Contacts of the helix formed by residues 373 - 391 (chain B) in PDB entry 1YY4
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 ILE 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B 4NA 3.8 28.3 - - + -
295B MET* 3.2 33.2 - - + -
298B LEU* 3.8 8.1 - - + -
367B GLY* 3.1 28.7 - - - +
370B VAL* 3.5 24.7 + - + -
372B GLY* 1.3 76.3 - - - +
374B LEU* 1.3 57.6 + - - +
375B GLU 3.0 2.5 - - - -
376B ILE* 2.8 28.9 + - + +
377B PHE* 2.8 44.9 + - + -
475B HIS* 3.9 4.3 - - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ARG* 3.0 66.4 - - + +
367B GLY 3.4 13.8 + - - +
368B LYS* 3.3 39.5 - - + +
370B VAL 5.7 0.2 - - - +
372B GLY* 5.3 1.8 - - - -
373B ILE* 1.3 83.4 - - - +
375B GLU* 1.3 62.4 + - - +
377B PHE* 3.7 6.3 - - + +
378B ASP* 2.8 36.4 + - - +
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLY* 4.4 13.6 - - - +
373B ILE 3.0 0.6 - - - +
374B LEU* 1.3 78.8 - - - +
376B ILE* 1.3 66.4 + - + +
378B ASP* 3.1 8.4 + - - +
379B MET* 3.1 44.4 + - + +
471B LYS* 3.2 31.2 + - - +
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Residues in contact with ILE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 4NA 2.4 55.4 - - + -
340B MET* 5.3 2.0 - - - -
372B GLY 4.5 2.9 - - - +
373B ILE* 2.8 14.9 + - + +
375B GLU* 1.3 83.2 - - + +
377B PHE* 1.3 68.4 + - + +
378B ASP 3.1 0.2 + - - -
379B MET* 3.3 14.0 - - + +
380B LEU* 3.0 46.4 + - + +
468B ALA* 5.2 5.2 - - + +
471B LYS* 3.5 30.1 - - + +
472B GLY* 3.8 7.2 - - - -
475B HIS* 3.5 14.1 - - + +
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Residues in contact with PHE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 4NA 5.6 1.6 - + - -
294B MET* 4.5 5.4 - - + -
298B LEU* 4.3 5.4 - - + -
354B LEU* 3.5 20.8 - - + +
356B PHE* 3.9 15.7 - + - -
362B LEU* 3.6 41.7 - - + -
363B ASP 4.6 9.4 - - - -
364B ARG* 4.7 9.9 - - - +
367B GLY* 4.3 17.0 - - - -
373B ILE* 2.8 60.3 + - + +
374B LEU* 3.7 11.4 - - + +
375B GLU 3.4 0.2 - - - -
376B ILE* 1.3 79.5 - - + +
378B ASP* 1.3 58.1 + - - +
380B LEU* 3.5 4.4 - - + +
381B LEU* 2.8 39.9 + - + +
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Residues in contact with ASP 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ARG* 3.0 48.9 + - - +
374B LEU* 2.8 27.5 + - - +
375B GLU* 3.5 6.8 + - - +
376B ILE 3.1 0.2 - - - -
377B PHE* 1.3 72.8 - - - +
379B MET* 1.3 60.7 + - - +
380B LEU 3.0 1.6 - - - -
381B LEU* 3.2 7.6 + - - +
382B ALA* 2.8 29.4 + - - +
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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
----------------------------------------------------------
410A MET* 5.1 24.9 - - + +
375B GLU* 3.1 36.9 + - + +
376B ILE* 3.3 19.1 - - - +
378B ASP* 1.3 78.7 - - - +
380B LEU* 1.3 59.8 + - - +
382B ALA* 3.7 8.5 - - - +
383B THR* 2.9 31.4 + - - +
464B HIS 6.1 0.4 - - - +
467B HIS* 4.5 22.9 - - + +
468B ALA* 3.8 37.0 - - + +
471B LYS* 4.7 12.6 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 4NA 4.9 7.4 - - + -
340B MET* 3.8 36.1 - - + -
343B LEU* 3.8 24.5 - - + -
344B MET* 4.1 14.1 - - + +
354B LEU* 4.1 17.3 - - + -
356B PHE* 4.8 5.2 - - + -
376B ILE* 3.0 42.9 + - + +
377B PHE* 3.5 11.2 - - + +
378B ASP 3.0 0.2 - - - -
379B MET* 1.3 77.1 - - - +
381B LEU* 1.3 58.7 + - - +
383B THR* 3.5 3.9 + - - -
384B THR* 2.7 32.9 + - - -
468B ALA* 4.2 11.4 - - + -
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLY* 3.8 35.9 - - - +
353B LYS 4.1 4.0 - - - +
354B LEU* 3.4 29.2 - - + -
364B ARG* 3.5 37.2 - - + -
377B PHE* 2.8 27.6 + - + +
378B ASP* 3.6 9.6 - - - +
