Contacts of the strand formed by residues 238 - 250 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ASN* 3.3 9.6 - - - -
191B ARG* 3.4 4.7 - - - -
192B PHE* 2.9 43.2 + - - +
237B TYR* 1.3 75.3 - - - +
239B LEU* 1.3 69.5 + - - +
240B TYR* 3.4 18.6 - - - -
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Residues in contact with LEU 239 (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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205A GLN* 3.9 32.8 - - + -
226A ALA* 3.7 19.7 - - + -
227A ARG* 3.0 44.8 + - - +
228A ASN* 2.9 16.7 + - + +
189B TYR* 3.7 17.3 - - - +
190B PHE 3.7 3.6 - - - -
191B ARG* 4.2 4.0 - - + -
237B TYR* 4.2 12.3 - - + -
238B GLY* 1.3 82.6 - - - +
240B TYR* 1.3 60.5 + - - +
98S GLU* 4.3 9.2 - - + -
99S MET* 4.0 30.1 - - + -
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Residues in contact with TYR 240 (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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226A ALA 3.9 0.4 + - - -
227A ARG* 3.2 36.9 + - - +
228A ASN* 3.4 15.3 + - - -
188B THR 3.6 0.9 - - - +
189B TYR* 4.3 1.0 - - - -
190B PHE* 2.8 45.6 + - + +
192B PHE* 3.8 11.1 - + - -
206B MET* 3.4 33.7 - - + -
227B ARG* 4.1 21.8 - - + -
228B ASN 3.9 14.4 - - - -
229B SER* 3.6 6.7 - - - -
230B CYS* 3.0 30.7 + - - +
237B TYR 5.1 0.7 + - - -
238B GLY* 3.4 25.9 - - - -
239B LEU* 1.3 74.6 - - - +
241B SER* 1.3 62.1 + - - +
242B ILE* 3.5 5.6 + - + +
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Residues in contact with SER 241 (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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224A LYS 4.5 1.4 + - - -
225A SER* 3.1 30.7 + - - -
226A ALA 2.9 30.9 + - - +
227A ARG* 4.3 7.4 - - - +
187B GLN* 4.6 10.9 - - - +
188B THR 3.8 4.9 - - - -
189B TYR* 3.2 21.2 - - - +
227B ARG* 6.2 0.2 - - - +
240B TYR* 1.3 70.9 - - - +
242B ILE* 1.3 62.1 + - - +
243B TYR* 4.0 1.0 + - - +
272B ALA 5.5 0.2 + - - -
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Residues in contact with ILE 242 (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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187B GLN* 3.1 5.8 - - - -
188B THR* 2.9 42.9 + - - +
190B PHE* 3.8 20.9 - - + -
206B MET* 3.5 26.2 - - + +
207B VAL 4.6 0.4 - - - +
208B GLN* 3.3 16.9 - - + +
225B SER* 3.6 39.7 - - - +
226B ALA* 4.6 1.3 - - - -
227B ARG* 4.5 22.9 - - + +
240B TYR 4.2 9.6 - - - +
241B SER* 1.3 76.5 - - - +
243B TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 243 (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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183A TYR* 2.7 24.7 + - - -
243A TYR* 3.4 30.1 - + - +
245A GLY 3.4 34.3 - - - -
183B TYR* 2.7 16.9 + - - -
185B TYR* 3.3 24.3 - + + +
186B SER 3.2 11.9 - - - -
187B GLN* 3.5 25.6 - - + +
225B SER* 4.5 1.6 + - - -
241B SER 4.0 1.6 + - - +
242B ILE* 1.3 78.8 - - - +
244B GLN* 1.3 79.9 + - - +
187D GLN* 4.2 1.6 - - - +
243D TYR* 3.4 40.1 - + - +
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Residues in contact with GLN 244 (chain B).
