Contacts of the strand formed by residues 379 - 389 (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 GLY 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B LYS* 6.4 0.7 - - - -
223B GLY 3.1 13.7 - - - -
224B LEU* 4.6 1.5 - - - +
225B TRP* 3.4 21.0 + - - -
274B PHE* 4.6 0.4 - - - -
375B VAL* 3.8 0.3 - - - -
376B ASN* 2.9 38.6 + - - +
378B GLU* 1.3 79.5 - - - +
380B SER* 1.3 62.4 + - - -
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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
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221B PHE* 3.9 8.0 - - - -
222B LYS* 3.4 6.3 - - - +
223B GLY 3.0 30.8 + - - +
225B TRP* 4.5 1.2 - - - -
274B PHE* 3.0 29.7 - - - -
281B MET* 3.4 11.1 - - - +
373B LEU* 4.2 13.6 - - - +
374B GLU 3.0 22.2 - - - -
375B VAL* 4.0 5.6 - - - -
376B ASN* 4.4 2.5 - - - +
379B GLY* 1.3 73.5 - - - -
381B GLU* 1.3 58.5 + - - +
412B ILE* 4.7 0.2 - - - +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 4.6 6.1 - - - +
197B ARG* 2.9 45.5 + - + +
220B TYR* 3.0 42.1 + - + +
221B PHE 3.4 5.4 - - - +
222B LYS* 4.0 21.3 + - + +
372B PHE* 3.9 8.8 - - + -
373B LEU* 3.3 3.5 - - - +
374B GLU* 3.0 40.1 + - - +
376B ASN* 6.1 0.4 - - - +
380B SER* 1.3 75.0 - - - +
382B ALA* 1.3 62.8 + - - +
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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
----------------------------------------------------------
77B PHE* 4.5 1.3 - - + -
220B TYR* 3.5 3.7 - - - -
221B PHE* 2.9 41.1 + - + +
372B PHE* 3.0 17.3 - - - +
373B LEU* 4.3 12.8 - - + -
381B GLU* 1.3 75.8 - - - +
383B ALA* 1.3 62.8 + - - +
412B ILE* 4.8 1.3 - - + -
422B PHE* 3.5 33.6 - - + -
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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
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194B THR* 4.0 17.3 - - - -
197B ARG* 4.0 15.5 - - + -
198B ILE* 3.7 20.4 - - + -
219B ILE 3.5 7.4 - - - +
220B TYR* 4.0 8.5 - - + -
371B ALA* 3.0 5.0 - - - +
372B PHE* 2.8 32.5 + - + +
382B ALA* 1.3 75.5 - - - +
384B ALA* 1.3 63.4 + - - +
422B PHE* 3.5 4.3 - - - -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 3.6 31.9 - - - +
82B SER* 4.1 4.7 + - - +
194B THR* 4.4 0.9 - - - +
198B ILE* 3.8 5.3 - - - +
218B THR* 3.3 2.6 + - - -
219B ILE* 3.1 33.4 + - + +
369B HIS* 3.9 8.7 - - + +
370B LYS 3.2 13.2 - - - +
371B ALA* 4.0 3.4 - - + -
383B ALA* 1.3 78.7 - - - +
385B SER* 1.3 67.8 + - - +
422B PHE* 4.0 3.4 - - + -
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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
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82B SER* 3.5 2.9 - - - -
190B VAL* 3.3 27.0 - - - +
194B THR* 4.2 1.2 - - - +
198B ILE* 4.0 6.1 - - - +
201B VAL* 4.2 17.9 - - - +
216B VAL* 5.4 0.7 - - - -
217B ASN 3.1 12.6 - - - -
218B THR* 3.1 17.8 + - - -
369B HIS* 3.2 10.3 - - - -
370B LYS 3.1 27.5 + - - -
384B ALA* 1.3 76.2 - - - +
386B THR* 1.3 65.6 + - - +
387B ALA* 4.2 0.4 - - - -
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Residues in contact with THR 386 (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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82B SER* 2.6 24.0 + - - -
83B ILE* 3.2 18.3 + - + -
86B ALA* 3.7 25.8 - - + +
87B PHE* 4.2 12.8 - - + -
215B LEU 4.0 0.2 - - - +
216B VAL* 3.3 4.3 - - - +
217B ASN* 2.9 30.3 + - - +
331B LEU* 4.0 18.8 - - + -
368B PHE 3.3 9.9 - - - +
369B HIS* 3.2 11.7 - - + -
385B SER* 1.3 73.1 - - - +
387B ALA* 1.3 63.4 + - - +
388B VAL* 4.1 4.3 - - + -
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Residues in contact with ALA 387 (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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201B VAL* 4.3 11.9 - - + -
202B ILE* 4.0 27.4 - - + -
214B VAL* 4.5 1.1 - - + -
215B LEU 3.3 6.1 - - - +
216B VAL* 3.7 17.3 - - + -
367B ALA* 3.4 2.6 - - - -
368B PHE* 2.9 40.2 + - + +
386B THR* 1.3 76.6 - - - +
388B VAL* 1.3 62.4 + - - +
389B VAL* 3.9 3.2 + - + -
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Residues in contact with VAL 388 (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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86B ALA* 4.3 14.4 - - + -
87B PHE* 3.9 34.5 - - + -
90B THR* 3.8 24.7 - - + +
214B VAL* 3.1 4.5 - - - +
215B LEU* 2.8 49.5 + - + +
364B VAL* 3.7 37.9 - - + -
367B ALA* 4.3 5.4 - - + +
386B THR* 4.7 0.9 - - + -
387B ALA* 1.3 73.4 - - - +
389B VAL* 1.3 62.2 + - - +
390B ILE* 4.7 0.2 - - + -
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.6 17.7 - - + -
206B ALA* 4.2 13.0 - - + +
207B ILE* 4.6 2.9 - - + -
211B THR* 4.5 10.8 - - + -
213B LEU 3.9 3.6 - - - -
214B VAL* 3.7 23.3 - - + -
364B VAL* 3.6 6.6 - - - +
365B SER* 2.9 37.9 + - - +
366B ASP 3.4 17.1 + - - +
368B PHE* 4.5 15.5 - - + -
387B ALA 4.7 2.2 - - - +
388B VAL* 1.3 73.8 - - - +
390B ILE* 1.3 61.9 + - - +
392B GLY* 3.9 18.6 - - - +
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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