Contacts of the strand formed by residues 227 - 233 (chain C) in PDB entry 1UHG
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 MET 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C SER* 3.8 0.5 - - - -
222C MET* 2.8 55.7 + - + +
225C GLU* 3.8 23.8 - - + +
226C LYS* 1.3 78.8 - - - +
228C LYS* 1.3 101.6 + - - +
229C ILE* 3.6 15.0 - - + +
244C LEU* 4.8 10.5 - - + -
245C LEU 3.2 19.3 - - - +
246C PRO* 4.0 3.4 - - + -
247C ASP* 3.7 5.3 + - - +
255C LEU* 4.2 18.8 - - + -
267C TRP* 4.2 25.6 - - + -
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Residues in contact with LYS 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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219C VAL* 4.5 10.7 - - + +
220C ALA 3.2 9.2 - - - +
221C SER* 3.7 22.0 - - - +
227C MET* 1.3 88.2 - - - +
229C ILE* 1.3 60.2 + - - +
243C VAL 3.6 1.0 - - - +
244C LEU* 3.7 0.2 - - - -
245C LEU* 2.9 38.2 + - + +
247C ASP* 3.9 13.0 - - - +
278C ILE* 5.6 1.0 - - - +
356C GLU* 4.6 13.2 + - - +
357C GLU 2.6 33.1 + - - -
358C PHE* 3.4 32.9 - - + +
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Residues in contact with ILE 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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219C VAL* 3.1 9.2 - - - +
220C ALA* 2.9 59.2 + - + +
222C MET* 5.0 0.4 - - + -
227C MET* 3.9 14.4 - - + -
228C LYS* 1.3 75.1 - - - +
230C LEU* 1.3 68.0 + - - +
242C LEU* 3.6 18.8 - - + -
243C VAL 2.9 41.7 - - - +
244C LEU* 3.7 11.4 - - + -
267C TRP* 4.1 13.0 - - + +
268C THR* 4.7 8.3 - - + -
273C MET* 3.9 19.5 - - + -
358C PHE* 3.9 2.0 - - - -
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Residues in contact with LEU 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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217C PHE* 3.6 16.4 - - + -
218C ARG 3.8 1.1 - - - -
219C VAL* 3.5 13.0 - - + -
229C ILE* 1.3 78.8 - - - +
231C GLU* 1.3 62.7 + - - +
232C LEU* 3.5 30.1 - - + -
241C MET 3.6 0.9 - - - +
242C LEU* 3.3 3.6 - - - -
243C VAL* 2.8 36.5 + - + +
278C ILE* 3.5 27.8 - - + -
280C VAL* 3.6 18.6 - - + -
282C LEU* 5.6 1.6 - - + -
358C PHE* 3.4 42.4 - - + -
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Residues in contact with GLU 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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217C PHE* 3.8 8.3 - - - -
218C ARG* 3.1 46.6 + - + +
230C LEU* 1.3 73.7 - - - +
232C LEU* 1.3 70.0 + - - +
233C PRO* 3.7 12.3 - - + +
240C SER* 2.9 33.2 + - - +
241C MET 3.3 2.9 - - - +
242C LEU* 3.6 18.2 - - + +
273C MET* 3.9 15.7 - - + +
369C LYS* 3.6 18.7 + - - -
371C ILE* 5.3 2.9 - - - +
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Residues in contact with LEU 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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184C TRP* 3.5 29.7 - - + -
188C PHE* 4.4 13.9 - - + -
217C PHE* 3.3 37.2 - - + -
230C LEU* 3.5 31.2 - - + +
231C GLU* 1.3 72.6 - - - +
233C PRO* 1.3 68.4 - - + +
240C SER* 3.4 2.0 - - - -
241C MET* 2.8 39.8 + - + +
243C VAL* 5.3 5.6 - - + -
280C VAL* 4.7 3.4 - - + -
282C LEU* 3.6 32.1 - - + -
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Residues in contact with PRO 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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184C TRP* 3.7 7.9 - - - +
185C GLU* 3.1 31.6 + - + +
186C LYS* 4.7 4.2 + - + +
217C PHE* 4.5 14.4 - - + -
231C GLU* 3.7 13.7 - - + +
232C LEU* 1.3 84.7 - - + +
234C PHE* 1.3 64.9 + - - +
237C GLY* 6.4 1.1 - - - -
239C MET 4.8 1.1 - - - +
240C SER* 4.0 12.6 - - - -
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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