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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185B TYR* 3.4 4.3 - - - +
186B SER 3.1 26.6 + - - +
208B GLN* 2.9 53.3 + - - +
210B ILE* 3.7 13.2 - - + +
223B MET* 3.5 23.1 + - + +
224B LYS 3.1 24.3 + - - -
225B SER* 3.3 9.1 + - - +
243B TYR* 1.3 85.4 - - - +
245B GLY* 1.3 58.5 + - - +
187D GLN* 3.2 29.7 + - - +
243D TYR* 4.3 3.6 - - - -
274D PHE* 5.2 0.2 - - + -
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Residues in contact with GLY 245 (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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183B TYR* 3.5 20.2 - - - -
184B ILE 3.0 15.0 - - - -
185B TYR* 4.1 0.9 - - - -
223B MET* 3.3 10.3 - - - -
244B GLN* 1.3 78.2 - - - +
246B GLY* 1.3 59.0 + - - -
185D TYR* 3.8 1.0 - - - -
243D TYR* 3.3 14.8 - - - -
274D PHE* 3.2 20.8 - - - -
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Residues in contact with GLY 246 (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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182B TYR 3.3 1.0 - - - +
183B TYR* 3.2 7.4 - - - -
184B ILE 2.8 30.3 + - - +
223B MET* 3.3 10.0 - - - -
245B GLY* 1.3 74.3 - - - -
247B ILE* 1.3 65.0 + - - -
248B PHE* 3.6 12.0 - - - -
125D HIS* 4.1 2.9 - - - -
185D TYR* 3.8 16.4 - - - -
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Residues in contact with ILE 247 (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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181B PHE* 3.8 15.9 - - + -
182B TYR 3.1 6.5 - - - +
183B TYR* 4.3 6.3 - - + -
246B GLY* 1.3 73.0 - - - -
248B PHE* 1.3 71.1 + - - +
280B VAL* 3.5 23.6 - - + -
123D ALA* 4.2 5.8 - - + -
124D ALA 3.8 7.4 - - - +
125D HIS* 3.3 23.1 + - + +
161D HIS 4.9 0.3 - - - +
163D PHE* 3.9 17.4 - - + -
185D TYR* 3.1 26.0 + - + +
277D ALA 3.8 16.4 - - - +
278D PHE* 3.3 36.8 - - + -
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Residues in contact with PHE 248 (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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181B PHE* 4.3 3.6 - - - -
182B TYR* 2.8 31.1 + - - +
184B ILE* 4.1 17.0 - - + -
212B LYS* 6.3 0.2 - - - +
222B LEU* 3.6 56.1 - - + -
223B MET* 3.6 32.3 - - + -
246B GLY* 3.6 17.7 - - - -
247B ILE* 1.3 76.7 - - - +
249B GLU* 1.3 65.3 + - - +
250B LEU* 3.5 7.2 + - + +
125D HIS* 3.5 23.8 - + - -
161D HIS* 3.7 34.5 - + + -
163D PHE* 4.9 2.2 - - - -
270D HIS 5.9 0.7 - - - -
274D PHE* 5.3 0.7 - + - -
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Residues in contact with GLU 249 (chain B).
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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179B LYS* 5.7 4.7 - - + -
180B GLY* 3.3 13.1 - - - +
181B PHE* 3.7 26.7 - - + -
212B LYS* 4.1 13.0 + - - -
248B PHE* 1.3 73.2 - - - +
250B LEU* 1.3 74.0 + - - +
251B LYS* 5.8 3.5 - - + +
254B ASP* 4.8 0.2 - - - +
121D ARG* 3.7 19.8 + - - -
163D PHE* 5.0 5.8 - - + +
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Residues in contact with LEU 250 (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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176B ILE* 3.5 38.1 - - + -
179B LYS* 3.0 7.3 - - - +
180B GLY 2.7 33.9 + - - -
182B TYR* 3.9 21.8 - - + -
184B ILE* 4.0 14.8 - - + -
212B LYS* 4.1 18.8 - - + -
222B LEU* 4.6 1.3 - - + -
248B PHE* 3.9 19.1 - - + +
249B GLU* 1.3 87.0 - - - +
251B LYS* 1.3 61.3 + - - +
254B ASP* 3.6 13.5 - - + +
256B ILE* 3.9 25.6 - - + -
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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