Contacts of the helix formed by residues 238 - 246 (chain C) in PDB entry 2UZ1
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 ASP 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C VAL* 4.6 1.6 - - - +
211C LEU 3.2 13.5 + - - +
212C GLY* 3.6 14.4 - - - -
213C SER* 4.3 3.6 + - - -
237C ALA* 1.3 77.2 - - - +
239C TYR* 1.3 65.8 + - - +
240C GLU* 3.3 8.6 + - - +
241C GLY 3.0 27.5 + - - -
242C LEU 3.1 7.6 + - - -
256C LEU* 3.8 5.4 - - - +
257C VAL* 4.0 11.7 - - + +
277C GLY 5.2 0.3 - - - +
278C ALA* 4.6 8.8 - - + +
279C ARG 5.3 1.4 + - - -
283C ASN* 3.8 34.1 + - + +
284C THR* 5.4 5.1 - - + +
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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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238C ASP* 1.3 74.3 - - - +
240C GLU* 1.3 63.2 + - - +
242C LEU* 3.2 17.2 + - - +
256C LEU* 3.9 17.9 - - + -
258C GLN* 3.8 26.4 + - - -
283C ASN* 3.6 25.5 - - + +
397C TYR* 3.4 32.8 - + - -
398C LEU* 4.4 7.8 - - - +
401C SER* 4.4 9.2 - - - -
412C PHE* 3.6 33.2 - + + +
414C CYS* 3.8 24.9 - - + +
415C HIS 3.5 23.6 - - - +
552C GLU* 5.5 2.3 + - - +
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Residues in contact with GLU 240 (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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62C ARG* 2.7 43.5 + - - +
91C ASP* 5.2 4.0 - - - +
213C SER* 3.5 34.1 - - - -
216C SER* 3.4 19.7 + - - -
217C ARG* 2.8 35.1 + - - +
238C ASP* 3.2 7.8 + - - +
239C TYR* 1.3 79.6 - - - +
241C GLY* 1.3 60.2 + - - +
242C LEU 3.3 0.4 + - - -
243C SER* 4.7 4.9 + - - -
412C PHE 4.1 9.7 - - - +
413C LEU* 4.2 6.0 - - - +
414C CYS 4.6 1.2 + - - +
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Residues in contact with GLY 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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211C LEU* 4.2 6.9 - - - +
212C GLY 4.1 14.5 - - - -
216C SER* 4.9 2.5 - - - -
237C ALA* 3.3 18.6 - - - +
238C ASP* 3.0 16.2 + - - -
240C GLU* 1.3 76.8 - - - +
242C LEU* 1.3 63.8 + - - +
243C SER 3.3 2.2 - - - -
244C MET* 3.0 25.0 + - - +
245C LEU* 4.0 1.7 + - - +
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Residues in contact with LEU 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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237C ALA* 3.8 6.7 - - + -
238C ASP 3.1 9.8 + - - +
239C TYR 3.2 16.2 + - - +
240C GLU 3.3 0.2 - - - -
241C GLY* 1.3 75.9 - - - +
243C SER* 1.3 57.1 + - - +
245C LEU* 3.0 43.6 + - + +
246C SER* 4.1 2.6 + - - -
253C ARG* 4.5 8.3 + - - +
255C GLY* 4.3 4.5 - - - -
256C LEU* 4.0 29.6 - - + +
404C MET* 3.7 38.1 - - + +
405C SER* 4.8 0.7 - - - -
409C PRO* 4.1 14.3 - - + +
412C PHE* 3.8 24.7 - - + -
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Residues in contact with SER 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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216C SER* 4.5 11.8 + - - -
221C LYS* 4.4 13.6 + - - -
239C TYR 4.8 0.8 + - - -
240C GLU 4.7 4.6 + - - -
241C GLY 3.2 0.2 + - - -
242C LEU* 1.3 77.8 - - - +
244C MET* 1.3 64.4 + - - +
245C LEU 3.1 1.1 - - - -
246C SER* 3.2 25.7 + - - -
247C GLY 4.9 0.3 + - - -
409C PRO* 3.7 12.0 - - - +
410C GLY 3.7 23.1 + - - +
411C GLY* 3.9 14.2 - - - -
412C PHE* 4.1 8.2 + - - +
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Residues in contact with MET 244 (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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211C LEU* 3.7 13.2 - - + -
215C ALA* 3.7 29.2 - - + +
216C SER* 3.8 18.4 - - - +
219C ALA* 3.8 19.5 - - - -
220C ARG 3.9 15.3 - - - +
221C LYS* 3.8 42.0 - - + +
224C LEU* 3.3 41.9 - - + +
241C GLY 3.0 13.5 + - - +
243C SER* 1.3 79.9 + - - +
245C LEU* 1.3 58.1 + - - +
246C SER 3.3 0.4 + - - -
247C GLY 4.8 2.2 + - - -
248C LEU* 4.4 2.4 - - - +
326C ILE* 5.3 4.0 - - + -
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Residues in contact with LEU 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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211C LEU* 3.9 15.7 - - + -
235C VAL* 3.4 51.1 - - + +
236C PHE 4.2 4.0 - - - +
237C ALA* 4.2 10.3 - - + -
241C GLY 4.2 0.2 - - - +
242C LEU* 3.0 22.6 + - + +
244C MET* 1.3 75.5 - - - +
246C SER* 1.3 62.6 + - - +
247C GLY 3.2 2.7 - - - -
248C LEU* 3.1 24.8 + - + +
253C ARG* 2.9 34.1 + - + +
254C GLY 4.9 0.7 - - - +
255C GLY* 3.7 34.8 - - - +
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Residues in contact with SER 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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221C LYS* 5.8 2.5 - - - -
242C LEU 4.4 0.7 + - - -
243C SER* 3.2 17.3 + - - -
244C MET 3.3 0.4 - - - -
245C LEU* 1.3 79.0 - - - +
247C GLY* 1.3 58.5 + - - +
248C LEU 3.4 1.5 + - - +
253C ARG* 4.3 1.4 + - - +
385C ALA* 6.1 3.1 - - - -
408C LYS* 3.2 49.6 - - - +
409C PRO* 2.7 32.1 + - - +
410C GLY* 5.6 0.4 - - - -
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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