Contacts of the helix formed by residues 286 - 300 (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 ASN 286 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E ARG* 5.6 0.7 - - - +
141E HIS* 5.2 0.9 + - - -
175E PRO* 3.8 7.8 - - - +
284P ILE* 2.8 22.4 + - + +
285P PRO* 1.3 77.7 + - + +
287P LYS* 1.3 67.3 + - - +
288P LEU* 3.4 9.2 + - - +
289P GLY* 2.8 27.4 + - - +
290P GLY* 3.0 19.4 + - - -
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Residues in contact with LYS 287 (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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140E THR 3.3 9.9 + - - -
141E HIS* 2.7 45.3 + - + +
142E LEU* 4.6 4.7 - - + -
175E PRO 3.2 18.4 + - - +
177E PRO* 3.9 29.7 - - + +
148P ASN* 5.9 0.2 - - - -
151P SER* 2.8 41.9 + - - -
152P ALA* 4.3 10.3 - - + +
286P ASN* 1.3 76.9 - - - +
288P LEU* 1.3 67.8 + - + +
290P GLY* 3.2 0.7 + - - -
291P VAL* 3.2 26.8 + - + +
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Residues in contact with LEU 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P ALA* 3.8 35.0 - - + +
154P PRO* 5.5 9.9 - - + -
286P ASN* 3.4 6.9 + - - +
287P LYS* 1.3 82.4 - - + +
289P GLY* 1.3 58.2 + - - +
291P VAL* 3.3 2.6 + - + +
292P LEU* 2.9 56.6 + - + +
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Residues in contact with GLY 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284P ILE* 3.8 15.9 - - - +
286P ASN* 2.8 23.2 + - - -
287P LYS 3.2 0.2 - - - -
288P LEU* 1.3 73.9 - - - +
290P GLY* 1.3 57.2 + - - +
292P LEU* 3.5 7.8 + - - +
293P ALA* 3.0 28.8 + - - +
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Residues in contact with GLY 290 (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* 6.2 0.4 - - - -
281P LEU* 3.5 34.0 - - - +
284P ILE* 3.9 10.7 - - - +
286P ASN 3.0 15.6 + - - -
287P LYS 3.8 3.1 - - - -
289P GLY* 1.3 73.6 - - - +
291P VAL* 1.3 59.6 + - - +
293P ALA* 3.4 2.1 + - - +
294P LEU* 2.9 30.0 + - - +
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Residues in contact with VAL 291 (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* 5.6 0.9 - - - +
142E LEU* 5.1 5.8 - - + -
149P LEU* 3.9 44.9 - - + +
152P ALA* 3.9 22.9 - - + -
281P LEU* 4.1 9.0 - - + -
287P LYS* 3.2 19.1 + - + +
288P LEU* 3.7 8.3 - - + +
290P GLY* 1.3 76.6 - - - +
292P LEU* 1.3 59.3 + - + +
294P LEU* 3.3 6.0 + - + +
295P ALA* 3.0 30.0 + - + +
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Residues in contact with LEU 292 (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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288P LEU* 2.9 48.8 + - + +
289P GLY* 3.8 7.0 - - - +
291P VAL* 1.3 77.3 - - + +
293P ALA* 1.3 60.0 + - - +
295P ALA* 3.4 7.6 + - + +
296P PHE* 2.8 32.7 + - - +
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Residues in contact with ALA 293 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280P ILE* 3.9 14.4 - - + -
284P ILE* 3.3 35.4 - - + -
289P GLY 3.0 9.2 + - - +
290P GLY 3.7 3.1 - - - +
292P LEU* 1.3 76.0 - - - +
294P LEU* 1.3 57.3 + - - +
296P PHE* 3.7 5.5 - - - -
297P SER* 2.8 30.7 + - - -
359P PHE* 3.7 12.9 - - + -
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Residues in contact with LEU 294 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P LEU* 3.7 37.5 - - + -
