Contacts of the helix formed by residues 339 - 355 (chain B) in PDB entry 4Y72
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 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLU* 3.6 28.0 - - + +
337B HIS 3.5 6.2 - - - +
338B PHE* 1.3 85.1 - - + +
340B PRO* 1.3 72.5 - - + +
341B SER* 3.9 5.6 - - - +
342B GLN* 3.0 33.7 + - + +
343B ILE* 3.1 10.4 + - - +
370B TYR* 4.3 8.1 - - + +
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Residues in contact with PRO 340 (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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181B GLU* 3.4 24.7 - - + +
300B LEU* 3.9 33.4 - - + -
301B PRO* 4.0 19.5 - - + +
304B PHE* 3.9 4.3 - - + -
326B MET* 3.9 2.8 - - - +
338B PHE 3.6 2.6 - - - +
339B PRO* 1.3 81.8 - - + +
341B SER* 1.3 55.3 + - - +
343B ILE* 3.4 11.4 + - + +
344B ALA* 2.9 29.3 + - - +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 5.4 2.0 - - - -
178B ARG* 3.1 12.5 + - - -
181B GLU* 2.6 36.0 + - - -
304B PHE* 3.5 29.1 - - - +
339B PRO* 3.9 0.9 - - - +
340B PRO* 1.3 72.0 - - - +
342B GLN* 1.3 56.4 + - - +
344B ALA* 3.5 2.4 + - - +
345B ALA* 3.0 28.1 + - - +
370B TYR* 2.4 32.4 + - - -
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PHE* 3.4 22.7 - - + -
339B PRO* 3.0 30.1 + - + +
341B SER* 1.3 77.1 + - - +
343B ILE* 1.3 59.8 + - - +
345B ALA 4.4 0.2 - - - +
346B GLY* 2.9 26.2 + - - -
370B TYR* 3.5 37.9 - - + +
374B SER* 2.8 30.9 + - - -
375B LEU* 3.8 10.0 - - + +
377B PRO* 5.7 0.8 - - - +
378B VAL* 4.0 15.2 - - + +
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Residues in contact with ILE 343 (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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326B MET* 3.6 24.0 - - + -
329B THR* 3.8 32.8 - - + +
335B MET* 3.6 31.9 - - + +
338B PHE* 3.6 30.3 - - + +
339B PRO 3.1 17.7 + - - +
340B PRO* 3.8 10.5 - - + +
342B GLN* 1.3 76.4 - - - +
344B ALA* 1.3 57.9 + - - +
346B GLY* 3.4 0.5 + - - -
347B ALA* 2.9 30.1 + - + +
378B VAL* 4.2 7.9 - - + +
382B LEU* 5.2 0.7 - - + -
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE* 3.7 12.6 - - + -
305B LEU* 3.7 33.3 - - - +
308B ALA* 5.8 1.3 - - + -
326B MET* 3.4 23.3 - - + +
340B PRO 2.9 18.4 + - - +
341B SER 3.7 1.6 - - - +
343B ILE* 1.3 77.7 - - - +
345B ALA* 1.3 61.6 + - - +
347B ALA* 3.8 1.9 - - - +
348B PHE* 3.0 23.9 + - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA* 5.8 0.7 - - - -
341B SER 3.0 18.3 + - - +
342B GLN 4.1 0.2 - - - +
343B ILE 3.3 0.2 - - - -
344B ALA* 1.3 75.0 - - - +
346B GLY* 1.3 57.4 + - - +
348B PHE* 3.3 7.4 + - - +
349B SER* 2.9 29.1 + - - -
360B TRP* 4.0 12.5 - - + -
368B LEU* 4.4 15.7 - - + -
370B TYR* 3.9 13.5 - - + -
375B LEU* 3.8 25.4 - - + +
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLN 2.9 17.6 + - - -
343B ILE 3.8 0.4 - - - -
345B ALA* 1.3 73.6 - - - +
347B ALA* 1.3 59.3 + - - +
349B SER* 3.4 0.4 + - - -
350B LEU* 2.9 31.7 + - - +
375B LEU* 3.8 12.2 - - - +
378B VAL* 4.2 7.9 - - - -
379B MET* 3.5 18.8 - - - +
382B LEU* 3.7 7.0 - - - -
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA* 3.6 28.4 - - + +
325B LEU* 3.6 16.3 - - + +
326B MET* 3.7 15.9 - - + +
343B ILE 2.9 18.5 + - - +
344B ALA 3.8 2.7 - - - +
346B GLY* 1.3 74.6 - - - +
348B PHE* 1.3 57.6 + - - +
351B ALA* 3.0 29.8 + - - +
