Contacts of the strand formed by residues 237 - 248 (chain B) in PDB entry 1G9Y
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 HIS 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ILE* 3.6 31.0 - - + -
228B LYS 3.3 5.8 - - - +
229B PRO* 3.6 24.4 - - + +
230B ASN 3.6 1.7 + - - +
233B TYR* 3.5 19.8 - - - +
235B PHE* 2.8 25.4 + - - +
236B LYS* 1.3 93.2 + - + +
238B GLN* 1.3 61.4 + - - +
239B LEU 4.2 0.2 + - - -
322B PHE* 3.8 22.5 - - + -
343B THR* 4.2 5.8 - - + +
347B THR* 4.5 11.5 + - - -
348B VAL* 4.0 34.0 - - + +
350B ALA* 5.3 7.0 - - + -
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Residues in contact with GLN 238 (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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226B GLN 3.4 0.3 - - - +
227B ILE* 3.4 6.8 - - - +
228B LYS* 2.8 53.1 + - + +
230B ASN* 5.0 2.6 + - + -
233B TYR* 2.9 39.6 + - + +
237B HIS* 1.3 74.5 - - - +
239B LEU* 1.3 78.9 + - - +
240B SER* 3.5 11.5 + - - +
420C T 4.7 1.6 - - - +
503D A 3.1 18.8 + - - +
504D A 3.1 42.0 + - - -
505D A 4.7 0.9 + - - -
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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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226B GLN 3.7 2.2 - - - +
227B ILE* 4.3 12.8 - - + -
237B HIS 4.2 0.6 + - - -
238B GLN* 1.3 85.2 + - - +
240B SER* 1.3 58.8 + - - +
241B LEU* 3.9 14.3 - - + +
308B ILE* 4.5 6.7 - - + -
312B LEU* 4.1 31.4 - - + +
315B ALA* 4.6 2.5 - - + -
322B PHE* 3.7 27.3 - - + -
325B VAL* 3.3 34.3 - - + -
326B CYS* 4.0 26.7 - - - -
329B VAL* 5.4 3.1 - - + -
503D A 4.5 9.2 + - - +
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Residues in contact with SER 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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224B ILE 4.6 0.2 - - - -
225B ALA* 3.5 2.4 - - - +
226B GLN* 2.7 45.1 + - - +
228B LYS* 2.7 43.8 + - - -
238B GLN* 3.5 12.1 + - - +
239B LEU* 1.3 72.7 - - - +
241B LEU* 1.3 67.4 + - - +
242B THR* 4.2 9.4 + - - -
279B SER* 5.7 0.2 + - - -
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Residues in contact with LEU 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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224B ILE 3.4 7.4 - - - +
225B ALA* 5.1 6.5 - - + -
239B LEU* 3.9 13.2 - - + +
240B SER* 1.3 87.9 + - - +
242B THR* 1.3 66.2 + - - +
279B SER* 3.5 26.2 + - - +
281B ILE* 5.6 2.7 - - + -
284B LEU* 4.0 13.5 - - + -
305B VAL* 3.4 25.6 - - + +
308B ILE* 4.0 24.7 - - + -
309B ILE* 3.3 34.1 - - + -
312B LEU* 4.9 9.2 - - + -
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Residues in contact with THR 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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222B SER 3.7 1.6 - - - +
223B ILE* 3.7 2.4 - - - +
224B ILE* 2.8 55.3 + - + +
226B GLN* 4.5 9.2 + - - -
228B LYS* 5.2 0.3 + - - -
240B SER* 4.2 9.0 + - - -
241B LEU* 1.3 80.0 + - - +
243B PHE* 1.3 73.5 + - - +
244B GLN* 4.2 17.5 - - + +
277B ILE* 3.9 23.6 - - + -
278B LEU 3.6 3.1 - - - -
279B SER* 3.7 6.5 + - - +
284B LEU* 4.6 3.8 - - - +
305B VAL* 5.9 0.4 - - - +