277P ALA* 3.4 41.5 - - + +
280P ILE* 4.6 5.3 - - - +
281P LEU* 4.1 7.4 - - + -
290P GLY 2.9 17.2 + - - +
291P VAL* 3.4 6.7 - - + +
292P LEU 3.2 0.2 - - - -
293P ALA* 1.3 76.7 - - - +
295P ALA* 1.3 64.3 + - - +
297P SER* 2.7 24.3 + - - -
298P ILE* 3.6 5.8 + - + +
3001P SMA 3.8 45.1 - - + +
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Residues in contact with ALA 295 (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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291P VAL* 3.0 18.3 + - + +
292P LEU* 3.7 10.5 - - + +
294P LEU* 1.3 77.4 - - - +
296P PHE* 1.3 58.6 + - - +
298P ILE* 3.3 7.2 + - - +
299P LEU* 2.9 44.4 + - + +
3001P SMA 5.6 3.6 - - - -
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Residues in contact with PHE 296 (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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292P LEU 2.8 18.4 + - - +
293P ALA* 3.9 5.4 - - - +
295P ALA* 1.3 73.5 - - - +
297P SER* 1.3 64.1 + - - +
298P ILE 3.0 2.2 - - - -
299P LEU* 4.3 9.2 - - + +
300P ILE* 2.9 65.4 + - + +
303P LEU* 4.0 25.6 - - + -
359P PHE* 3.4 24.0 - + + -
363P LEU* 4.2 15.0 - - + -
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Residues in contact with SER 297 (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* 4.3 7.2 - - - -
277P ALA* 4.3 6.6 - - - +
280P ILE* 3.7 28.7 - - - -
293P ALA 2.8 15.8 + - - -
294P LEU* 2.7 20.3 + - - -
296P PHE* 1.3 77.2 - - - +
298P ILE* 1.3 71.7 + - - +
300P ILE* 3.6 4.3 - - - +
301P LEU* 5.2 0.5 - - - +
358P TYR* 2.7 28.8 + - - -
359P PHE* 3.9 12.3 - - - -
3007P PEE 4.7 3.3 - - - +
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Residues in contact with ILE 298 (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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117P VAL* 4.6 4.5 - - + +
120P LEU* 4.2 19.7 - - + -
121P LEU* 3.6 33.2 - - + -
124P MET* 3.7 25.4 - - + -
276P PHE* 3.7 22.9 - - + -
277P ALA* 5.0 3.6 - - + -
294P LEU* 3.9 7.6 - - + +
295P ALA* 3.3 5.1 + - - +
296P PHE 3.0 0.2 - - - -
297P SER* 1.3 89.4 - - - +
299P LEU* 1.3 65.5 + - - +
300P ILE 3.1 1.6 - - - -
301P LEU* 3.1 28.0 + - + +
3001P SMA 4.1 20.0 - - - -
3007P PEE 4.8 4.5 - - + -
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Residues in contact with LEU 299 (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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117P VAL* 4.8 9.0 - - + -
121P LEU* 4.1 26.5 - - + -
295P ALA* 2.9 36.3 + - + +
296P PHE* 4.4 9.4 - - + +
298P ILE* 1.3 71.9 - - + +
300P ILE* 1.3 56.3 + - - +
301P LEU 3.0 6.1 - - - -
302P ALA* 2.9 32.4 + - + +
303P LEU* 4.0 3.1 + - - +
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Residues in contact with ILE 300 (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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296P PHE* 2.9 47.9 + - + +
297P SER* 3.6 16.8 - - - +
299P LEU* 1.3 75.6 - - - +
301P LEU* 1.3 64.3 + - + +
302P ALA 3.0 0.2 - - - -
303P LEU* 2.8 28.0 + - + +
304P ILE* 3.4 7.6 + - + +
358P TYR* 4.0 10.8 - - + +
359P PHE* 3.8 20.9 - - + -
362P ILE* 3.8 32.1 - - + -
363P LEU* 3.8 29.4 - - + -
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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