Contacts of the helix formed by residues 364 - 377 (chain B) in PDB entry 1ZDT
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 364 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B TYR* 4.0 5.4 - - - -
362B GLN 4.3 1.1 - - - +
363B LEU* 1.3 76.0 - - - +
365B ARG* 1.3 58.7 + - - +
366B GLN* 3.2 15.9 + - - +
367B GLU* 2.9 35.8 + - - +
368B PHE* 3.0 24.1 + - - +
404B TYR* 2.6 20.4 + - - -
409B TYR* 2.5 29.8 + - - +
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Residues in contact with ARG 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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231B LEU* 3.8 24.5 + - + +
234B GLU* 3.2 36.9 + - - +
235B PRO 3.9 10.5 + - - -
236B ASP* 5.3 2.6 - - - +
237B GLU* 5.5 4.8 - - - +
312B TYR* 3.4 25.4 + - - +
316B GLN* 4.0 20.8 - - - +
364B ASP* 1.3 76.5 - - - +
366B GLN* 1.3 63.7 + - - +
368B PHE* 3.5 6.8 - - + +
369B VAL* 3.0 34.4 + - + +
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Residues in contact with GLN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 4.7 6.8 - - + +
227B ILE* 3.9 27.2 - - + +
231B LEU* 3.9 23.7 - - + +
364B ASP* 3.2 13.6 - - - +
365B ARG* 1.3 80.6 + - - +
367B GLU* 1.3 64.1 + - - +
369B VAL* 3.4 6.7 - - - +
370B CYS* 3.2 23.2 + - - +
404B TYR* 3.1 46.4 + - + +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 3.4 16.7 - - + +
364B ASP* 2.9 33.9 + - - +
366B GLN* 1.3 73.6 - - - +
368B PHE* 1.3 67.0 + - - +
370B CYS* 3.2 1.0 + - - +
371B LEU* 2.9 31.8 + - + +
401B LEU* 4.0 13.7 - - + -
404B TYR* 3.6 15.9 - - + -
405B THR* 3.8 5.0 - - + +
409B TYR* 3.1 19.8 - - - -
415B LYS* 2.9 35.1 + - - -
419B LEU* 3.9 19.9 - - + +
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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
----------------------------------------------------------
234B GLU* 3.7 25.1 - - + -
308B PHE* 3.4 36.7 - + - -
309B ASP* 5.0 11.7 - - - -
312B TYR* 3.4 66.0 - + + -
363B LEU* 3.8 8.4 - - + +
364B ASP 3.0 13.2 + - - +
365B ARG* 3.5 11.9 - - + +
366B GLN 3.4 0.2 - - - -
367B GLU* 1.3 77.4 - - - +
369B VAL* 1.3 73.1 + - + +
371B LEU* 3.6 2.1 - - - +
372B LYS* 3.0 41.3 + - + +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ILE* 4.1 8.1 - - + +
230B LEU* 3.6 39.0 - - + +
231B LEU* 4.1 19.7 - - + -
234B GLU* 3.8 37.7 - - + +
279B TRP* 4.9 1.7 - - - +
365B ARG* 3.0 20.9 + - + +
366B GLN* 3.4 13.9 - - - +
368B PHE* 1.3 87.5 - - + +
370B CYS* 1.3 64.4 + - - +
372B LYS* 3.5 8.8 + - - +
373B PHE* 3.3 15.6 + - - +
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Residues in contact with CYS 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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226B LEU* 4.7 5.2 - - - -
227B ILE* 4.1 20.0 - - + -
230B LEU* 3.9 7.2 - - - -
366B GLN 3.2 18.1 + - - +
367B GLU 3.2 3.7 + - - +
368B PHE 3.2 0.6 - - - -
369B VAL* 1.3 79.1 - - - +
371B LEU* 1.3 56.7 + - - +
373B PHE* 3.1 5.9 + - - +
374B ILE* 2.9 30.7 + - - +
397B ALA* 3.4 32.3 - - - -
400B ALA* 4.3 3.1 - - - -
401B LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.7 23.1 - - + -
358B LEU* 5.6 1.3 - - + -
363B LEU* 3.9 23.8 - - + -
367B GLU 2.9 22.0 + - - +
368B PHE 3.6 3.4 - - - +
370B CYS* 1.3 74.8 - - - +
372B LYS* 1.3 62.9 + - - +
374B ILE* 3.4 7.7 + - + +
