Contacts of the strand formed by residues 242 - 250 (chain B) in PDB entry 3H90
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 THR 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B GLY* 5.8 5.4 - - - -
76B GLY* 5.9 1.3 - - - -
238B GLN* 3.1 3.8 - - - +
239B SER* 3.1 34.4 + - - +
240B GLY 3.4 0.2 - - - -
241B PRO* 1.3 88.0 - - + +
243B ARG* 1.3 60.4 + - - +
244B PHE* 3.3 26.1 + - + -
277B GLY 3.8 21.8 - - - +
279B ASP* 5.1 3.0 - - - +
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Residues in contact with ARG 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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210B LEU* 3.6 31.2 - - + -
214B GLU* 3.0 39.8 + - - -
237B ARG 4.3 0.7 - - - +
238B GLN* 3.5 30.1 + - + +
241B PRO 3.8 6.1 + - - +
242B THR* 1.3 74.0 - - - +
244B PHE* 1.3 58.5 + - - +
245B ILE* 4.7 5.6 - - + -
275B PHE* 3.6 30.4 - - - +
276B PRO* 5.2 6.5 + - - +
278B SER* 3.3 23.3 + - - +
279B ASP* 2.7 34.0 + - - +
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Residues in contact with PHE 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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73B PHE* 3.6 29.6 - + + -
74B GLY* 3.9 22.2 - - - -
210B LEU* 5.1 0.2 - - - +
235B ARG 4.5 0.7 - - - -
236B THR* 3.4 4.3 - - - -
237B ARG* 2.6 68.9 + - + +
239B SER* 3.8 29.2 - - - -
242B THR* 3.3 26.0 - - + -
243B ARG* 1.3 72.9 - - - +
245B ILE* 1.3 65.6 + - - +
246B GLN* 4.4 2.0 - - + -
279B ASP* 3.4 37.7 - - + -
73D PHE* 6.0 1.8 - - + -
235D ARG* 4.5 1.1 - - - -
246D GLN* 5.8 2.2 - - - -
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Residues in contact with ILE 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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210B LEU* 4.7 4.3 - - + -
218B ILE* 3.6 37.2 - - + -
234B LEU* 4.1 18.4 - - + -
235B ARG 3.7 2.9 - - - -
236B THR* 4.3 5.4 - - + -
243B ARG* 4.7 6.1 - - + -
244B PHE* 1.3 81.2 - - - +
246B GLN* 1.3 67.7 + - - +
247B ILE* 4.9 5.8 - - + +
271B ILE* 3.8 25.4 - - + -
275B PHE* 5.1 3.8 - - + -
278B SER* 4.3 16.8 - - - +
279B ASP 2.8 9.8 + - - +
280B VAL* 3.0 23.3 - - + -
281B ILE* 2.8 28.5 + - - +
282B ILE* 6.1 0.2 - - + -
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Residues in contact with GLN 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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233B ASP* 4.2 1.1 - - - -
234B LEU* 3.0 8.7 - - - +
235B ARG* 2.8 70.8 + - + +
237B ARG* 5.4 1.4 - - - +
244B PHE* 5.6 1.1 - - + -
245B ILE* 1.3 80.0 - - - +
247B ILE* 1.3 60.5 + - - +
248B HIS* 5.7 0.4 - - + -
281B ILE* 3.3 18.8 - - + +
73D PHE* 3.4 29.4 - - + -
237D ARG* 5.3 1.8 - - - +
244D PHE* 5.7 1.4 - - - -
246D GLN* 3.6 23.8 - - - +
281D ILE* 4.0 27.2 - - + +
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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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218B ILE* 4.8 1.8 - - + -
219B ILE* 4.7 7.0 - - + -
222B VAL* 3.9 24.9 - - + -
231B ALA* 3.8 22.4 - - + -
232B HIS 4.8 0.9 - - - +
233B ASP 3.1 13.7 - - - +
234B LEU* 3.7 30.1 - - + -
245B ILE* 5.1 5.2 - - + -
246B GLN* 1.3 76.3 - - - +
248B HIS* 1.3 74.7 + - - +
249B LEU* 4.1 13.2 - - + -
271B ILE* 5.6 0.9 - - + -
281B ILE 3.2 4.3 + - - +
282B ILE* 3.5 28.1 - - + -
283B HIS* 2.9 25.1 + - - +
281D ILE* 4.6 0.7 - - - +
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Residues in contact with HIS 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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231B ALA* 3.1 27.9 - - - +
232B HIS* 3.1 29.0 + + + +
233B ASP* 3.1 35.4 + - + +
246B GLN 5.7 0.4 - - - -
247B ILE* 1.3 82.4 - - - +
249B LEU* 1.3 61.1 + - - +
283B HIS* 3.2 31.2 - + + +
285B ASP* 3.1 4.7 + - - +
292B ZN 4.7 1.8 - - - -
294B ZN 2.2 31.2 - - - -
281D ILE* 4.3 14.4 - - + +
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Residues in contact with LEU 249 (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 VAL* 3.5 32.5 - - + -
228B VAL* 4.1 16.2 - - + -
230B GLY 3.6 1.3 - - - +
231B ALA* 4.4 2.0 - - + -
247B ILE* 4.1 9.1 - - + -
248B HIS* 1.3 77.6 - - - +
250B GLU* 1.3 61.1 + - - +
251B MET* 3.4 29.3 + - + +
263B VAL* 4.3 0.7 - - + -
264B ALA* 4.1 5.8 - - - -
267B VAL* 3.9 28.0 - - + -
282B ILE* 3.7 27.4 - - + -
283B HIS 2.8 7.7 + - - +
284B GLN* 3.4 3.2 - - + +
285B ASP* 2.8 29.6 + - - +
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Residues in contact with GLU 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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228B VAL* 3.7 1.9 - - - -
229B SER* 2.8 34.4 + - - +
230B GLY* 2.6 40.3 + - - +
231B ALA 3.9 1.6 + - - -
232B HIS* 2.9 43.4 + - + +
249B LEU* 1.3 70.7 - - - +
251B MET* 1.3 67.4 + - - +
285B ASP* 3.2 6.3 - - + +
286B PRO 3.9 12.8 - - - +
289B VAL* 4.3 21.2 - - + +
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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