Contacts of the strand formed by residues 366 - 375 (chain B) in PDB entry 1ATH
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 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B SER* 2.6 23.4 + - - -
332B LYS* 3.3 11.3 - - - +
344B PHE* 4.4 6.7 - - - -
364B VAL* 3.8 5.0 - - - +
365B SER* 1.3 82.4 + - - +
367B ALA* 1.3 69.1 + - - +
368B PHE* 3.2 35.2 - - + -
389B VAL* 3.4 20.5 + - + +
392B GLY 5.3 0.7 - - - +
394B SER* 3.7 17.9 + - - +
395B LEU 2.9 26.9 + - - +
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Residues in contact with ALA 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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87B PHE* 3.7 33.0 - - + -
330B SER* 3.4 1.7 - - - -
331B LEU* 2.8 41.5 + - + -
332B LYS 4.8 0.4 - - - +
344B PHE* 4.3 8.5 - - + -
366B ASP* 1.3 83.4 + - - +
368B PHE* 1.3 61.3 + - - +
386B THR* 4.8 0.4 - - + -
387B ALA 3.4 9.6 - - - +
388B VAL* 4.3 9.6 - - + +
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Residues in contact with PHE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B VAL* 4.1 21.3 - - + +
202B ILE* 5.2 2.5 - - + -
203B PRO* 3.6 27.6 - - + -
206B ALA* 3.9 18.4 - - + -
329B PHE 3.7 5.2 - - - +
330B SER* 4.0 15.3 - - - -
331B LEU* 3.4 6.1 - - - +
366B ASP* 3.2 50.7 - - + -
367B ALA* 1.3 74.7 - - - +
369B HIS* 1.3 58.4 + - - +
385B SER 3.9 0.2 - - - +
386B THR* 3.3 3.8 - - - -
387B ALA* 2.9 41.4 + - + +
389B VAL* 4.5 10.5 - - + -
395B LEU* 3.7 26.5 - - + -
396B ASN* 4.7 6.7 - - + -
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Residues in contact with HIS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.9 8.3 - - + -
79B SER 3.4 37.2 + - - -
82B SER* 3.6 8.9 + - - -
83B ILE* 3.3 15.9 - - + -
201B VAL* 4.8 2.7 - - - -
328B GLY* 3.0 2.3 - - - -
329B PHE* 2.8 58.4 + + + +
331B LEU* 3.6 13.2 - - + -
368B PHE* 1.3 75.7 - - - +
370B LYS* 1.3 91.8 + - - +
371B ALA* 4.2 0.8 + - - +
384B ALA* 3.9 7.2 - - + +
385B SER 3.2 9.8 + - - -
386B THR* 3.2 24.0 - - - -
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Residues in contact with LYS 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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197B ARG 3.6 6.5 + - - -
198B ILE* 3.4 26.2 - - + +
199B THR* 3.3 28.5 - - - +
200B ASP* 3.1 26.9 + - - +
201B VAL* 4.5 6.9 - - + +
326B GLU* 4.6 16.2 + - - -
327B ASP 3.2 15.5 - - - +
328B GLY* 4.0 7.0 - - - +
369B HIS* 1.3 84.0 + - - +
371B ALA* 1.3 66.3 + - - +
384B ALA* 3.2 2.3 - - - -
385B SER 3.1 28.4 + - - -
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Residues in contact with ALA 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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77B PHE* 3.6 38.6 - - + +
78B LEU* 4.0 12.6 - - - -
198B ILE* 3.7 4.9 - - - +
326B GLU* 3.5 4.7 - - - +
327B ASP 2.8 28.6 + - - +
369B HIS* 4.0 0.4 - - + -
370B LYS* 1.3 77.0 - - - +
372B PHE* 1.3 61.5 + - - +
383B ALA 3.0 13.7 - - - +
384B ALA* 4.0 7.4 - - + -
422B PHE* 5.1 0.2 - - + -
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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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77B PHE* 3.2 11.3 - - - -
197B ARG* 3.5 55.9 - - + -
198B ILE* 4.0 14.4 - - + -
324B ARG* 3.6 44.9 - - + -
325B ILE 3.6 5.4 - - - -
326B GLU* 3.4 31.4 - - + +
371B ALA* 1.3 75.9 - - - +
373B LEU* 1.3 60.1 + - - +
374B GLU* 3.9 14.1 - - + -
381B GLU* 3.9 22.7 - - - -
382B ALA* 3.0 8.8 - - - -
383B ALA 2.8 26.6 + - - +
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Residues in contact with LEU 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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77B PHE* 3.5 34.3 - - + -
281B MET* 4.6 1.1 - - + -
323B PHE* 4.1 16.6 - - + -
324B ARG* 3.3 5.8 - - - +
325B ILE* 2.9 48.8 + - + +
372B PHE* 1.3 76.2 - - - +
374B GLU* 1.3 69.6 + - - +
375B VAL* 4.1 17.7 - - + -
380B SER* 4.2 8.5 - - - -
381B GLU 3.3 11.7 - - - +
382B ALA* 4.5 2.2 - - + -
410B VAL* 4.4 18.2 - - + -
412B ILE* 3.9 24.7 - - + -
426B VAL* 4.9 0.2 - - + -
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Residues in contact with GLU 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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197B ARG* 4.6 3.6 + - - -
323B PHE 3.3 15.0 - - - +
324B ARG* 3.1 37.7 + - + -
372B PHE* 3.9 17.2 - - + -
373B LEU* 1.3 78.1 - - - +
375B VAL* 1.3 66.5 + - - +
376B ASN* 3.7 21.0 + - + +
379B GLY 3.8 0.9 - - - +
380B SER* 3.0 25.4 - - - -
381B GLU* 3.0 23.8 + - + +
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Residues in contact with VAL 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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225B TRP* 3.8 17.0 - - + -
252B MET* 3.9 9.9 - - + -
281B MET* 4.3 15.9 - - + -
320B MET* 3.7 29.8 - - - -
321B PRO 4.1 1.6 - - - +
322B ARG* 3.6 5.0 - - - +
323B PHE* 2.9 61.2 + - + +
373B LEU* 4.1 16.6 - - + -
374B GLU* 1.3 75.6 - - - +
376B ASN* 1.3 67.0 + - - +
379B GLY 3.8 2.7 - - - -
380B SER* 4.0 0.9 - - - -
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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