Contacts of the strand formed by residues 379 - 393 (chain B) in PDB entry 1ATT
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 GLU 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B LYS* 4.6 2.2 - - - +
225B LEU* 3.7 17.0 - - + +
226B TRP* 3.0 22.2 + - - -
229B LYS* 4.1 14.0 - - + +
230B PHE 5.3 0.2 - - - +
232B PRO* 3.7 21.5 - - - +
323B ARG* 5.7 0.2 + - - -
377B ASN* 3.3 23.0 + - - +
378B GLU* 1.3 93.4 - - - +
380B GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 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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223B LYS* 3.5 9.5 + - - +
224B GLY 3.3 13.2 - - - -
226B TRP* 3.1 18.4 - - - -
375B GLU 3.7 3.1 - - - +
377B ASN* 2.9 34.9 + - - +
379B GLU* 1.3 74.2 - - - +
381B SER* 1.3 61.9 + - - -
382B GLU* 3.9 0.7 + - - +
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Residues in contact with SER 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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222B PHE* 3.9 9.3 - - - -
223B LYS* 3.6 2.3 + - - -
224B GLY 3.0 30.0 + - - +
226B TRP* 3.1 25.7 - - - -
275B PHE* 3.3 18.0 - - - -
282B MET* 3.3 20.9 - - - +
374B LEU* 4.4 6.1 - - - -
375B GLU 3.1 9.4 - - - -
376B VAL* 3.6 5.4 - - - +
380B GLY* 1.3 71.6 - - - -
382B GLU* 1.3 59.2 + - - +
383B ALA 4.2 0.4 - - - -
413B ILE* 4.7 1.3 - - - -
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 5.4 0.2 - - - +
198B ARG* 2.8 46.9 + - - -
221B TYR* 2.8 30.8 + - + +
222B PHE 3.4 13.7 - - - +
223B LYS* 3.7 19.2 - - + +
373B PHE* 3.3 20.4 - - - -
374B LEU 3.6 0.9 - - - -
375B GLU* 2.8 36.0 + - + +
380B GLY 3.9 1.3 + - - +
381B SER* 1.3 73.9 - - - +
383B ALA* 1.3 60.4 + - - +
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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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78B PHE* 4.0 2.7 - - + -
221B TYR* 3.8 2.5 - - - -
222B PHE* 2.9 32.1 + - + +
373B PHE* 3.1 16.6 - - - +
374B LEU* 4.0 9.0 - - + -
381B SER 4.2 0.6 - - - -
382B GLU* 1.3 75.3 - - - +
384B ALA* 1.3 64.4 + - - +
413B ILE* 3.6 29.6 - - + -
423B PHE* 3.8 15.4 - - + -
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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
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195B THR* 4.1 2.0 - - - -
198B ARG* 3.8 13.2 - - + -
199B ILE* 3.6 24.7 - - + -
220B ILE 3.5 8.5 - - - +
221B TYR* 3.8 21.5 - - + +
372B ALA* 3.5 4.0 - - - +
373B PHE* 3.0 27.8 + - + +
383B ALA* 1.3 75.9 - - - +
385B ALA* 1.3 62.8 + - - +
423B PHE* 3.6 8.6 - - - -
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Residues in contact with ALA 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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80B SER* 3.5 33.9 - - - +
83B SER* 4.4 5.4 - - - -
195B THR* 3.6 7.8 - - - +
199B ILE* 3.8 4.2 - - - +
219B THR* 3.6 3.8 - - - -
220B ILE* 2.7 40.1 + - + +
370B HIS* 4.6 1.6 - - - +
371B LYS 3.8 9.6 - - - +
372B ALA* 5.2 0.7 - - - -
384B ALA* 1.3 76.9 - - - +
386B SER* 1.3 64.3 + - - +
423B PHE* 3.8 5.6 - - + -
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Residues in contact with SER 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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83B SER* 3.3 7.2 - - - -
191B ILE* 3.0 37.1 - - - +
199B ILE* 4.0 15.5 - - - -
202B VAL* 4.4 10.2 - - - +
218B ASN 3.2 12.4 + - - -
370B HIS* 3.2 33.0 - - - -
371B LYS 3.3 6.5 + - - -
385B ALA* 1.3 78.0 - - - +
387B THR* 1.3 66.8 + - - +
