Contacts of the strand formed by residues 238 - 250 (chain D) in PDB entry 1D0G
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 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B ASN* 3.3 10.1 - - - -
191D ARG* 3.3 5.4 - - - -
192D PHE* 2.9 42.7 + - - +
237D TYR* 1.3 74.8 - - - +
239D LEU* 1.3 67.6 + - - +
240D TYR* 3.4 18.8 - - - -
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Residues in contact with LEU 239 (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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205B GLN* 3.9 35.9 - - + -
226B ALA* 3.8 14.8 - - + -
227B ARG* 3.1 43.6 + - - +
228B ASN* 2.9 18.6 + - + +
189D TYR* 3.8 20.2 - - - +
190D PHE 3.6 4.3 - - - -
191D ARG* 4.2 7.2 - - - -
237D TYR* 4.1 7.9 - - + -
238D GLY* 1.3 80.4 - - - +
240D TYR* 1.3 61.0 + - - +
98T GLU* 4.4 6.7 - - + -
99T MET* 3.6 28.0 - - + -
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Residues in contact with TYR 240 (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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227B ARG* 3.4 38.2 + - - +
228B ASN* 3.4 14.2 + - - -
189D TYR* 4.1 1.6 - - - -
190D PHE* 2.8 40.9 + - + +
192D PHE* 3.9 11.5 - + - -
206D MET* 3.5 37.2 - - + -
227D ARG* 4.0 14.8 - - + -
228D ASN 3.9 15.0 - - - -
229D SER* 3.8 5.8 - - - -
230D CYS* 2.8 32.9 + - - +
237D TYR 5.3 0.7 + - - -
238D GLY* 3.4 26.8 - - - -
239D LEU* 1.3 75.9 - - - +
241D SER* 1.3 63.1 + - - +
242D ILE* 3.5 8.8 + - + +
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Residues in contact with SER 241 (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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224B LYS 4.5 1.0 + - - -
225B SER* 3.1 28.8 + - - -
226B ALA 2.8 33.1 + - - +
227B ARG* 4.5 6.8 - - - +
187D GLN* 4.4 11.7 - - - -
188D THR 3.7 5.4 - - - -
189D TYR* 3.2 20.5 - - - +
227D ARG* 5.9 0.7 - - - +
240D TYR* 1.3 72.8 - - - +
242D ILE* 1.3 62.0 + - - +
243D TYR 4.2 0.9 + - - -
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Residues in contact with ILE 242 (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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187D GLN* 3.1 5.3 - - - -
188D THR* 2.9 39.4 + - - +
190D PHE* 3.7 23.3 - - + -
206D MET* 3.5 27.1 - - + +
207D VAL* 4.7 0.7 - - - -
208D GLN* 3.3 14.9 - - + +
225D SER* 3.5 42.0 - - - +
226D ALA 4.7 0.2 - - - -
227D ARG* 4.3 23.3 - - + -
240D TYR* 3.9 9.6 - - + +
241D SER* 1.3 79.8 - - - +
243D TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 243 (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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187A GLN* 4.3 1.6 - - - +
243A TYR* 3.4 38.6 - + - +
183B TYR* 2.8 17.1 + - - -
243B TYR* 3.4 34.1 - + - +
244B GLN* 4.3 1.3 - - - -
245B GLY 3.3 32.5 - - - -
183D TYR* 2.7 21.7 + - - -
185D TYR* 3.2 30.5 - + + +
186D SER 3.3 12.3 - - - -
187D GLN* 3.7 25.1 - - + +
208D GLN* 5.0 0.2 - - - -
225D SER* 4.3 4.2 + - - -
241D SER 4.1 1.2 + - - -
242D ILE* 1.3 76.6 - - - +
244D GLN* 1.3 74.7 + - - +
274D PHE* 4.7 0.2 - + - -
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Residues in contact with GLN 244 (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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187A GLN* 3.0 36.0 + - - +
243A TYR* 4.2 5.2 - - - -
185D TYR* 3.3 4.9 - - - +
