Contacts of the helix formed by residues 371 - 391 (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 THR 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B TRP* 4.0 2.0 - - - +
365B GLN* 3.8 27.8 - - + +
370B TYR* 1.3 76.4 - - - +
372B GLU* 1.3 63.8 + - - +
373B GLU* 3.6 13.2 + - - +
374B SER* 2.8 43.5 + - - -
375B LEU* 3.2 10.3 + - - +
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Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B SER* 4.4 5.6 + - - +
353B LYS* 2.8 34.7 + - - -
359B GLU* 5.8 1.3 - - - +
360B TRP* 3.6 39.6 + - + +
365B GLN* 4.8 1.0 + - - -
371B THR* 1.3 73.8 - - - +
373B GLU* 1.3 65.8 + - - +
375B LEU* 3.0 18.1 + - - +
376B LEU* 3.2 16.2 + - + +
379B MET* 5.4 4.5 - - - +
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B THR* 3.3 10.5 + - - +
372B GLU* 1.3 79.6 - - - +
374B SER* 1.3 62.2 + - - +
375B LEU 3.2 0.7 + - - -
376B LEU* 3.2 26.8 + - + +
377B PRO* 3.6 5.5 - - - +
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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
----------------------------------------------------------
342B GLN* 2.8 25.7 + - - -
370B TYR* 3.6 20.7 - - - +
371B THR* 2.8 42.0 + - - -
373B GLU* 1.3 73.9 - - - +
375B LEU* 1.3 58.3 + - - +
377B PRO* 3.8 9.0 - - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLN* 3.8 25.6 - - + +
345B ALA* 3.8 25.4 - - + +
346B GLY* 3.8 7.9 - - - +
349B SER* 4.1 9.0 - - - +
360B TRP* 3.7 39.9 - - + -
370B TYR* 3.7 24.0 - - + -
371B THR 3.2 12.7 + - - +
372B GLU* 3.0 10.1 + - - +
374B SER* 1.3 74.5 - - - +
376B LEU* 1.3 65.7 + - - +
377B PRO* 3.3 3.1 - - - -
378B VAL* 2.9 8.5 + - - +
379B MET* 2.9 29.1 + - + +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LYS* 6.6 0.2 - - - -
372B GLU* 3.2 13.6 + - + +
373B GLU* 3.4 16.8 - - + +
375B LEU* 1.3 77.4 - - - +
377B PRO* 1.4 70.5 - - + +
379B MET* 3.2 10.7 + - + +
380B GLN* 2.9 47.8 + - - +
425B LEU* 3.8 26.9 - - + -
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Residues in contact with PRO 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PHE* 4.2 18.6 - - + -
342B GLN* 5.8 0.4 - - - +
373B GLU 3.6 10.1 - - - +
374B SER* 3.8 9.4 - - - +
375B LEU 3.6 3.4 - - - -
376B LEU* 1.4 94.1 - - + +
378B VAL* 1.3 60.8 + - + +
380B GLN* 3.6 13.5 + - - +
381B HIS* 3.1 33.2 + - + +
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 4.0 13.2 - - + -
338B PHE* 3.6 42.6 - - + -
342B GLN* 4.0 35.7 - - + +
343B ILE* 4.2 8.7 - - - -
346B GLY* 4.2 7.2 - - - -
375B LEU* 2.9 10.2 + - - +
377B PRO* 1.3 74.4 - - - +
379B MET* 1.3 61.2 + - - +
381B HIS* 3.2 4.9 + - - +
382B LEU* 2.9 45.2 + - + +
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Residues in contact with MET 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLY* 3.5 22.7 - - - +
349B SER* 3.2 21.8 - - - -
350B LEU* 3.3 38.0 - - + +
353B LYS* 3.2 34.1 - - + -
372B GLU* 5.3 5.2 - - - +
375B LEU* 2.9 26.9 + - - +
376B LEU* 3.2 11.9 + - + +
378B VAL* 1.3 77.0 - - - +
380B GLN* 1.3 56.6 + - - +
382B LEU* 3.5 9.9 + - - +
383B ALA* 3.0 28.6 + - - +
425B LEU* 4.3 14.8 - - + +
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Residues in contact with GLN 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 2.9 47.0 + - - +
377B PRO* 3.8 13.4 - - - +
379B MET* 1.3 76.8 - - - +
381B HIS* 1.3 57.4 + - + +
383B ALA* 3.3 2.8 + - - +
384B LYS* 2.9 29.1 + - - +
425B LEU* 3.5 35.9 - - + +
426B ALA* 4.0 1.2 - - - -
428B ALA* 3.1 32.4 + - - +
429B VAL* 3.8 15.9 - - + +
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Residues in contact with HIS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 4.4 0.2 + - - -
334B ASP* 4.4 18.5 + - + -
335B MET* 3.5 26.4 - - + +
337B HIS* 5.8 0.8 - - - -
338B PHE* 3.8 24.6 - + - -
377B PRO* 3.1 22.4 + - + +
378B VAL 3.2 5.9 + - - +
380B GLN* 1.3 75.7 - - + +
382B LEU* 1.3 66.2 + - - +
384B LYS* 3.2 29.8 + - - +
385B ASN* 2.9 29.6 + - - -
