Contacts of the strand formed by residues 230 - 238 (chain D) in PDB entry 2Y05
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 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D GLY* 5.2 0.2 - - - -
211D TYR* 3.6 30.1 - - - +
212D ASP 3.6 20.4 - - - +
214D TYR* 3.8 25.4 - - + +
226D VAL* 3.6 18.2 - - - +
227D ILE* 3.2 19.4 + - - +
228D GLY 5.2 1.0 - - - +
229D GLN* 1.3 79.6 - - - +
231D LYS* 1.3 59.4 + - - +
234D GLY* 3.8 4.0 - - - -
235D ARG 3.8 24.7 - - - +
236D ILE* 4.3 6.7 - - + -
263D GLN* 2.8 26.0 + - - +
265D LEU* 3.4 26.5 - - + -
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D THR* 5.3 2.9 + - - -
209D ASP* 3.5 33.0 - - + +
210D GLY 3.7 16.8 - - - -
211D TYR 2.9 23.4 + - - +
212D ASP* 2.9 42.8 + - - +
229D GLN 3.6 0.4 + - - -
230D MET* 1.3 76.6 - - - +
232D LYS* 1.3 66.7 + - - +
234D GLY 2.9 19.6 + - - +
263D GLN* 3.5 4.0 - - - +
265D LEU* 3.4 8.3 - - - +
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Residues in contact with LYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LYS* 1.3 77.8 - - - +
233D PHE* 1.3 97.3 + - + +
234D GLY* 3.2 1.0 + - - -
262D TYR 3.5 23.1 - - - +
263D GLN* 3.3 26.4 - - - +
264D GLU* 3.3 24.2 - - - -
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Residues in contact with PHE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LYS* 1.3 90.9 - - + +
234D GLY* 1.3 67.8 + - - +
235D ARG* 3.5 18.9 + - - +
263D GLN 2.8 11.9 + - - -
264D GLU* 3.4 52.5 - - + -
266D ARG* 4.9 2.6 + - - +
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Residues in contact with GLY 234 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211D TYR 4.7 0.7 - - - -
212D ASP* 3.5 14.6 - - - -
230D MET* 3.8 13.7 - - - -
231D LYS* 2.9 19.7 + - - -
232D LYS 3.1 1.5 - - - -
233D PHE* 1.3 78.7 - - - +
235D ARG* 1.3 58.6 + - - -
236D ILE* 5.2 0.2 - - - -
265D LEU* 3.4 10.0 - - - +
266D ARG* 2.8 27.5 + - - +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ILE 4.7 4.5 - - - +
137D CYS* 3.0 39.1 + - - +
138D GLY* 3.4 16.1 + - - -
143D GLU* 3.8 15.6 + - - +
212D ASP* 3.1 39.1 + - - +
213D CYS* 3.3 18.5 - - - +
214D TYR 3.0 23.9 + - - +
230D MET* 3.8 1.2 - - - +
233D PHE 3.7 15.1 + - - +
234D GLY* 1.3 74.7 - - - +
236D ILE* 1.3 63.1 + - - +
237D ALA 4.0 0.3 + - - -
266D ARG* 3.3 27.8 - - + +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ILE* 4.4 4.5 - - - +
137D CYS* 4.7 1.1 - - - -
214D TYR* 3.4 37.0 - - + +
216D ASP* 4.3 7.0 - - + +
227D ILE* 3.8 22.2 - - + -
230D MET* 4.3 9.9 - - + -
234D GLY 5.1 1.1 - - - +
235D ARG* 1.3 77.6 - - - +
237D ALA* 1.3 69.2 + - - +
238D ILE* 3.9 13.5 - - + -
265D LEU* 4.3 8.1 - - + -
266D ARG* 2.8 11.8 + - - +
267D MET* 3.5 40.7 - - + -
268D GLU* 3.0 26.3 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLY 3.8 14.8 - - - +
136D ILE* 3.8 12.8 - - + -
137D CYS* 3.5 24.7 - - - -
214D TYR 2.9 9.0 + - - +
215D PHE* 4.5 9.2 - - + -
216D ASP* 3.0 26.0 + - - +
236D ILE* 1.3 74.1 - - - +
238D ILE* 1.3 60.2 + - - +
239D CYS* 3.2 4.0 + - - +
268D GLU 3.5 5.6 - - - -
270D PHE* 4.1 9.9 - - + -
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Residues in contact with ILE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ASP* 4.1 10.5 - - - +
236D ILE* 4.2 14.6 - - + -
237D ALA* 1.3 70.9 - - - +
239D CYS* 1.3 60.4 + - - +
240D GLY* 4.8 11.2 - - - +
241D ALA* 6.1 2.0 - - + -
267D MET* 4.0 27.4 - - + +
268D GLU 2.7 21.4 + - - +
269D ALA* 3.2 35.8 - - + +
270D PHE* 3.4 10.4 + - - +
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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
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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