Contacts of the strand formed by residues 227 - 239 (chain C) in PDB entry 5CQD
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 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C LEU* 3.4 3.8 - - - -
224C ASP* 3.0 40.8 + - - +
225C ASN 3.5 3.9 + - - +
226C GLY* 1.3 77.7 - - - +
228C SER* 1.3 62.6 + - - +
229C VAL* 6.4 0.4 - - - -
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Residues in contact with SER 228 (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 GLU* 3.2 24.0 + - - -
222C ARG 3.5 4.7 - - - -
223C LEU* 3.2 20.0 - - - +
226C GLY 4.1 2.1 + - - -
227C THR* 1.3 79.5 - - - +
229C VAL* 1.3 66.5 + - - +
230C LYS 4.1 1.2 + - - -
274C ARG* 3.4 13.0 + - - -
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Residues in contact with VAL 229 (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 GLU* 3.4 1.7 - - - -
222C ARG* 2.8 60.2 + - + +
224C ASP* 4.0 22.7 - - + +
227C THR* 6.4 0.4 - - - -
228C SER* 1.3 75.2 - - - +
230C LYS* 1.3 66.0 + - - +
231C MET* 3.8 4.9 + - + +
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Residues in contact with LYS 230 (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 GLU* 2.7 45.3 + - + +
220C VAL 3.6 12.8 - - - +
221C GLU* 3.1 36.8 + - + +
228C SER* 4.1 1.8 + - - -
229C VAL* 1.3 76.3 - - - +
231C MET* 1.3 69.4 + - - +
232C ASP* 3.8 9.9 + - - +
235C MET* 4.7 11.4 - - - -
343C TYR* 3.6 13.7 + - - +
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Residues in contact with MET 231 (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 VAL* 3.1 22.0 + - + +
221C GLU 4.2 2.0 - - - -
222C ARG* 3.9 34.5 - - + +
229C VAL* 4.1 5.6 - - + +
230C LYS* 1.3 76.6 - - - +
232C ASP* 1.3 64.8 + - - +
233C GLN 3.2 1.1 - - - +
234C HIS* 3.1 61.3 + - + +
235C MET* 3.8 10.9 - - - +
265C LEU 5.0 0.2 - - - +
266C GLN 6.0 0.9 - - - +
267C LEU* 4.7 1.1 - - + -
273C TYR* 4.1 19.7 - - + -
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Residues in contact with ASP 232 (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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230C LYS* 4.2 10.0 - - - +
231C MET* 1.3 71.6 - - - +
233C GLN* 1.3 72.6 + - + +
234C HIS 3.3 0.6 + - - -
235C MET* 4.2 23.4 + - - +
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Residues in contact with GLN 233 (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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231C MET* 3.2 1.2 - - + -
232C ASP* 1.3 89.3 + - + +
234C HIS* 1.3 72.0 + - + +
235C MET 3.4 9.7 + - - +
265C LEU* 5.8 0.9 - - - +
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Residues in contact with HIS 234 (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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218C TYR* 3.9 9.9 - - - -
219C GLU* 3.4 3.5 - - - -
220C VAL* 3.2 42.5 + - + +
231C MET* 3.1 49.0 + - + +
233C GLN* 1.3 89.5 - - + +
235C MET* 1.3 61.4 + - - +
264C SER 5.3 0.2 + - - -
265C LEU* 2.8 54.3 + - + -
266C GLN* 5.8 2.9 - - - -
267C LEU* 4.5 4.5 - - + -
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Residues in contact with MET 235 (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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218C TYR* 3.4 16.4 + - - +
219C GLU* 3.8 27.6 - - + +
220C VAL 4.9 0.2 - - - +
230C LYS* 4.7 11.9 - - + -
231C MET 3.8 15.7 - - - +
232C ASP* 4.2 18.5 - - - +
233C GLN 3.4 6.6 + - - +
234C HIS* 1.3 82.4 - - - +
236C GLY* 1.3 58.5 + - - +
343C TYR* 4.3 3.1 - - - +
347C THR* 3.3 34.3 - - + -
348C PHE* 4.1 10.1 - - + -
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Residues in contact with GLY 236 (chain C).
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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191C TYR 6.1 0.2 - - - -
217C CYS* 3.4 3.1 - - - -
218C TYR* 2.8 44.8 + - - +
235C MET* 1.3 77.4 - - - +
237C PHE* 1.3 65.8 + - - -
348C PHE* 3.5 12.3 - - - -
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Residues in contact with PHE 237 (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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191C TYR* 3.0 29.8 - - - -
192C LEU 4.4 0.7 - - - -
193C MET* 3.4 39.7 - - + -
215C TYR* 3.8 32.1 - + - -
216C LEU 3.0 14.4 - - - +
217C CYS* 3.7 17.9 - - - -
218C TYR* 3.8 1.5 - - - -
236C GLY* 1.3 78.7 - - - +
238C LEU* 1.3 77.9 + - - +
348C PHE* 4.3 11.9 - + - -
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Residues in contact with LEU 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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214C THR 3.7 0.3 - - - +
215C TYR* 3.4 6.9 - - - -
216C LEU* 2.7 42.5 + - + +
218C TYR* 4.1 9.4 - - + +
237C PHE* 1.3 86.2 - - - +
239C CYS* 1.3 60.5 + - - +
254C ALA* 3.8 13.8 - - + +
257C ARG* 3.8 30.3 - - + +
258C PHE* 3.4 50.7 - - + +
261C LEU* 4.0 22.2 - - + -
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Residues in contact with CYS 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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213C GLN* 3.7 12.3 - - - +
214C THR 3.1 15.0 - - - +
215C TYR* 3.8 31.0 - - + -
237C PHE* 5.3 0.2 - - - -
238C LEU* 1.3 74.6 - - - +
240C ASN* 1.3 75.2 + - - +
241C GLU* 4.2 14.8 - - - -
254C ALA* 3.7 6.5 - - - +
257C ARG* 2.8 29.1 + - - +
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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