYS* 1.4 74.9 - - - +
184P GLY* 1.3 62.3 + - - +
185P GLY 3.9 0.2 + - - -
189P ASP* 4.4 4.3 - - - +
199P LEU* 4.5 10.1 - - + -
225P PRO* 4.1 0.4 - - - -
226P GLY 3.2 25.7 + - - +
228P TYR* 3.6 26.1 + - + -
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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