Contacts of the helix formed by residues 364 - 376 (chain B) in PDB entry 1Y2C
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 SER 364 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B MET* 6.0 0.4 - - - -
362B ASN 4.4 0.5 + - - -
363B ALA* 1.3 76.3 + - - +
365B VAL* 1.3 64.4 + - - +
366B GLU* 3.3 5.6 + - - -
367B LYS* 3.3 38.2 + - - +
368B SER* 2.9 28.8 + - - -
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Residues in contact with VAL 365 (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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333B THR* 3.9 25.8 - - + -
337B MET* 3.9 35.8 - - + +
341B PHE* 4.7 10.5 - - + -
363B ALA* 3.8 5.8 - - + -
364B SER* 1.3 72.8 - - - +
366B GLU* 1.3 69.7 + - - +
368B SER* 3.4 5.6 + - - -
369B GLN* 3.1 28.6 + - - +
406B TYR* 4.9 2.2 - - + -
501B EDO 4.2 14.6 - - - +
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Residues in contact with GLU 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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364B SER* 4.5 2.4 - - - -
365B VAL* 1.3 84.9 + - - +
367B LYS* 1.3 66.6 + - - +
369B GLN* 3.2 4.5 + - - +
370B VAL* 3.1 26.0 + - - +
406B TYR* 3.9 14.3 - - + +
409B THR* 3.2 30.1 - - - +
410B ILE* 4.0 15.9 - - + +
501B EDO 2.8 40.0 + - - +
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Residues in contact with LYS 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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364B SER* 3.3 31.2 + - - +
366B GLU* 1.3 77.5 + - + +
368B SER* 1.3 58.5 + - - +
370B VAL* 3.3 3.9 + - - +
371B GLY* 3.0 24.4 + - - -
410B ILE* 3.7 35.2 - - + -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B MET* 5.7 1.1 - - - -
357B MET* 3.6 43.0 - - - +
364B SER* 2.9 25.1 + - - -
365B VAL* 3.7 6.5 - - - -
367B LYS* 1.3 77.9 - - - +
369B GLN* 1.3 58.8 + - - +
371B GLY* 3.4 1.6 + - - +
372B PHE* 2.9 28.6 + - - +
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Residues in contact with GLN 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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329B TYR* 2.6 37.1 + - - +
333B THR* 3.8 24.1 - - + +
336B ILE* 5.0 1.4 - - - +
337B MET* 5.1 1.0 - - - -
357B MET* 4.1 12.9 - - - +
365B VAL 3.1 17.6 + - - +
366B GLU 3.2 7.8 + - - +
368B SER* 1.3 75.2 + - - +
370B VAL* 1.3 64.7 + - - +
372B PHE* 3.3 11.0 + - - +
373B ILE* 3.0 30.8 + - - +
406B TYR* 4.0 22.4 - - + -
1003B 3DE 2.9 40.0 + - - +
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Residues in contact with VAL 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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366B GLU 3.1 15.4 + - - +
367B LYS* 3.8 8.1 - - - +
369B GLN* 1.3 74.6 - - - +
371B GLY* 1.3 57.3 + - - +
373B ILE* 3.4 7.1 + - - +
374B ASP* 2.8 52.0 + - - +
403B ARG* 3.5 26.0 - - - +
406B TYR* 4.0 6.7 - - + -
407B GLN* 3.6 46.0 - - + +
410B ILE* 4.2 4.0 - - + -
540B EDO 4.1 6.1 - - - +
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Residues in contact with GLY 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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367B LYS 3.0 14.3 + - - -
368B SER* 3.8 3.8 - - - -
369B GLN 3.2 0.2 - - - -
370B VAL* 1.3 75.8 - - - +
372B PHE* 1.3 58.3 + - - +
375B TYR* 2.9 45.5 + - - +
540B EDO 4.0 13.6 + - - -
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Residues in contact with PHE 372 (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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273B MET* 5.3 3.4 - - + -
319B LEU* 4.0 17.5 - - + -
322B PRO* 3.9 17.7 - - + -
357B MET* 5.9 0.4 - - - -
368B SER 2.9 19.4 + - - +
369B GLN* 3.5 17.9 - - - +
371B GLY* 1.3 73.7 - - - +
373B ILE* 1.3 63.0 + - - +
376B ILE* 3.1 35.2 + - + +
377B VAL* 3.1 46.8 + - + -
1003B 3DE 3.5 72.2 - + + +
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Residues in contact with ILE 373 (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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322B PRO* 4.0 22.9 - - + -
329B TYR* 3.4 27.8 - - + +
369B GLN* 3.0 21.2 + - + +
370B VAL* 3.8 4.0 - - - +
372B PHE* 1.3 78.4 - - + +
374B ASP* 1.3 65.3 + - - +
377B VAL* 3.9 5.4 - - - -
378B HIS* 2.8 42.5 + - + +
379B PRO* 3.4 0.7 - - - +
399B LEU* 3.9 18.8 - - + -
402B ASN 4.8 0.2 - - - +
403B ARG* 3.7 49.4 - - + +
406B TYR* 5.3 1.3 - - + -
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Residues in contact with ASP 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 VAL* 2.8 22.1 + - - +
371B GLY 4.0 1.3 - - - +
373B ILE* 1.3 74.9 - - - +
375B TYR* 1.3 61.6 + - + +
378B HIS* 4.8 3.6 - - - +
379B PRO* 3.4 18.4 - - - +
403B ARG* 2.9 48.0 + - - +
540B EDO 2.9 36.9 + - - -
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Residues in contact with TYR 375 (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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276B HIS* 4.7 2.3 + - - -
277B MET* 5.4 4.9 - - - +
371B GLY* 2.9 31.2 + - - +
374B ASP* 1.3 80.1 - - + +
376B ILE* 1.3 75.7 + - + +
379B PRO* 3.7 12.0 - - - +
540B EDO 3.3 38.0 + - - -
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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
----------------------------------------------------------
273B MET* 4.0 16.6 - - + -
276B HIS* 3.7 39.3 + - + -
277B MET* 5.3 4.0 - - + -
319B LEU* 3.8 20.0 - - + -
372B PHE* 3.1 29.8 + - + +
374B ASP 3.7 0.4 - - - -
375B TYR* 1.3 95.5 - - + +
377B VAL* 1.3 67.0 + - - +
378B HIS 3.6 1.1 - - - -
379B PRO* 3.5 2.3 - - - +
380B LEU* 3.3 23.6 + - - +
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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