382B LEU* 3.5 15.1 - - + +
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Residues in contact with PHE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.1 9.2 - - + -
308B ALA* 3.8 33.4 - - + -
309B SER* 3.5 26.5 - - - -
312B GLY 6.3 0.4 - - - -
318B GLN* 3.1 40.7 + - + +
322B ALA* 4.2 6.0 - - + +
344B ALA 3.0 17.7 + - - +
345B ALA* 3.4 8.3 - - - +
347B ALA* 1.3 73.6 - - - +
349B SER* 1.3 66.4 + - - +
351B ALA 3.2 1.2 + - - -
352B LEU* 3.0 40.5 + - + +
360B TRP* 4.2 14.4 - + + -
364B LEU* 3.9 22.7 - - + -
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA 2.9 17.1 + - - -
346B GLY 3.7 4.0 - - - -
348B PHE* 1.3 76.2 - - - +
350B LEU* 1.3 62.1 + - - +
352B LEU* 3.4 9.6 + - - +
353B LYS* 3.3 29.5 + - - +
360B TRP* 3.6 29.7 + - - +
372B GLU* 4.4 6.8 + - - +
375B LEU* 4.1 7.9 - - - +
379B MET* 3.2 22.0 - - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.1 17.9 - - + -
346B GLY 2.9 19.1 + - - +
347B ALA 4.0 3.4 - - - +
349B SER* 1.3 74.0 - - - +
351B ALA* 1.3 67.7 + - - +
353B LYS* 3.0 4.0 + - + +
354B ILE* 2.9 45.4 + - + +
379B MET* 3.3 32.5 - - + +
382B LEU* 3.7 30.3 - - + -
383B ALA* 4.2 11.0 - - + +
386B VAL* 5.6 1.3 - - + -
417B LEU* 6.5 0.2 - - + -
421B LEU* 4.4 5.2 - - + -
422B VAL* 5.1 2.5 - - + -
425B LEU* 3.7 19.5 - - + -
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLN* 3.4 33.2 - - - +
321B LEU* 3.9 28.5 - - + -
322B ALA* 4.0 4.3 - - + +
325B LEU* 4.0 1.7 - - + +
347B ALA 3.0 19.4 + - - +
348B PHE 3.2 0.2 + - - -
350B LEU* 1.3 77.7 - - - +
352B LEU* 1.3 62.4 + - - +
354B ILE* 3.2 1.2 + - - +
355B LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLN* 3.5 20.6 + - + +
348B PHE* 3.0 31.9 + - + +
349B SER* 3.4 14.1 - - - +
350B LEU 3.2 0.2 - - - -
351B ALA* 1.3 76.8 - - - +
353B LYS* 1.3 58.5 + - + +
356B ASP* 2.9 7.3 + - - -
357B ASN* 2.8 56.4 + - + +
358B GLY* 3.8 12.9 + - - +
359B GLU* 4.0 18.4 - - - +
360B TRP* 4.6 2.2 - - + -
364B LEU* 3.9 28.3 - - + -
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Residues in contact with LYS 353 (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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349B SER* 3.3 14.3 + - - +
350B LEU 3.0 6.1 + - - +
352B LEU* 1.3 75.9 - - - +
354B ILE* 1.3 65.3 + - - +
356B ASP* 3.4 12.3 + - - +
358B GLY 4.6 10.1 - - - +
359B GLU* 5.5 9.7 - - - +
360B TRP 5.5 0.2 - - - +
372B GLU* 2.8 28.2 + - - -
376B LEU* 6.6 0.2 - - - -
379B MET* 3.2 34.5 - - + -
421B LEU* 4.1 39.3 - - + +
425B LEU* 5.0 2.7 - - + -
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 3.8 24.5 - - + -
325B LEU* 5.3 1.1 - - + -
350B LEU* 2.9 42.0 + - + +
351B ALA 3.7 5.2 - - - +
353B LYS* 1.3 78.4 - - - +
355B LEU* 1.3 63.2 + - + +
356B ASP* 3.3 1.6 + - - +
414B LEU* 4.9 1.6 - - + -
416B GLN* 3.5 46.4 - - + +
417B LEU* 4.1 17.3 - - + +
419B SER* 4.7 2.5 - - - +
421B LEU* 4.6 5.2 - - + -
422B VAL* 3.2 34.5 - - + -
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLU* 3.8 33.7 - - + +
318B GLN* 3.7 35.2 - - - +
321B LEU* 3.7 19.5 - - + -
351B ALA 3.0 9.4 + - - +
354B ILE* 1.3 77.2 - - + +
356B ASP* 1.3 71.3 + - - +
357B ASN* 3.3 26.5 + - - +
414B LEU* 3.8 26.7 - - + -
416B GLN* 4.2 16.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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