186D SER 3.2 27.7 + - - +
208D GLN* 3.0 50.5 + - - +
210D ILE* 3.7 12.5 - - + +
223D MET* 3.3 25.0 + - + +
224D LYS 3.1 16.1 + - - -
225D SER* 3.6 11.0 - - - +
243D TYR* 1.3 87.7 - - - +
245D GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 245 (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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185A TYR* 3.9 0.9 - - - -
243A TYR* 3.2 15.9 - - - -
274A PHE* 3.2 20.1 - - - -
183D TYR* 3.7 18.8 - - - -
184D ILE 2.9 14.8 - - - -
185D TYR* 4.0 0.2 - - - -
223D MET* 3.2 10.7 - - - -
244D GLN* 1.3 80.3 - - - +
246D GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 246 (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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125A HIS* 4.1 3.1 - - - -
185A TYR* 3.6 17.3 - - - -
182D TYR 3.4 0.2 - - - +
183D TYR* 3.6 10.4 - - - -
184D ILE* 2.9 27.4 + - - +
223D MET* 3.3 10.0 - - - -
245D GLY* 1.3 74.6 - - - -
247D ILE* 1.3 59.8 + - - -
248D PHE* 3.4 16.7 - - - -
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Residues in contact with ILE 247 (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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123A ALA* 4.2 4.9 - - + -
124A ALA 3.7 17.7 - - - +
125A HIS* 3.3 25.8 + - + +
161A HIS 4.9 0.3 - - - +
163A PHE* 3.8 22.5 - - + -
185A TYR* 3.0 23.5 + - + +
277A ALA 3.7 9.2 - - - +
278A PHE* 3.3 41.3 - - + -
181D PHE* 3.9 9.9 - - + -
182D TYR 3.2 6.7 - - - +
183D TYR* 4.2 2.9 - - + -
246D GLY* 1.3 69.6 - - - -
248D PHE* 1.3 70.1 + - - +
280D VAL* 3.5 24.9 - - + -
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Residues in contact with PHE 248 (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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125A HIS* 3.3 23.1 - + - -
161A HIS* 3.7 35.9 - + + -
163A PHE* 4.9 2.5 - - - -
270A HIS* 5.9 1.3 - + - -
274A PHE* 5.4 0.7 - + - -
181D PHE* 4.5 3.1 - - - -
182D TYR* 2.9 31.4 + - - +
184D ILE* 4.1 20.9 - - + -
212D LYS* 6.3 0.4 - - - +
222D LEU* 3.6 38.8 - - + -
223D MET* 3.6 43.1 - - + -
246D GLY* 3.4 17.7 - - - -
247D ILE* 1.3 78.3 - - - +
249D GLU* 1.3 62.1 - - - +
250D LEU* 3.5 11.4 + - + +
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Residues in contact with GLU 249 (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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121A ARG* 4.1 9.5 + - - -
158A ARG* 3.5 38.0 + - - +
163A PHE* 5.0 7.7 - - + +
179D LYS* 5.7 6.0 - - + -
180D GLY* 3.4 13.0 - - - +
181D PHE* 3.8 33.7 - - + -
212D LYS* 4.0 7.1 + - - -
248D PHE* 1.3 74.0 - - - +
250D LEU* 1.3 70.1 + - - +
251D LYS* 5.8 2.3 - - + +
254D ASP* 4.6 0.2 - - - +
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Residues in contact with LEU 250 (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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176D ILE* 3.7 36.6 - - + -
178D GLU 4.4 0.3 - - - +
179D LYS* 3.0 6.6 - - - +
180D GLY 2.9 31.4 + - - -
182D TYR* 3.9 19.1 - - + -
184D ILE* 3.9 24.7 - - + -
212D LYS* 4.0 19.5 - - + -
222D LEU* 4.7 0.9 - - + -
248D PHE* 3.9 14.6 - - + +
249D GLU* 1.3 85.5 - - - +
251D LYS* 1.3 61.6 + - - +
254D ASP* 3.5 14.1 - - + +
256D ILE* 4.0 21.1 - - + -
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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