Contacts of the strand formed by residues 226 - 230 (chain B) in PDB entry 2GD4
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* 3.0 8.3 - - - -
183B ALA 2.7 47.1 + - - -
184B GLY* 4.6 0.6 - - - -
189B ASP* 3.9 19.3 + - - -
225B TYR* 1.3 71.7 - - - +
227B ILE* 1.3 60.5 + - - -
228B TYR* 3.3 13.2 - - - -
393C ARG* 4.7 5.2 - - - -
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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
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168B CYS* 4.3 0.7 - - - -
172B SER* 5.4 2.0 - - - +
176B ILE* 4.3 9.0 - - + -
180B MET* 4.0 20.2 - - + -
181B PHE 3.4 2.9 - - - +
182B CYS* 3.6 28.5 - - - -
213B VAL* 4.5 0.7 - - - +
214B SER* 3.2 19.7 + - - -
215B TRP* 3.4 84.1 + - + +
216B GLY* 4.1 1.6 - - - -
225B TYR 3.7 10.8 - - - +
226B GLY* 1.3 70.9 - - - -
228B TYR* 1.3 71.5 + - - +
393C ARG* 4.7 1.4 + - - +
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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* 3.1 35.3 - - + +
160B VAL* 4.4 3.5 - - - +
180B MET* 3.4 3.4 - - - -
181B PHE* 2.9 55.3 + + + -
183B ALA* 3.1 34.2 + - + +
189B ASP* 3.4 19.1 + - - -
190B ALA* 3.8 11.1 - - + +
199B HIS* 3.4 19.3 - + + -
211B GLY 4.3 0.2 - - - -
212B ILE 3.1 9.2 - - - +
213B VAL* 3.9 26.7 - - + -
214B SER* 4.2 2.7 - - - +
226B GLY* 3.3 24.2 - - - -
227B ILE* 1.3 75.4 - - - +
229B THR* 1.3 64.2 + - - +
230B LYS 3.2 0.9 + - - -
393C ARG* 5.9 0.7 - - - -
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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
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99B TYR 5.5 0.5 + - - -
102B ASP* 2.7 40.3 + - - +
103B ILE* 4.3 9.4 - - + -
179B ASN 3.6 6.6 + - - +
180B MET* 4.6 1.3 - - - +
211B GLY* 2.7 14.0 - - - -
212B ILE* 2.6 58.3 + - + -
214B SER* 4.2 8.1 - - - -
228B TYR* 1.3 68.3 - - - +
230B LYS* 1.3 63.0 + - - +
231B VAL* 2.9 4.9 + - - +
234B PHE* 4.3 14.8 - - + -
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 2.7 28.5 + - - -
131B MET* 3.9 20.0 - - - +
165B ARG* 4.4 10.5 - - - +
178B GLN 3.5 19.9 + - - +
179B ASN* 2.6 24.1 + - - +
180B MET 3.7 12.8 - - - +
181B PHE* 3.8 9.6 - - + -
210B THR 4.0 0.7 - - - -
228B TYR 3.2 2.8 + - - -
229B THR* 1.3 67.6 - - - +
231B VAL* 1.3 68.3 + - - +
232B THR* 2.7 40.5 + - + +
233B ALA* 3.1 18.1 + - + +
234B PHE* 3.5 14.9 - - - -
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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
------------------------------------------------------------
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