Contacts of the helix formed by residues 360 - 374 (chain B) in PDB entry 2PY5
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 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B PHE* 3.4 35.2 - + - -
211B PHE* 4.9 0.4 - + - -
258B MET* 3.5 58.4 + - + +
263B LEU* 3.9 8.7 - - + -
358B GLY* 3.2 1.0 - - - -
359B LEU* 1.3 82.1 - - + +
361B LYS* 1.3 66.3 + - - +
362B ASP 3.3 2.2 + - - -
363B PHE* 3.4 5.9 + - + +
364B ILE* 3.0 39.4 + - + +
389B LEU* 3.8 9.0 - - + -
393B PHE* 3.8 25.4 - + - -
429B MET* 3.5 40.6 - - + -
433B ILE* 4.4 1.8 - - + -
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Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 3.0 66.3 + - + +
260B SER* 5.2 1.2 - - - +
357B THR* 4.8 5.4 - - - -
358B GLY* 3.4 38.2 + - - +
359B LEU 3.6 0.6 - - - -
360B PHE* 1.3 76.5 - - - +
362B ASP* 1.3 65.6 + - - +
365B ASP* 2.8 38.7 + - - +
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Residues in contact with ASP 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 3.7 28.7 - - + +
358B GLY 5.2 0.2 + - - -
359B LEU 5.4 0.4 + - - -
360B PHE 3.4 0.4 - - - -
361B LYS* 1.3 81.9 - - - +
363B PHE* 1.3 65.7 + - - +
365B ASP* 3.8 9.9 - - - +
366B LYS* 3.0 25.1 + - - +
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B SER* 3.6 24.9 - - - -
197B GLY 3.9 4.5 - - - -
198B PHE* 3.6 36.6 - + + -
201B ILE* 3.6 18.6 - - + +
360B PHE* 3.4 7.5 + - - +
361B LYS 3.4 0.4 - - - -
362B ASP* 1.3 79.6 - - - +
364B ILE* 1.3 72.4 + - + +
366B LYS* 3.3 1.2 + - - +
367B TRP* 3.2 55.0 + + - +
385B MET* 3.5 38.8 - - + -
386B LEU* 4.4 9.2 - - + -
389B LEU* 3.7 24.7 - - + -
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PRO* 3.4 33.2 - - + +
258B MET* 3.8 23.8 - - + -
259B TYR* 3.6 27.8 - - + +
360B PHE* 3.0 27.6 + - + +
363B PHE* 1.3 79.1 - - + +
365B ASP* 1.3 60.9 + - - +
368B THR* 2.7 49.1 + - - +
386B LEU* 3.9 18.8 - - + -
480B LEU* 4.8 7.4 - - + -
9002B EDO 3.9 7.4 - - - -
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 2.7 30.3 + - - -
361B LYS* 2.8 28.9 + - - +
362B ASP* 3.8 9.9 - - - +
364B ILE* 1.3 76.6 - - - +
366B LYS* 1.3 61.2 + - - +
368B THR* 4.1 0.3 - - - -
369B TYR* 3.0 25.5 + - - +
9002B EDO 2.9 18.6 + - - -
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Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ILE* 4.3 18.6 - - + +
362B ASP 3.0 18.5 + - - +
363B PHE* 3.6 5.6 - - - +
364B ILE 3.3 0.2 - - - -
365B ASP* 1.3 77.0 - - - +
367B TRP* 1.3 94.9 + - + +
369B TYR* 3.4 5.2 + - - +
370B ILE* 3.2 39.5 + - + +
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Residues in contact with TRP 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLN* 4.7 18.2 - - - -
185B LEU* 4.3 19.3 - - + -
197B GLY* 5.7 1.4 - - - -
201B ILE* 5.6 0.2 - - - +
363B PHE* 3.2 44.5 + + - +
366B LYS* 1.3 108.8 - - + +
368B THR* 1.3 60.9 + - - +
370B ILE* 3.4 31.4 + - + +
371B LYS* 2.8 29.3 + - - +
378B ILE* 6.0 0.2 - - + -
381B LEU* 4.8 2.9 - - + -
382B ALA* 3.5 33.4 - - + +
385B MET* 3.6 43.2 - - + +
386B LEU* 3.7 26.4 - - + +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE* 2.7 38.3 + - - +
367B TRP* 1.3 74.5 - - - +
369B TYR* 1.3 58.4 + - - +
371B LYS* 3.2 11.6 + - + +
372B THR* 2.9 48.9 + - + +
386B LEU* 3.9 12.0 - - - +
480B LEU* 6.0 0.2 - - - +
9002B EDO 3.6 25.9 - - - +
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Residues in contact with TYR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B ASP 3.0 20.0 + - - +
366B LYS* 3.5 5.8 - - - +
368B THR* 1.3 76.3 - - - +
370B ILE* 1.3 62.6 + - + +
372B THR* 2.7 20.4 + - - -
373B THR* 2.7 53.4 + - + +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLN* 5.2 5.6 - - - +
366B LYS* 3.2 26.9 + - + +
367B TRP* 3.5 41.7 - - + +
368B THR 3.3 0.2 - - - -
369B TYR* 1.3 84.6 - - + +
371B LYS* 1.3 63.6 + - - +
373B THR* 3.3 6.1 + - - -
374B SER* 2.6 32.5 + - - +
378B ILE* 3.6 29.2 - - + +
382B ALA* 3.8 12.8 - - + -
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Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B SER* 4.0 18.0 + - - -
367B TRP 2.8 21.5 + - - +
368B THR* 3.2 9.8 + - + +
370B ILE* 1.3 73.6 - - - +
372B THR* 1.3 69.2 + - + +
373B THR 3.3 0.3 + - - -
374B SER 3.4 15.6 - - - +
379B LYS* 3.7 32.7 - - + +
382B ALA* 3.6 13.1 - - + +
383B LYS* 3.9 34.1 - - + +
386B LEU* 4.4 14.2 - - + +
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Residues in contact with THR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B THR* 2.9 31.9 + - + +
369B TYR* 2.7 27.4 + - - -
371B LYS* 1.3 81.8 - - + +
373B THR* 1.3 65.3 + - - +
374B SER 3.5 2.4 + - - +
379B LYS* 6.2 0.2 - - - +
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Residues in contact with THR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TYR* 2.7 58.3 + - + +
370B ILE* 3.5 7.4 + - - +
371B LYS 3.2 0.2 - - - -
372B THR* 1.3 84.3 - - - +
374B SER* 1.3 60.7 + - - +
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B ILE* 2.6 27.1 + - - +
371B LYS 3.4 11.3 + - - +
372B THR 3.5 2.1 - - - +
373B THR* 1.3 82.9 + - - +
375B GLU* 1.3 76.3 + - - +
378B ILE* 3.6 22.6 - - - +
379B LYS* 3.7 25.0 + - - +
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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