429B VAL* 3.6 24.8 - - + +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.3 37.9 - - + +
326B MET* 4.6 0.9 - - - +
328B LEU* 5.0 2.9 - - + +
329B THR* 3.3 23.6 - - + +
335B MET* 4.3 0.7 - - + -
343B ILE* 4.9 0.7 - - + +
346B GLY 3.7 8.3 - - - +
347B ALA* 3.5 36.6 - - + +
350B LEU* 3.7 15.0 - - + -
378B VAL* 2.9 29.9 + - + +
379B MET* 3.5 9.0 - - - +
381B HIS* 1.3 74.7 - - - +
383B ALA* 1.3 62.8 + - - +
385B ASN* 3.0 18.9 + - - +
386B VAL* 3.0 17.8 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 4.2 8.7 - - + +
379B MET 3.0 17.6 + - - +
380B GLN 3.3 4.7 + - - +
382B LEU* 1.3 72.4 - - - +
384B LYS* 1.3 67.4 + - - +
386B VAL* 3.2 11.2 + - - +
387B VAL* 3.0 26.0 + - - +
422B VAL* 3.6 29.1 - - + +
425B LEU* 3.8 15.3 - - + -
426B ALA* 3.7 3.8 - - - +
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Residues in contact with LYS 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 2.7 37.8 + - - -
334B ASP* 4.3 9.5 + - - -
380B GLN 2.9 15.8 + - - +
381B HIS* 3.2 37.0 + - - +
383B ALA* 1.3 74.0 - - - +
385B ASN* 1.3 65.0 + - - +
387B VAL* 3.2 5.7 + - - +
388B MET* 3.0 46.8 + - + +
426B ALA* 3.6 23.2 - - + +
429B VAL* 4.4 13.9 - - + +
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Residues in contact with ASN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 4.3 30.4 + - + +
329B THR* 5.1 1.4 - - - +
331B LEU* 5.9 1.4 - - - +
332B ASP* 2.9 35.3 + - - +
335B MET* 3.8 9.3 - - - -
381B HIS 2.9 25.5 + - - -
382B LEU* 3.0 11.5 + - - +
384B LYS* 1.3 76.9 - - - +
386B VAL* 1.3 60.2 + - - +
388B MET* 3.2 24.6 + - - +
389B VAL* 3.1 28.5 + - + +
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 5.2 3.6 - - + -
325B LEU* 3.6 28.7 - - + -
328B LEU* 4.0 9.4 - - + -
350B LEU* 5.6 2.0 - - + -
382B LEU 3.0 14.5 + - - +
383B ALA* 3.2 11.0 + - - +
385B ASN* 1.3 72.7 - - - +
387B VAL* 1.3 66.4 + - - +
389B VAL* 3.5 6.6 - - + +
390B ASN* 3.0 34.0 + - - +
417B LEU* 3.7 48.0 - - + +
418B ASN* 5.5 0.2 - - - +
422B VAL* 4.1 6.5 - - + -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA 3.0 16.6 + - - +
384B LYS* 3.5 8.5 - - - +
386B VAL* 1.3 75.7 - - - +
388B MET* 1.3 65.5 + - + +
390B ASN* 4.9 1.1 - - - -
391B GLN* 2.9 52.6 + - - +
393B LEU* 4.0 14.8 - - + -
417B LEU 5.9 0.2 - - - +
422B VAL* 4.4 10.1 - - + -
423B GLN* 4.0 26.7 - - - +
426B ALA* 3.7 19.1 - - + -
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 5.1 1.1 - - - +
384B LYS* 3.0 34.5 + - + +
385B ASN* 3.2 41.9 + - - +
387B VAL* 1.3 79.9 - - + +
389B VAL* 1.3 61.2 + - + +
392B GLY* 3.3 2.4 + - - -
393B LEU* 2.9 51.6 + - + +
394B THR* 3.6 22.3 - - + +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 3.6 20.4 - - - +
328B LEU* 4.4 17.7 - - + -
385B ASN* 3.1 16.4 + - + +
386B VAL* 3.5 10.3 - - - +
388B MET* 1.3 76.4 - - + +
390B ASN* 1.3 75.9 + - - +
391B GLN 3.5 0.2 + - - -
392B GLY 3.9 0.9 + - - -
394B THR* 3.7 20.6 - - + -
396B HIS 3.9 14.8 - - - +
397B MET* 3.5 28.5 - - - +
400B LYS* 3.8 20.3 + - + +
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Residues in contact with ASN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 4.5 2.3 + - - -
386B VAL* 3.0 25.1 + - + +
387B VAL* 4.1 2.2 - - - +
389B VAL* 1.3 85.2 - - - +
391B GLN* 1.3 64.9 + - + +
392B GLY 3.6 0.7 + - - -
400B LYS* 3.5 27.2 + - - +
412B SER 4.2 10.6 + - - +
413B THR 6.2 0.2 - - - -
414B LEU 5.0 1.6 + - - -
417B LEU* 3.9 21.2 - - - +
418B ASN* 3.0 34.5 + - - +
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Residues in contact with GLN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 2.9 37.6 + - - +
390B ASN* 1.3 86.3 - - + +
392B GLY* 1.3 61.7 + - - +
393B LEU* 3.3 25.3 + - + +
418B ASN* 5.2 7.1 - - - +
423B GLN* 2.9 35.3 + - - +
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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
------------------------------------------------------------
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