Contacts of the helix formed by residues 246 - 258 (chain C) in PDB entry 3UYS
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 SER 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C CYS* 6.3 0.4 - - - -
244C TYR 3.1 6.2 + - - -
245C PRO* 1.3 68.6 - - - +
247C GLU* 1.3 75.5 + - - -
248C PHE 3.3 0.4 - - - -
249C ALA* 3.1 12.6 + - - +
250C THR* 3.0 28.6 + - - -
279C ARG* 5.5 1.0 + - - -
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Residues in contact with GLU 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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245C PRO* 2.7 14.9 + - - +
246C SER* 1.3 89.2 + - - +
248C PHE* 1.3 52.2 + - + +
250C THR* 3.2 8.0 + - - -
251C TYR* 2.8 35.2 + - - +
272C LEU* 3.6 38.4 - - + +
273C PHE* 3.9 20.0 - - + -
276C LEU* 3.8 24.8 - - + +
279C ARG* 3.1 30.1 + - - -
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Residues in contact with PHE 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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102C LEU* 3.8 28.5 - - + -
105C VAL* 4.1 15.9 - - + -
106C LEU* 4.0 16.6 - - + -
200C GLY 5.9 0.4 - - - +
203C LEU* 4.3 17.3 - - + -
204C MET* 3.8 20.4 - - + -
207C ASN* 3.5 30.7 - - - -
241C CYS* 4.1 4.5 - - + -
244C TYR* 4.4 3.4 - - + -
245C PRO* 3.2 40.1 + - + +
247C GLU* 1.3 75.4 - - - +
249C ALA* 1.3 58.6 + - - +
251C TYR* 3.5 7.2 + - - +
252C LEU* 3.0 32.6 + - - +
273C PHE* 3.5 24.0 - + - -
276C LEU* 4.3 4.3 - - + -
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Residues in contact with ALA 249 (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 ILE* 3.6 28.7 - - + +
238C GLU* 4.9 5.2 - - + -
241C CYS* 3.7 19.5 - - + +
246C SER* 3.1 12.5 + - - +
248C PHE* 1.3 76.3 - - - +
250C THR* 1.3 61.3 + - - +
252C LEU 3.4 0.3 + - - -
253C ASN* 2.8 39.4 + - - +
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Residues in contact with THR 250 (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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246C SER* 3.0 20.8 + - - -
247C GLU* 3.4 12.5 - - - -
249C ALA* 1.3 76.5 - - - +
251C TYR* 1.3 60.2 + - - +
253C ASN* 3.1 7.5 + - - +
254C PHE* 2.8 29.7 + - + +
268C TYR* 3.7 24.7 - - + +
272C LEU* 3.9 16.6 - - + -
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Residues in contact with TYR 251 (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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113C ILE* 4.3 10.3 - - + -
196C LEU* 2.5 43.8 + - + +
197C GLU* 4.8 0.7 - - - -
199C LEU* 3.6 18.6 - - + +
200C GLY* 3.4 25.8 - - - -
203C LEU* 4.9 2.9 - - + -
247C GLU 2.8 20.0 + - - +
248C PHE* 3.6 6.3 - - - +
250C THR* 1.3 73.5 - - - +
252C LEU* 1.3 66.7 + - - +
254C PHE* 3.2 3.3 + - - +
255C CYS* 3.1 35.1 + - - -
269C LEU* 3.9 36.1 - - + +
272C LEU* 4.1 10.1 - - + +
273C PHE* 3.5 34.5 - + + -
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Residues in contact with LEU 252 (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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197C GLU* 4.1 12.1 - - + +
200C GLY* 3.8 33.2 - - - +
201C TYR* 4.0 19.5 - - + -
204C MET* 4.3 8.1 - - + -
237C ILE* 3.5 21.1 - - + -
240C LEU* 3.6 31.2 - - + -
241C CYS* 3.9 18.8 - - - -
248C PHE 3.0 16.6 + - - +
249C ALA 3.8 2.9 - - - +
251C TYR* 1.3 79.5 - - + +
253C ASN* 1.3 61.3 + - - +
255C CYS* 3.5 4.3 + - - +
256C ARG* 3.2 27.9 + - + +
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Residues in contact with ASN 253 (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 ILE* 3.8 25.7 - - - +
238C GLU 5.8 0.2 - - - +
249C ALA* 2.8 29.5 + - - +
250C THR* 3.5 7.7 - - + +
252C LEU* 1.3 74.2 - - - +
254C PHE* 1.3 65.4 + - - +
256C ARG* 3.3 6.5 + - - +
257C SER* 3.0 25.1 + - - -
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Residues in contact with PHE 254 (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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250C THR* 2.8 14.1 + - + +
251C TYR* 3.2 9.6 + - - +
253C ASN* 1.3 76.9 - - - +
255C CYS* 1.3 63.1 + - - +
257C SER* 3.0 22.4 + - - -
258C LEU* 3.2 35.8 + - + +
264C PRO* 5.0 0.2 - - + -
265C ASP* 4.0 33.0 - - + -
268C TYR* 3.4 33.4 - + + -
269C LEU* 3.9 24.7 - - + -
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Residues in contact with CYS 255 (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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193C ARG* 4.3 9.7 - - - +
196C LEU* 3.7 25.6 - - - -
197C GLU* 4.1 24.5 - - + +
251C TYR* 3.1 42.9 + - - +
252C LEU* 3.9 4.9 - - - +
253C ASN 3.3 0.2 - - - -
254C PHE* 1.3 80.1 - - - +
256C ARG* 1.3 63.0 + - - +
257C SER 3.0 1.1 + - - -
258C LEU* 3.3 32.3 + - + +
269C LEU* 4.6 9.2 - - - -
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Residues in contact with ARG 256 (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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182C ILE* 3.7 40.5 - - + +
183C ASN* 3.3 39.5 + - - +
186C LEU* 5.7 2.2 - - - +
193C ARG* 5.7 0.2 + - - -
197C GLU* 3.6 29.8 + - + +
201C TYR* 5.4 1.1 - - - +
237C ILE* 4.4 12.8 - - + -
252C LEU* 3.2 20.1 + - + +
253C ASN* 3.7 9.2 - - - +
254C PHE 3.2 0.4 - - - -
255C CYS* 1.3 75.4 - - - +
257C SER* 1.3 60.3 + - - +
258C LEU 4.4 2.7 - - - +
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Residues in contact with SER 257 (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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253C ASN 3.0 13.9 + - - -
254C PHE* 3.0 12.8 + - - -
255C CYS 3.0 0.4 - - - -
256C ARG* 1.3 80.2 - - - +
258C LEU* 1.3 71.0 + - - +
259C ARG* 3.4 7.1 + - - +
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Residues in contact with LEU 258 (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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193C ARG* 2.8 51.8 + - + -
196C LEU* 4.6 1.8 - - + -
254C PHE* 3.6 32.8 - - + +
255C CYS* 3.3 33.3 + - + +
256C ARG 4.4 3.1 - - - +
257C SER* 1.3 84.2 - - - +
259C ARG* 1.3 61.1 + - - +
262C ASP* 3.9 22.2 - - + +
263C LYS 4.8 1.6 - - - +
264C PRO* 4.1 27.1 - - + -
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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