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Residues in contact with PHE 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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213B LEU* 5.1 1.8 - - + -
217B VAL* 3.5 43.1 - - + -
222B SER 3.6 2.9 - - - -
223B ILE* 4.4 12.3 - - + +
242B THR* 1.3 73.1 - - - +
244B GLN* 1.3 65.6 + - - +
245B VAL* 3.6 15.5 - - + -
262B ILE* 4.3 3.4 - - + -
276B TYR* 3.4 34.8 - + - -
277B ILE* 3.6 0.7 - - - -
278B LEU* 2.9 39.4 + - + +
284B LEU* 3.6 24.2 - - + +
287B PHE* 3.5 39.3 - + - -
288B LEU* 4.3 12.6 - - + -
291B LEU* 4.3 3.6 - - + -
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Residues in contact with GLN 244 (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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221B GLY* 3.2 2.8 - - - -
222B SER* 2.8 54.2 + - - +
224B ILE* 3.8 16.8 - - + +
242B THR* 4.2 11.2 - - + +
243B PHE* 1.3 80.2 - - - +
245B VAL* 1.3 65.2 + - - +
246B THR* 3.5 19.0 + - - -
268B ARG* 5.5 2.1 + - - -
270B ARG* 4.8 0.2 - - - +
275B ASP* 4.0 13.2 + - + +
276B TYR 3.0 13.5 - - - +
277B ILE* 4.3 10.8 - - + +
415C G 4.3 3.0 - - - -
416C A 3.1 31.4 + - - +
417C C 4.5 8.8 + - - -
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Residues in contact with VAL 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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213B LEU* 5.0 0.4 - - + -
216B PHE* 3.2 38.1 - - + -
217B VAL* 4.2 12.3 - - + -
220B ASP* 4.0 8.3 - - + +
221B GLY* 4.6 1.3 - - - -
243B PHE* 3.6 28.9 - - + -
244B GLN* 1.3 80.1 - - - +
246B THR* 1.3 65.1 + - - +
255B LEU* 3.7 15.4 - - + +
258B LEU* 4.1 14.8 - - + -
275B ASP* 3.4 2.8 - - - -
276B TYR* 2.8 39.7 + - + -
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Residues in contact with THR 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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220B ASP* 3.3 20.5 + - - +
244B GLN* 3.5 16.6 + - - -
245B VAL* 1.3 74.4 - - - +
247B GLN* 1.3 80.8 + - - +
270B ARG* 3.7 9.0 + - - +
273B VAL* 3.2 28.5 - - + -
274B SER 3.6 3.4 - - - -
275B ASP* 2.7 18.1 + - - +
414C C 3.1 37.4 - - + +
415C G 3.9 4.6 - - - -
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Residues in contact with GLN 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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18A ASP 4.9 1.0 - - - +
97A LEU* 3.5 15.6 - - + +
216B PHE* 3.5 15.2 - - + -
220B ASP* 2.9 23.2 + - - +
246B THR* 1.3 89.6 + - - +
248B LYS* 1.3 69.5 + - - +
251B ARG* 2.9 44.8 + - + +
254B PHE* 5.3 3.6 - - + -
255B LEU* 4.1 24.6 - - + +
273B VAL* 4.4 3.6 - - - -
274B SER* 2.9 33.1 + - - +
414C C 3.1 23.4 + - - -
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Residues in contact with LYS 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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137A ASP* 4.4 6.1 + - - +
247B GLN* 1.3 73.2 - - - +
249B THR* 1.3 62.5 + - - +
250B GLN* 2.9 43.8 - - + +
251B ARG* 2.8 44.7 + - - +
252B ARG* 4.6 0.3 - - - -
272B SER* 3.5 21.3 - - - +
273B VAL* 4.2 4.5 - - - -
413C A 3.1 47.5 + - + +
414C C 2.7 21.6 + - - +
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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