Contacts of the helix formed by residues 374 - 385 (chain B) in PDB entry 1YA8
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 ASP 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B LEU* 1.3 77.3 - - - +
375B GLN* 1.3 55.1 + - - +
376B LYS* 2.7 43.3 + - - +
377B THR* 2.5 32.5 + - - -
378B ALA* 2.9 19.7 + - - +
404B LEU* 5.4 0.4 - - - -
410B THR* 5.4 3.6 - - + -
413B LYS* 4.0 9.4 - - - +
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Residues in contact with GLN 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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374B ASP* 1.3 72.0 + - - +
376B LYS* 1.3 58.8 + - + +
378B ALA* 3.8 4.8 - - - +
379B MET* 3.0 44.8 + - + +
400B THR* 3.3 30.2 + - - +
401B GLU* 4.1 14.1 + - - +
404B LEU* 2.8 39.0 - - - +
405B GLY* 3.9 4.3 + - - -
413B LYS* 3.8 14.0 + - - +
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASP* 2.7 23.9 + - - +
375B GLN* 1.3 73.3 - - + +
377B THR* 1.3 65.8 + - - +
378B ALA 3.0 0.7 - - - -
379B MET* 2.7 27.8 + - + +
380B SER* 3.0 10.4 + - - -
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Residues in contact with THR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.4 26.9 - - + -
374B ASP* 2.5 27.7 + - - -
376B LYS* 1.3 72.9 - - - +
378B ALA* 1.3 51.5 + - - +
380B SER* 2.7 13.4 + - - -
381B LEU* 2.5 48.3 + - + +
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Residues in contact with ALA 378 (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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373B LEU* 4.0 14.9 - - + +
374B ASP 2.9 16.1 + - - +
375B GLN 3.8 2.2 - - - +
377B THR* 1.3 77.5 - - - +
379B MET* 1.3 56.2 + - - +
381B LEU* 4.7 0.9 - - - -
382B LEU* 3.0 34.5 + - - +
400B THR* 3.5 14.1 - - + -
404B LEU* 3.2 35.7 - - + -
417B PHE* 3.9 7.5 - - + -
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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
----------------------------------------------------------
375B GLN* 3.0 34.3 - - + +
376B LYS* 2.7 21.9 + - + +
378B ALA* 1.3 75.7 - - - +
380B SER* 1.3 57.9 + - - +
382B LEU 4.3 0.4 - - - -
383B TRP* 3.5 14.0 + - - +
393B LYS* 4.7 4.5 + - - -
396B ILE* 3.2 27.7 - - + +
397B PRO* 4.0 31.4 - - - -
400B THR* 3.3 22.4 - - - +
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS 3.0 9.2 + - - -
377B THR* 2.7 17.0 + - - -
379B MET* 1.3 78.9 - - - +
381B LEU* 1.3 63.9 + - - -
382B LEU 3.3 0.2 - - - -
383B TRP* 3.4 4.5 + - - +
384B LYS* 3.1 55.3 + - - +
393B LYS* 5.7 2.0 - - - +
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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
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306B LEU* 5.8 1.3 - - + -
308B LEU* 5.0 7.0 - - + -
366B TYR* 3.5 26.2 - - + +
367B PRO* 3.8 42.8 - - + +
368B LEU* 4.0 12.3 - - + -
373B LEU* 4.5 16.2 - - + -
377B THR* 2.5 24.8 + - + +
378B ALA* 4.0 0.4 - - - +
380B SER* 1.3 71.1 - - - +
382B LEU* 1.3 57.7 + - - +
384B LYS* 3.4 8.5 + - + -
385B SER* 2.7 38.2 + - - +
417B PHE* 3.7 25.4 - - + -
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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
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378B ALA 3.0 17.4 + - - +
379B MET 4.6 0.7 - - - +
381B LEU* 1.3 78.6 - - - +
383B TRP* 1.3 62.7 + - - +
385B SER* 3.1 17.1 + - - -
386B TYR* 3.4 5.5 + - - -
389B VAL* 3.4 33.1 - - + +
391B ILE* 3.8 18.6 - - + +
396B ILE* 3.9 26.7 - - + +
399B ALA* 4.3 7.2 - - + -
400B THR* 4.2 17.3 - - + +
417B PHE* 3.7 16.5 - - + -
420B LEU* 3.7 30.5 - - + -
421B ILE* 4.6 3.1 - - + -
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Residues in contact with TRP 383 (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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312B PRO* 3.2 38.8 - - + +
313B ARG* 4.1 34.8 - - - -
379B MET 3.5 18.0 + - - +
380B SER* 3.4 6.2 + - - +
381B LEU 3.3 0.4 - - - -
382B LEU* 1.3 78.8 - - - +
384B LYS* 1.3 61.0 + - + +
386B TYR* 2.9 49.9 + + - +
391B ILE 3.0 28.7 - - - -
392B ALA* 3.9 1.6 - - - -
393B LYS* 3.0 63.6 - - + +
396B ILE* 3.6 10.5 - - + +
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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
----------------------------------------------------------
306B LEU* 4.3 10.6 - - + +
307B ASP 4.8 5.7 - - - +
308B LEU* 3.8 47.4 + - + +
309B GLN* 6.1 0.2 - - - +
310B GLY 6.0 1.1 - - - +
312B PRO* 4.1 17.5 - - + +
380B SER* 3.1 37.2 + - - +
381B LEU* 3.8 8.5 - - + +
383B TRP* 1.3 75.8 - - + +
385B SER* 1.3 57.3 + - - +
386B TYR 2.9 5.8 - - - -
387B PRO* 3.0 21.2 - - - +
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 4.4 7.1 - - - +
366B TYR* 2.5 40.6 + - - -
381B LEU* 2.7 19.1 + - - +
382B LEU* 3.3 15.5 - - - -
383B TRP 3.0 0.8 - - - -
384B LYS* 1.3 73.6 - - - +
386B TYR* 1.3 56.5 + - - +
387B PRO* 3.2 6.1 - - - -
388B LEU* 2.9 25.8 + - - +
389B VAL* 3.0 18.5 + - - +
421B ILE* 4.9 4.7 - - - -
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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