Contacts of the helix formed by residues 240 - 250 (chain C) in PDB entry 3PII
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 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C ALA 3.3 4.5 + - - -
239C VAL* 1.3 76.1 - - - +
241C LYS* 1.3 66.5 + - - +
242C PRO* 3.1 15.6 - - - +
243C ALA* 3.1 20.4 + - - +
244C PHE* 3.0 23.0 + - - +
263C PRO* 5.6 0.2 - - - -
265C GLU* 4.8 9.4 - - - -
267C MET* 4.2 7.9 - - - -
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Residues in contact with LYS 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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240C SER* 1.3 70.9 - - - +
242C PRO* 1.4 65.4 - - + +
244C PHE* 3.9 1.9 - - - +
245C GLN* 3.0 29.8 + - - +
265C GLU* 3.6 34.6 + - - +
266C GLU 3.2 20.0 + - - +
267C MET* 3.2 37.6 + - + +
268C PRO* 5.3 1.3 - - + -
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Residues in contact with PRO 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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240C SER* 3.1 18.8 - - - +
241C LYS* 1.4 93.9 - - + +
243C ALA* 1.3 63.1 + - - +
245C GLN* 3.9 6.0 - - + +
246C SER* 3.0 25.1 + - - -
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Residues in contact with ALA 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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171C TYR* 3.8 17.5 - - + -
236C VAL* 4.2 11.0 - - + -
238C ALA 3.3 20.6 - - - +
240C SER* 3.1 23.2 + - - +
242C PRO* 1.3 80.1 - - - +
244C PHE* 1.3 62.0 + - - +
246C SER* 3.2 4.5 + - - -
247C ALA* 3.1 19.4 + - - +
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Residues in contact with PHE 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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269B ILE* 4.8 0.9 - - + -
236C VAL* 4.6 6.4 - - + +
239C VAL* 4.6 8.1 - - + -
240C SER 3.0 17.0 + - - +
241C LYS 3.9 2.7 - - - +
243C ALA* 1.3 73.1 - - - +
245C GLN* 1.3 74.6 + - + +
246C SER 3.0 0.7 + - - -
247C ALA* 3.1 6.3 + - - -
248C TYR* 2.9 48.4 + + + -
257C CYS* 4.7 5.6 - - - -
259C LEU* 4.1 34.8 - - + -
267C MET* 3.6 28.7 - - + -
268C PRO 5.3 2.2 - - - -
269C ILE* 3.4 34.3 - - + -
270C PRO* 5.4 0.7 - - + -
281C ILE* 4.0 20.0 - - + -
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Residues in contact with GLN 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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266B GLU* 4.5 8.5 - - - +
241C LYS 3.0 20.2 + - - +
242C PRO* 3.5 6.7 + - + +
244C PHE* 1.3 78.9 - - + +
246C SER* 1.3 64.5 + - - +
248C TYR* 3.6 11.3 - - - +
249C ASN* 2.8 55.2 + - - +
268C PRO 5.5 2.7 - - - +
270C PRO* 4.1 23.4 - - - +
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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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171C TYR* 3.1 28.5 + - - -
215C PRO* 4.8 6.2 - - - +
220C ALA* 3.5 21.1 - - - +
221C ALA* 4.3 4.4 + - - +
242C PRO 3.0 14.4 + - - -
243C ALA* 3.5 4.3 - - - -
244C PHE 3.0 0.2 - - - -
245C GLN* 1.3 73.6 - - - +
247C ALA* 1.3 69.8 + - - +
249C ASN* 2.8 17.7 + - - +
250C SER* 3.1 10.6 + - - -
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Residues in contact with ALA 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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171C TYR* 3.2 27.2 + - + -
234C ALA* 3.8 11.4 - - + -
236C VAL* 3.8 25.8 - - + -
243C ALA 3.1 12.3 + - - +
244C PHE 3.7 5.4 - - - +
246C SER* 1.3 71.3 - - - +
248C TYR* 1.3 66.6 + - - +
250C SER* 2.4 25.4 + - - -
251C ILE* 3.1 12.5 + - - +
257C CYS* 4.2 4.7 - - - -
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Residues in contact with TYR 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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244C PHE* 2.9 49.4 + + + +
245C GLN* 3.6 16.2 - - - +
247C ALA* 1.3 73.0 - - - +
249C ASN* 1.3 78.3 + - - +
250C SER 3.3 0.2 + - - -
251C ILE* 3.7 24.7 - - - +
257C CYS* 4.3 3.9 - - + -
270C PRO* 3.6 22.9 - - + +
273C ASP* 3.4 14.9 + - + +
274C THR* 3.0 45.2 + - - -
277C ASN* 5.0 1.7 + - - -
279C ILE* 3.9 34.7 - - + +
281C ILE* 4.3 6.5 - - + -
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Residues in contact with ASN 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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221C ALA* 3.7 17.6 - - + +
245C GLN* 2.8 44.7 + - - +
246C SER* 2.8 10.5 + - - +
248C TYR* 1.3 86.5 - - - +
250C SER* 1.3 59.3 + - - +
251C ILE 4.0 5.3 - - - +
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Residues in contact with SER 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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169C ALA* 4.9 0.2 - - - +
171C TYR* 3.3 8.9 + - - -
221C ALA* 3.6 19.0 - - - +
224C MET* 3.5 32.7 - - - +
230C GLY* 3.4 9.4 - - - -
231C VAL* 3.2 25.4 + - - +
234C ALA* 4.9 0.2 - - - +
246C SER 3.1 7.3 + - - -
247C ALA* 2.4 29.8 + - - -
249C ASN* 1.3 76.1 - - - +
251C ILE* 1.3 66.0 + - - +
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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