380B LEU* 1.3 74.6 - - - +
382B ALA* 1.3 57.2 + - - +
384B THR* 3.1 10.1 + - - -
385B SER* 2.8 32.7 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A MET 4.1 18.8 - - - +
378B ASP 2.8 16.2 + - - +
379B MET* 3.7 10.5 - - - +
380B LEU 3.2 0.2 - - - -
381B LEU* 1.3 76.0 - - - +
383B THR* 1.3 64.0 + - - +
385B SER* 2.9 18.8 + - - -
386B ARG* 3.0 11.6 + - - +
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Residues in contact with THR 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A MET* 5.7 1.2 - - - -
344B MET* 3.4 20.0 - - + -
379B MET* 2.9 18.0 + - - +
380B LEU* 3.9 0.4 - - - -
382B ALA* 1.3 77.6 - - - +
384B THR* 1.3 62.5 + - - +
386B ARG* 3.1 9.0 + - - +
387B PHE* 2.9 51.9 + - + -
461B LEU* 4.8 8.1 - - + -
464B HIS* 3.8 32.1 + - + +
465B VAL* 4.3 10.5 - - + -
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B MET* 3.5 37.5 - - - +
347B SER* 3.9 15.6 - - - +
348B ILE* 4.0 6.7 - - + -
353B LYS 5.8 0.4 - - - +
354B LEU* 4.9 2.6 - - - +
380B LEU 2.7 20.0 + - - -
381B LEU* 3.2 13.0 - - - -
382B ALA 3.1 0.6 - - - -
383B THR* 1.3 76.3 - - - +
385B SER* 1.3 52.3 + - - +
387B PHE* 2.9 12.2 + - - +
388B ARG* 2.7 56.0 + - - +
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PRO* 5.5 2.6 - - - +
352B GLY 5.8 1.0 + - - -
381B LEU* 2.8 15.8 + - - +
382B ALA* 2.9 11.8 + - - -
384B THR* 1.3 75.1 - - - +
386B ARG* 1.3 53.0 + - - +
388B ARG* 3.1 23.3 + - - +
389B GLU* 2.7 36.5 + - - +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 5.7 2.8 - - - +
430A LEU* 5.6 10.6 - - - +
382B ALA 3.0 10.5 + - - +
383B THR* 3.3 11.2 - - - +
384B THR 3.1 0.2 - - - -
385B SER* 1.3 76.5 - - - +
387B PHE* 1.3 58.7 + - - +
389B GLU* 3.1 25.2 + - - +
390B LEU* 2.8 58.5 + - - +
457B ASN* 3.6 29.7 + - - +
460B MET* 5.4 4.8 - - - +
461B LEU* 3.2 45.3 - - + +
464B HIS* 6.0 0.9 - - - +
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B MET* 3.8 31.6 - - + -
344B MET* 4.0 12.8 - - + +
348B ILE* 3.8 13.9 - - + -
383B THR* 2.9 46.7 + - + -
384B THR* 2.9 10.2 + - - +
386B ARG* 1.3 77.3 - - - +
388B ARG* 1.3 56.3 + - - +
390B LEU* 3.4 3.7 + - - -
391B LYS 2.8 21.8 + - - -
392B LEU* 2.9 51.5 + - + +
400B VAL* 5.2 7.9 - - + -
458B LEU* 4.7 10.8 - - + -
461B LEU* 3.5 32.8 - - + -
462B LEU* 6.0 0.7 - - + -
465B VAL* 4.4 4.3 - - + -
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B SER 3.4 9.5 + - - -
348B ILE* 2.6 43.4 + - + +
349B ASP* 4.6 2.6 - - - +
350B HIS 3.6 0.6 + - - -
351B PRO* 3.2 49.1 - - - +
384B THR* 2.7 21.7 + - - +
385B SER* 3.1 43.7 + - - +
387B PHE* 1.3 69.1 - - - +
389B GLU* 1.3 61.5 + - - +
391B LYS* 2.7 30.5 + - - +
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B SER 2.7 21.2 + - - +
386B ARG* 3.4 28.3 + - - +
388B ARG* 1.3 75.5 - - - +
390B LEU* 1.3 65.5 + - + +
391B LYS* 3.2 9.9 + - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 2.8 53.8 + - - +
387B PHE* 3.8 4.7 - - - +
389B GLU* 1.3 79.6 - - + +
391B LYS* 1.3 62.4 + - - +
392B LEU 4.7 1.3 - - - +
454B ARG* 2.5 39.7 + - + +
457B ASN* 3.9 33.0 - - + +
458B LEU* 4.1 16.4 - - + -
461B LEU* 3.9 15.0 - - + -
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Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE* 6.4 0.4 - - - -
387B PHE 2.8 4.2 + - - -
388B ARG* 2.7 24.9 + - - +
389B GLU 3.5 10.5 - - - +
390B LEU* 1.3 81.8 - - - +
392B LEU* 1.3 65.5 + - - +
393B GLN* 3.5 25.0 + - - +
454B ARG* 3.6 11.1 + - - +
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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