Contacts of the helix formed by residues 274 - 283 (chain P) in PDB entry 1PP9
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 PHE 274 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P PHE* 4.3 3.4 - + - -
124P MET* 3.7 48.9 - - + -
127P ALA* 4.8 0.4 - - + -
128P PHE* 4.5 10.3 - - + -
146P ILE* 4.8 0.4 - - + -
270P PRO* 4.1 7.0 - - + -
271P GLU* 3.0 38.3 + - - +
273P TYR* 1.3 104.8 - + - +
275P LEU* 1.3 65.3 + - - +
276P PHE* 3.4 4.7 - - - -
277P ALA* 3.3 5.9 + - - +
278P TYR* 3.0 21.7 + - - +
3001P SMA 3.6 64.1 - - + +
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Residues in contact with LEU 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269P LYS* 4.7 7.0 - - + -
270P PRO* 3.8 28.5 - - + +
271P GLU 3.5 2.4 + - - +
272P TRP* 3.2 35.5 + - + +
274P PHE* 1.3 79.0 - - - +
276P PHE* 1.3 56.7 + - - +
278P TYR* 3.6 3.2 - - + +
279P ALA* 2.9 30.5 + - - +
335P LEU 3.8 2.9 - - - +
336P THR* 3.7 33.4 - - + +
339P GLY* 3.3 31.6 - - - +
340P GLY* 4.0 8.1 - - - +
3008P JZR 5.7 2.0 - - - +
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Residues in contact with PHE 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P TYR* 3.5 23.1 - + - -
124P MET* 4.6 3.8 - - + -
272P TRP 4.8 0.2 + - - -
273P TYR 3.9 11.9 - - - -
274P PHE* 4.7 0.9 - - - -
275P LEU* 1.3 78.1 - - - +
277P ALA* 1.3 86.1 + - + +
279P ALA* 3.4 3.8 + - - +
280P ILE* 3.2 34.0 + - + +
297P SER* 4.3 11.0 - - - -
298P ILE* 3.7 28.5 - - + -
332P LEU* 3.9 21.1 - - + +
335P LEU* 4.0 23.7 - - + +
336P THR* 3.9 16.6 + - - +
358P TYR* 4.9 1.6 - - - -
3007P PEE 3.6 44.4 - - + -
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Residues in contact with ALA 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274P PHE 3.3 7.5 + - - +
275P LEU 3.3 0.4 - - - -
276P PHE* 1.3 101.2 - - + +
278P TYR* 1.3 60.0 + - - +
280P ILE* 3.3 7.6 + - - +
281P LEU* 3.0 23.6 + - - +
294P LEU* 3.4 34.0 - - + +
297P SER* 4.3 4.9 - - - +
298P ILE* 5.0 2.0 - - + -
3001P SMA 3.9 16.2 - - + -
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Residues in contact with TYR 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E PRO 4.5 1.4 + - - -
160E CYS* 2.9 28.3 + - - -
161E HIS* 3.5 13.7 - + - -
268P ILE 3.9 14.9 + - - -
269P LYS* 5.0 0.7 - - + -
270P PRO* 3.4 32.3 - - + -
274P PHE 3.0 17.2 + - - +
275P LEU* 3.3 3.3 + - + +
277P ALA* 1.3 73.2 - - - +
279P ALA* 1.3 62.2 + - - +
281P LEU* 3.4 1.3 + - - +
282P ARG* 2.8 62.8 + - + +
339P GLY* 3.2 32.5 - - - -
3001P SMA 3.2 43.7 - - + +
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Residues in contact with ALA 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275P LEU 2.9 10.3 + - - +
276P PHE 3.5 5.4 - - - +
278P TYR* 1.3 79.9 - - - +
280P ILE* 1.3 56.4 + - - +
282P ARG* 3.4 8.3 + - - +
283P SER* 2.7 34.4 + - - +
335P LEU* 3.2 39.9 - - + +
338P ILE* 4.4 10.3 - - + +
339P GLY* 3.9 13.7 - - - +
355P SER* 4.4 1.1 - - - -
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Residues in contact with ILE 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276P PHE* 3.2 22.9 + - + +
277P ALA* 3.6 7.6 - - - +
279P ALA* 1.3 72.9 - - - +
281P LEU* 1.3 67.3 + - - +
283P SER* 3.2 15.8 + - - -
284P ILE* 3.9 10.5 - - + +
293P ALA* 3.9 33.4 - - + +
294P LEU* 4.6 0.9 - - - +
297P SER* 3.7 24.7 - - - +
335P LEU* 3.9 20.6 - - + -
355P SER* 3.4 23.0 + - - +
358P TYR* 4.1 17.5 - - + -
359P PHE* 4.2 12.1 - - + -
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Residues in contact with LEU 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E HIS* 4.0 16.4 - - + +
142E LEU* 4.7 4.3 - - + -
161E HIS* 3.6 31.6 - - + +
175E PRO* 5.8 1.3 - - + +
149P LEU* 4.0 25.6 - - + -
277P ALA 3.0 17.2 + - - +
278P TYR 3.9 3.6 - - - +
280P ILE* 1.3 78.0 - - - +
282P ARG* 1.3 65.5 + - - +
283P SER 3.1 1.4 + - - -
284P ILE* 3.3 19.8 + - - +
290P GLY* 3.5 37.9 - - - +
291P VAL* 3.9 6.5 - - + +
294P LEU* 4.1 15.0 - - + -
3001P SMA 4.5 10.1 - - + +
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Residues in contact with ARG 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E PRO 5.5 1.4 + - - -
160E CYS 4.9 0.2 + - - -
161E HIS* 3.7 43.0 - - + +
175E PRO* 5.8 4.3 - - - +
278P TYR* 2.8 57.1 + - + +
279P ALA* 3.7 5.5 - - - +
280P ILE 3.3 0.4 - - - -
281P LEU* 1.3 78.7 - - - +
283P SER* 1.3 59.8 + - - +
284P ILE 3.3 5.2 + - - +
285P PRO* 5.1 0.3 - - - +
338P ILE* 2.9 29.5 + - - +
339P GLY* 3.9 6.1 + - - -
341P GLN 2.9 29.0 + - - -
342P PRO* 4.7 3.4 + - - +
343P VAL* 3.5 40.5 - - + +
347P TYR* 6.2 0.2 - - - +
348P ILE* 6.1 0.3 - - - +
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Residues in contact with SER 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279P ALA 2.7 20.8 + - - -
280P ILE 3.6 7.6 - - - -
281P LEU 3.1 1.4 + - - -
282P ARG* 1.3 77.7 - - - +
284P ILE* 1.3 62.8 + - - +
285P PRO* 3.5 5.6 - - - +
338P ILE* 5.7 0.9 - - - +
348P ILE* 4.9 3.4 + - - -
351P GLY* 3.4 22.7 + - - -
352P GLN* 3.3 44.3 + - - +
355P SER* 3.5 11.3 + - - -
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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