Contacts of the strand formed by residues 237 - 248 (chain C) in PDB entry 3ASK
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 PHE 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C MET* 4.0 18.2 - - + -
150C ALA* 3.9 16.2 - - + -
151C TRP 5.5 0.2 - - - +
152C PHE* 3.7 31.2 - + - -
191C TYR* 4.3 10.5 - - - -
226C ASN* 3.2 5.7 - - - -
227C TYR 3.0 31.2 + - - -
228C ASN* 6.0 2.9 - - - -
229C PRO* 5.9 1.6 - - + -
236C GLY* 1.3 80.9 - - - -
238C TRP* 1.3 71.2 + + - +
239C TYR* 3.5 21.2 - - + -
298C SER* 4.7 11.7 - - - -
299C GLY 4.3 10.8 - - - -
300C PRO 4.3 15.3 - - - -
301C SER* 3.8 21.3 - - - -
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Residues in contact with TRP 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ALA* 3.2 3.8 - - - -
151C TRP* 2.7 46.6 + - - +
153C GLU* 6.0 0.7 - - + -
224C MET* 4.1 19.1 - - + -
225C LEU* 3.4 24.5 - - - -
226C ASN* 3.7 27.4 - - + +
237C PHE* 1.3 81.2 - + + +
239C TYR* 1.3 62.1 + - - +
276C GLU* 3.3 45.3 - - + -
278C PHE* 3.7 24.9 - + - -
296C ARG* 3.4 40.9 - - + +
297C LYS 3.5 20.1 + - - -
298C SER* 3.3 25.4 + - - -
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Residues in contact with TYR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C MET* 3.2 31.2 + - - +
149C GLY 4.8 0.7 - - - -
150C ALA* 3.7 20.2 - - + -
151C TRP* 4.7 2.7 - - - -
224C MET* 3.4 3.3 - - - -
225C LEU* 2.9 36.0 + - + +
227C TYR* 3.0 32.5 - - + -
229C PRO* 3.7 18.6 - - + +
237C PHE* 3.5 37.2 - - + +
238C TRP* 1.3 73.7 - - - +
240C ASP* 1.3 66.1 + - - +
241C ALA 3.9 0.2 + - - -
259C VAL* 3.5 27.1 - - + -
260C VAL 3.8 8.5 - - - +
261C LEU* 3.4 22.2 - - + -
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Residues in contact with ASP 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ARG* 4.6 6.5 + - - +
149C GLY 5.2 0.8 + - - -
151C TRP* 3.5 19.4 + - - +
205C ARG* 2.5 37.3 + - - -
222C VAL* 5.1 6.8 - - + +
223C VAL 3.2 3.8 - - - +
224C MET* 3.9 4.9 - - - +
239C TYR* 1.3 75.3 - - - +
241C ALA* 1.3 60.3 + - - +
259C VAL* 3.8 0.3 - - - -
260C VAL* 2.8 44.4 + - + +
280C ILE* 3.6 16.7 - - + +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLN 3.7 0.7 - - - +
222C VAL* 3.4 6.5 - - - +
223C VAL* 2.8 36.5 + - - +
225C LEU* 3.8 26.9 - - + -
240C ASP* 1.3 76.1 - - - +
242C GLU* 1.3 61.7 + - - +
257C ALA* 3.9 13.7 - - + -
258C ASN 3.2 16.2 - - - +
259C VAL* 3.8 10.5 - - + -
260C VAL* 4.7 1.8 - - - -
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C GLY* 3.4 30.5 - - - +
221C GLN 3.4 4.5 - - - +
222C VAL* 4.3 14.2 - - + +
241C ALA* 1.3 73.6 - - - +
243C ILE* 1.3 73.2 + - - +
244C SER* 3.4 1.0 + - - -
257C ALA* 3.2 1.7 - - - -
258C ASN* 2.8 57.2 + - + +
260C VAL* 5.4 1.0 - - - +
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Residues in contact with ILE 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C LEU* 3.4 45.5 - - + -
218C GLU 3.9 11.0 - - - +
219C VAL* 3.6 24.2 - - + +
220C GLY* 2.7 29.8 + - - -
221C GLN* 2.9 17.0 + - + +
223C VAL* 4.3 24.0 - - + -
225C LEU* 5.0 1.6 - - + -
242C GLU* 1.3 74.2 - - - +
244C SER* 1.3 60.7 - - - +
245C ARG 4.2 1.3 - - - +
246C LYS* 4.4 5.2 - - + -
255C LEU* 4.0 21.1 - - + -
256C TYR 3.9 6.3 - - - +
257C ALA* 3.7 11.2 - - + -
277C VAL* 5.0 0.2 - - + -
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Residues in contact with SER 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C VAL* 3.5 18.3 - - - +
242C GLU* 3.4 2.8 + - - -
243C ILE* 1.3 74.8 - - - +
245C ARG* 1.3 62.6 + - - +
256C TYR* 2.8 30.3 + - - +
257C ALA* 3.6 5.0 + - - -
258C ASN* 4.1 22.1 + - - -
268C ASP* 3.9 14.2 + - - -
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C VAL* 3.6 7.6 - - - +
243C ILE* 4.2 0.2 - - - +
244C SER* 1.3 83.2 + - - +
246C LYS* 1.3 78.5 + - - +
247C ARG* 5.5 9.2 - - + +
255C LEU* 4.3 0.5 - - - +
256C TYR* 2.9 73.4 + - + +
268C ASP* 3.3 33.1 + - - -
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C TRP* 2.8 59.1 + - + +
215C GLN* 4.6 4.9 + - - +
217C LEU* 2.6 38.5 + - + +
219C VAL* 4.3 14.4 - - + +
243C ILE* 4.4 6.1 - - + -
245C ARG* 1.3 86.8 - - - +
247C ARG* 1.3 62.7 + - - +
254C GLU 3.3 4.5 - - - -
255C LEU* 4.2 13.0 - - + -
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C TRP* 4.4 1.8 - - - -
245C ARG* 5.5 10.8 - - + +
246C LYS* 1.3 76.4 - - - +
248C GLU* 1.3 62.1 + - - +
249C THR* 3.5 23.0 - - + +
252C ALA 3.8 1.9 - - - +
254C GLU* 2.8 81.9 + - + +
256C TYR* 4.9 4.5 - - + -
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C TRP* 3.4 29.9 + - + -
247C ARG* 1.3 76.2 - - - +
249C THR* 1.3 74.9 + - - +
252C ALA 3.6 2.5 - - - -
253C ARG* 4.1 18.2 - - + +
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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