375B ILE* 3.0 28.4 + - - +
401B LEU* 3.9 24.9 - - + -
419B LEU* 4.2 29.2 - - + +
420B LEU* 4.5 0.9 - - + -
422B CYS* 6.5 0.2 - - + -
423B LEU* 3.4 33.4 - - + +
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Residues in contact with LYS 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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234B GLU* 3.3 26.3 + - - +
235B PRO* 4.5 4.0 - - - +
276B ILE* 4.8 12.7 - - - +
279B TRP* 3.4 53.1 - - + +
305B LEU* 3.6 24.1 - - + +
308B PHE* 3.9 20.5 - - + -
309B ASP* 5.9 3.4 + - + +
368B PHE* 3.0 39.1 + - + +
369B VAL* 3.5 11.0 - - - +
371B LEU* 1.3 74.6 - - - +
373B PHE* 1.3 58.1 + - - +
375B ILE* 3.4 2.2 + - - -
376B LEU* 3.1 25.3 + - - +
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 4.3 18.2 - - + -
230B LEU* 3.5 35.7 - - + -
279B TRP* 4.1 2.7 - - - -
283B CYS* 4.1 14.4 - - + -
284B MET* 3.6 34.1 - - + -
285B VAL* 4.8 2.5 - - + -
369B VAL 3.3 2.3 + - - +
370B CYS 3.1 9.9 + - - +
372B LYS* 1.3 77.9 - - - +
374B ILE* 1.3 64.4 + - - +
376B LEU* 3.3 10.7 + - + +
377B PHE* 3.1 50.1 + + + +
393B ALA* 3.8 26.9 - - + -
396B LYS* 6.0 0.2 - - + -
397B ALA* 3.5 19.3 - - + -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B CYS* 2.9 23.7 + - - +
371B LEU* 3.5 12.6 - - + +
373B PHE* 1.3 73.7 - - - +
375B ILE* 1.3 66.0 + - - +
377B PHE* 3.3 4.2 + - - +
378B SER* 2.9 27.0 + - - -
394B GLN* 5.6 1.1 - - - +
397B ALA* 3.6 38.1 - - + +
398B ASN* 4.4 6.3 - - + +
401B LEU* 4.0 26.0 - - + -
420B LEU* 4.7 9.9 - - + -
423B LEU* 3.8 20.9 - - + -
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Residues in contact with ILE 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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300B ASN* 4.7 0.2 + - - -
301B CYS* 3.6 16.2 - - + +
304B GLU* 3.7 26.7 - - + +
305B LEU* 3.3 23.6 - - + -
308B PHE* 3.9 36.3 - - + -
371B LEU 3.0 19.9 + - - +
372B LYS 3.6 5.8 - - - +
373B PHE 3.3 0.2 - - - -
374B ILE* 1.3 75.2 - - - +
376B LEU* 1.3 63.7 + - - +
378B SER* 2.4 28.2 + - - +
423B LEU* 4.1 25.6 - - + -
426B VAL* 4.7 7.2 - - + -
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Residues in contact with LEU 376 (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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279B TRP* 3.8 27.6 - - + -
280B ALA* 4.2 10.8 - - + -
283B CYS* 4.7 2.2 - - - -
286B PHE* 3.8 35.0 - - + -
297B LEU* 3.7 21.7 - - + +
298B LEU* 4.1 20.2 - - + -
300B ASN* 5.3 1.0 + - - -
301B CYS* 3.9 17.2 - - - +
305B LEU* 4.8 2.5 - - + -
372B LYS 3.1 11.8 + - - +
373B PHE* 3.3 16.4 - - + +
375B ILE* 1.3 82.6 - - - +
377B PHE* 1.3 80.2 + - + +
378B SER 3.6 0.7 + - - -
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Residues in contact with PHE 377 (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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285B VAL* 3.7 13.5 - - + -
286B PHE* 3.5 35.4 - + + -
289B LEU* 4.1 7.0 - - + -
297B LEU* 3.8 23.1 - - + -
373B PHE* 3.1 54.6 + + + +
374B ILE* 3.5 4.0 - - - +
375B ILE 3.2 0.2 - - - -
376B LEU* 1.3 92.3 - - + +
378B SER* 1.3 54.7 + - - +
379B LEU* 2.9 3.4 + - - +
390B VAL* 4.2 20.3 - - + +
393B ALA* 3.8 19.1 - - + +
394B GLN* 2.6 49.6 + - + +
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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