Contacts of the helix formed by residues 272 - 280 (chain C) in PDB entry 2PWP
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 PRO 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B SER* 6.1 2.0 - - - +
259B TYR* 3.8 41.7 - - + +
264B ASN* 3.8 3.6 - - - +
194C LEU* 4.1 33.9 - - + -
219C ASN* 5.9 1.6 - - + +
270C LYS 4.5 2.2 - - - +
271C LEU* 1.3 91.3 - - + +
273C ALA* 1.3 66.1 - - - +
274C PHE* 3.2 23.3 - - + -
275C LEU* 2.9 18.3 + - + +
276C LEU* 3.2 8.0 + - - +
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Residues in contact with ALA 273 (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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257B LEU* 3.7 14.1 - - + +
258B LYS 3.6 17.9 + - - -
259B TYR 3.1 17.1 + - - +
260B TYR 4.0 9.0 - - - +
261B ASN* 4.4 13.7 - - + +
264B ASN* 4.3 0.4 - - - +
271C LEU 3.6 1.4 + - - -
272C PRO* 1.3 69.8 - - - +
274C PHE* 1.3 64.2 + - - +
275C LEU 3.3 0.2 + - - -
276C LEU* 3.3 8.0 + - - +
277C LYS* 3.2 21.9 + - - +
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Residues in contact with PHE 274 (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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61B PHE* 3.9 23.6 - + - -
258B LYS* 2.8 38.4 + - + +
259B TYR* 5.2 0.2 - + - -
194C LEU* 3.6 39.9 - - + -
195C TRP* 4.3 11.2 - + - -
198C VAL* 4.3 9.9 - - + -
272C PRO* 3.1 18.3 + - + -
273C ALA* 1.3 74.6 - - - +
275C LEU* 1.3 72.2 + - + +
277C LYS* 3.4 11.1 + - - +
278C GLU* 3.1 30.7 + - + +
501C GOL 3.6 41.3 - - - +
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Residues in contact with LEU 275 (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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194C LEU* 3.7 31.4 - - + -
198C VAL* 4.4 31.0 - - + -
201C ILE* 4.7 11.4 - - + -
202C LYS* 6.2 0.2 - - + -
217C TYR* 3.8 23.8 - - + -
271C LEU* 3.8 19.7 - - + -
272C PRO* 2.9 14.7 + - + +
274C PHE* 1.3 90.8 - - + +
276C LEU* 1.3 67.9 + - - +
278C GLU* 3.0 4.8 + - + +
279C ILE* 2.8 39.8 + - + +
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Residues in contact with LEU 276 (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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261B ASN* 3.7 26.9 - - - +
269C PHE 5.7 1.1 - - - +
271C LEU* 4.0 34.3 - - + +
272C PRO 3.2 8.8 + - - +
273C ALA* 3.6 9.4 - - - +
275C LEU* 1.3 77.3 - - - +
277C LYS* 1.3 58.0 + - - +
279C ILE* 3.2 12.9 + - + +
280C GLU* 3.0 31.4 + - - +
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Residues in contact with LYS 277 (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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273C ALA 3.2 9.5 + - - +
274C PHE* 3.5 13.9 - - - +
275C LEU 3.1 0.2 - - - -
276C LEU* 1.3 76.8 - - - +
278C GLU* 1.3 65.6 + - + +
280C GLU* 3.4 19.9 + - + +
281C ASN* 3.6 17.4 + - - +
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Residues in contact with GLU 278 (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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198C VAL* 3.8 31.6 - - + +
202C LYS* 3.0 38.5 + - + -
274C PHE* 3.1 20.6 + - + +
275C LEU* 3.0 11.5 + - + +
277C LYS* 1.3 77.2 - - + +
279C ILE* 1.3 60.6 + - - +
281C ASN* 2.9 33.2 + - - +
282C ILE* 3.9 0.2 - - - +
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Residues in contact with ILE 279 (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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201C ILE* 5.1 2.2 - - + -
202C LYS* 5.5 1.3 - - + -
205C ILE* 3.9 32.5 - - + -
209C LYS* 5.2 4.3 + - - +
217C TYR* 4.6 6.1 - - + -
271C LEU* 4.0 18.8 - - + -
275C LEU* 2.8 42.6 + - + +
276C LEU* 3.2 12.3 + - + +
278C GLU* 1.3 76.8 - - - +
280C GLU* 1.3 62.1 + - + +
281C ASN 3.3 0.7 + - - -
282C ILE* 3.4 31.7 + - + +
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Residues in contact with GLU 280 (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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276C LEU 3.0 15.1 + - - +
277C LYS* 3.5 15.0 - - + +
278C GLU 3.2 0.2 - - - -
279C ILE* 1.3 77.5 - - + +
281C ASN* 1.3 63.4 + - - +
282C ILE* 3.3 5.4 + - - +
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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