Contacts of the strand formed by residues 226 - 230 (chain B) in PDB entry 4D9R
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B CYS* 3.2 10.4 - - - +
183B ALA 2.9 33.1 + - - -
184B GLU 5.3 0.2 - - - -
185B SER* 4.0 5.3 - - - -
189B ASP* 4.0 8.1 - - - -
218B ARG* 3.8 18.2 - - - -
224B LYS 3.7 0.4 + - - -
225B PRO* 1.3 73.6 - - - +
227B ILE* 1.3 59.3 + - - -
228B TYR* 3.5 15.8 - - - -
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 4.4 18.8 - - + -
172B HIS* 3.5 32.3 - - + +
175B ALA* 6.3 0.7 - - + -
176B ILE* 3.7 21.5 - - + -
180B LEU* 3.9 34.3 - - + -
181B MET 3.6 6.5 - - - +
182B CYS* 4.7 0.4 - - - -
190B SER* 5.9 0.4 - - - -
213B VAL* 4.1 1.9 - - - +
214B THR* 2.7 40.7 + - - +
216B GLY 5.5 5.8 - - - +
218B ARG* 4.2 18.2 - - + +
225B PRO 3.7 5.1 + - - +
226B GLY* 1.3 75.7 - - - +
228B TYR* 1.3 72.3 + - - +
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.4 2.2 - - + +
160B LEU* 3.5 20.1 - - - +
180B LEU* 3.5 5.6 - - - +
181B MET* 2.8 51.4 + - + +
182B CYS 4.5 0.4 - - - -
183B ALA* 3.5 27.0 - - + +
189B ASP* 4.2 4.5 + - - -
190B SER* 2.9 36.8 + - - -
199B LEU* 3.9 39.9 - - + -
211B GLY* 4.4 6.3 - - - -
212B VAL 3.3 7.0 - - - +
213B VAL* 3.7 23.8 - - + -
214B THR* 3.8 1.8 - - - -
226B GLY* 3.5 23.0 - - - -
227B ILE* 1.3 78.9 - - - +
229B THR* 1.3 63.0 + - - +
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B HIS 5.3 0.4 - - - +
102B ASP* 4.1 12.2 + - - +
103B LEU* 3.8 30.7 - - + -
179B ARG 3.9 5.6 - - - +
180B LEU* 3.8 9.8 - - + +
211B GLY* 3.0 6.9 - - - -
212B VAL* 2.7 33.5 + - - +
214B THR* 2.3 33.7 + - - +
228B TYR* 1.3 69.7 - - - +
230B ARG* 1.3 63.0 + - - +
231B VAL* 3.3 3.5 + - - +
234B TYR* 3.6 31.0 - - + +
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 2.8 30.5 + - - +
129B ASP* 3.1 54.7 + - - +
130B VAL* 5.2 2.6 - - - +
165B ARG* 3.5 17.0 - - - +
178B GLU* 2.9 28.3 + - - +
179B ARG 3.1 13.8 + - - +
180B LEU 3.7 7.4 - - - -
181B MET* 3.7 28.2 - - + +
210B GLU* 3.5 10.0 + - - +
211B GLY* 4.7 0.2 - - - -
229B THR* 1.3 68.6 - - - +
231B VAL* 1.3 65.7 - - - +
232B ALA* 3.3 8.3 - - + +
233B SER* 3.2 19.6 + - - +
234B TYR* 3.3 17.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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