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Residues in contact with THR 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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83B SER* 2.7 22.5 + - - -
84B ILE* 3.3 14.5 + - + -
87B ALA* 3.5 31.0 - - + -
88B PHE* 4.5 9.2 - - + -
216B LEU 4.8 0.2 - - - -
217B VAL* 3.5 1.4 - - - +
218B ASN* 3.2 25.6 + - - +
332B VAL* 5.1 2.9 - - + -
369B PHE 3.1 15.5 - - - +
370B HIS* 3.2 15.4 + - - +
386B SER* 1.3 72.9 + - - +
388B VAL* 1.3 68.1 + - - +
389B ILE* 4.0 14.1 - - + -
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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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191B ILE* 4.7 3.8 - - + -
202B VAL* 3.6 37.2 - - + -
203B ILE* 3.9 30.3 - - + -
215B VAL* 3.9 24.9 - - + -
216B LEU 3.6 6.5 - - - -
217B VAL* 3.8 10.1 - - + -
367B ASP 4.0 0.2 - - - +
368B ALA* 3.3 1.7 - - - -
369B PHE* 2.9 40.9 + - + -
386B SER* 4.8 0.4 - - - +
387B THR* 1.3 77.4 - - - +
389B ILE* 1.3 62.9 + - - +
390B SER* 4.1 1.5 + - - +
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Residues in contact with ILE 389 (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 ALA* 3.7 27.6 - - + +
88B PHE* 3.4 36.8 - - + -
91B THR* 4.0 12.6 - - + +
214B LEU 3.7 0.3 - - - +
215B VAL* 3.4 3.4 - - - -
216B LEU* 3.2 35.5 + - + +
365B VAL* 3.9 31.6 - - + -
367B ASP 3.4 3.8 - - - -
368B ALA* 3.7 16.4 - - + -
387B THR* 4.0 6.1 - - + -
388B VAL* 1.3 76.2 - - - +
390B SER* 1.3 61.3 + - - +
391B ILE* 3.5 9.5 + - + -
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Residues in contact with SER 390 (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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203B ILE* 5.6 2.2 - - - -
207B ALA* 4.0 6.4 + - - +
208B ILE* 3.7 29.2 - - - -
212B THR* 3.8 7.4 - - - -
214B LEU 3.6 4.5 - - - -
215B VAL* 4.0 4.9 - - - -
365B VAL* 3.7 1.2 - - - -
366B SER* 2.7 49.1 + - - -
367B ASP* 2.9 21.9 + - - +
369B PHE* 5.2 1.8 - - - -
388B VAL* 4.1 3.3 + - - +
389B ILE* 1.3 70.8 - - - +
391B ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 391 (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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91B THR* 4.6 10.3 - - + -
212B THR* 3.6 3.6 - - - -
213B VAL* 2.9 22.5 + - + -
214B LEU* 2.8 20.5 + - + +
216B LEU* 3.7 28.5 - - + -
352B LEU* 3.7 18.6 - - + -
355B ILE* 3.4 27.8 - - + -
363B LEU* 3.5 34.1 - - + -
364B TYR 3.1 11.9 - - - +
365B VAL* 4.5 3.6 - - + +
389B ILE* 3.5 9.8 + - + -
390B SER* 1.3 75.5 - - - +
392B ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 392 (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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209B ASN* 6.0 1.3 - - - +
211B PHE* 3.7 20.4 - - + +
212B THR* 3.9 15.0 - - + -
213B VAL* 4.0 2.9 - - - +
363B LEU* 3.3 8.2 - - - -
364B TYR* 2.8 46.5 + - + +
366B SER* 4.6 8.3 - - - +
390B SER 3.8 0.2 + - - -
391B ILE* 1.3 73.8 - - - +
393B GLY* 1.3 69.2 + - - +
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Residues in contact with GLY 393 (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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211B PHE* 3.8 10.6 + - - +
213B VAL* 3.8 4.8 - - - +
362B ASP* 3.3 24.9 - - - -
363B LEU* 3.8 7.3 - - - +
364B TYR* 3.0 18.4 + - - -
392B ALA* 1.3 78.7 - - - +
394B ARG* 1.3 60.8 + - - -
395B SER* 3.1 16.5 + - - +
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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