Contacts of the strand formed by residues 226 - 230 (chain J) 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 GLY 226 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J TYR* 4.4 1.6 - - - -
181J PHE 3.7 0.2 - - - +
182J CYS* 3.1 24.4 - - - -
183J ALA 3.1 13.5 + - - -
189J ASP* 3.9 16.3 + - - -
215J PHE 4.0 0.7 - - - -
216J GLY* 4.6 1.1 - - - -
225J PRO* 1.3 73.6 - - - +
227J VAL* 1.3 62.2 + - - -
228J TYR* 3.8 7.8 - - - -
710J PBZ 3.8 20.2 - - - -
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Residues in contact with VAL 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J CYS* 5.8 0.7 - - - -
172J TYR* 3.6 31.2 - - + -
176J TYR* 6.1 0.4 - - + -
180J MET* 3.4 33.7 - - + -
181J PHE 3.4 7.9 - - - +
182J CYS* 4.5 4.5 - - - -
213J VAL* 4.5 0.5 - - - +
214J SER* 3.2 18.1 + - - -
215J PHE* 2.7 67.9 + - + +
226J GLY* 1.3 73.3 - - - +
228J TYR* 1.3 68.6 + - - +
710J PBZ 4.9 1.4 + - - -
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Residues in contact with TYR 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J VAL* 4.1 10.7 - - + +
160J VAL* 4.4 5.9 - - + +
180J MET* 3.2 4.4 - - - -
181J PHE* 2.8 56.2 + + + +
183J ALA* 3.6 31.5 + - + -
189J ASP* 3.8 8.7 + - - -
190J SER* 2.6 23.2 + - - -
199J LEU* 3.8 33.2 - - + -
212J LEU 3.1 23.6 - - - +
213J VAL* 3.7 28.0 - - + -
214J SER* 4.1 3.4 - - - -
226J GLY* 3.8 16.8 - - - -
227J VAL* 1.3 77.9 - - - +
229J THR* 1.3 64.1 + - - +
710J PBZ 5.9 0.9 - - - -
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Residues in contact with THR 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J ALA* 5.5 0.3 - - - +
102J ASP* 3.2 34.4 + - - +
103J LEU* 3.9 23.6 - - + -
179J SER 3.7 8.5 - - - +
180J MET* 4.6 0.7 - - - +
181J PHE* 3.5 1.3 - - - -
211J GLY* 3.2 20.1 - - - -
212J LEU* 2.9 28.0 + - - +
214J SER* 3.9 6.0 - - - -
228J TYR* 1.3 70.3 - - - +
230J ASN* 1.3 60.8 + - - +
231J LEU* 2.9 16.4 + - + +
234J PHE* 3.9 21.5 - - + -
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Residues in contact with ASN 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J CYS* 4.8 1.0 - - - +
129J PRO* 3.3 27.2 - - - +
178J PRO 3.3 16.2 + - - +
179J SER 3.0 27.8 + - - -
180J MET* 3.6 7.7 + - - +
181J PHE* 3.4 20.2 - - + +
210J GLN 4.7 0.7 - - - +
228J TYR 3.3 1.2 + - - -
229J THR* 1.3 70.0 - - - +
231J LEU* 1.3 52.1 + - - +
232J CYS* 3.2 10.8 + - - -
233J LYS* 2.8 51.1 + - - +
234J PHE* 3.6 6.6 - - - -
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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