Contacts of the helix formed by residues 367 - 377 (chain B) in PDB entry 4LEY
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 PHE 367 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B TRP* 3.5 44.6 - + + -
319B PRO* 5.8 0.2 - - + -
322B THR* 3.8 23.6 - - + -
345B PHE* 4.3 11.2 - - + -
365B LEU* 4.0 30.3 - - + -
366B SER* 1.3 82.3 + - - +
368B SER* 1.3 64.0 + - - +
369B HIS* 3.2 15.7 - + + -
370B THR* 3.2 2.8 + - - -
371B GLU* 3.0 31.8 + - - +
467B HIS* 4.3 7.9 - + - -
469B PHE* 3.6 48.5 - + + -
470B ILE* 4.3 10.3 - - + -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 3.6 33.5 + - - +
198B GLY 5.3 1.1 - - - -
202B GLU* 4.6 1.9 - - - +
215B MET* 4.0 12.7 - - - -
366B SER* 3.4 14.3 + - - -
367B PHE* 1.3 78.0 + - - +
369B HIS* 1.3 58.3 + - - +
371B GLU* 3.8 15.3 + - - +
372B LYS* 2.9 29.5 + - - +
424B LYS* 5.7 0.7 - - - +
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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
----------------------------------------------------------
195B LEU* 3.8 29.9 - - + +
197B THR* 4.4 1.2 - - - +
215B MET* 5.3 0.6 - - - -
318B TRP* 4.2 4.8 - - - -
343B GLU* 4.4 17.5 - - + +
344B PRO* 2.9 23.4 + - + -
345B PHE* 4.6 0.4 - - - -
346B TYR* 3.4 37.4 - + - +
366B SER 4.0 2.2 - - - -
367B PHE* 3.6 24.9 - + - -
368B SER* 1.3 78.6 + - - +
370B THR* 1.3 77.7 + - - -
372B LYS* 3.3 8.7 - - - +
373B TYR* 3.0 26.2 + - - +
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B TRP* 3.6 13.9 - - + -
326B LEU* 4.5 4.3 - - + -
340B LEU* 3.9 36.6 + - + +
367B PHE* 3.2 8.1 + - - +
369B HIS* 1.3 96.6 + - - +
371B GLU* 1.3 60.6 + - - +
373B TYR* 3.2 6.9 + - - +
374B ILE* 2.9 37.6 + - + +
469B PHE* 3.7 27.6 - - + -
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 3.8 2.2 - - - -
367B PHE* 3.0 26.9 + - - +
368B SER* 3.8 11.9 + - - +
370B THR* 1.3 72.8 - - - +
372B LYS* 1.3 60.6 + - - +
374B ILE* 3.3 7.4 + - - +
375B LEU* 2.9 35.7 + - - +
421B TYR* 2.7 39.9 + - - -
424B LYS* 2.8 30.8 + - - +
428B PHE* 3.7 23.1 - - + -
469B PHE* 3.8 15.2 - - + -
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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
----------------------------------------------------------
195B LEU* 4.3 15.6 - - + +
196B ASN* 2.6 39.4 + - - +
197B THR* 4.6 5.8 - - + -
201B TYR* 4.1 24.5 - - + +
202B GLU* 3.7 17.8 + - + +
368B SER 2.9 17.7 + - - +
369B HIS* 3.3 6.5 - - - +
371B GLU* 1.3 77.9 - - - +
373B TYR* 1.3 64.0 + - - +
375B LEU* 3.3 1.7 + - - +
376B ASN* 3.0 41.2 + - - +
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Residues in contact with TYR 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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332B LEU* 5.7 1.8 - - + -
336B VAL* 4.1 29.5 - - + +
340B LEU* 3.6 32.8 - - + -
369B HIS 3.0 13.9 + - - +
370B THR* 3.2 7.4 + - - +
372B LYS* 1.3 76.1 - - - +
374B ILE* 1.3 54.6 + - + +
376B ASN* 3.2 1.5 + - - -
377B ASN* 2.7 80.3 + - + +
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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
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326B LEU* 3.9 28.3 - - + -
328B ILE* 4.8 1.3 - - + -
331B TRP* 3.7 28.7 - - + -
332B LEU* 4.2 17.0 - - + -
340B LEU* 4.7 6.7 - - + -
370B THR* 2.9 29.3 + - + +
371B GLU* 3.7 7.4 - - - +
372B LYS 3.3 0.2 - - - -
373B TYR* 1.3 74.9 - - + +
375B LEU* 1.3 67.9 + - - +
377B ASN 3.1 23.6 + - - -
378B HIS* 3.2 7.3 + - - +
428B PHE* 4.3 20.2 - - + -
431B TRP* 4.7 3.1 - - + -
468B TYR* 4.6 10.3 - - + -
469B PHE* 4.5 8.3 - - + -
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Residues in contact with LEU 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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202B GLU* 3.8 30.7 - - + +
204B VAL* 4.0 11.9 - - + -
371B GLU 2.9 25.0 + - - +
372B LYS 3.7 3.8 - - - +
374B ILE* 1.3 76.5 - - - +
376B ASN* 1.3 59.6 + - - +
378B HIS* 3.0 23.2 + - - +
395B LYS* 3.1 35.6 - - + -
398B LEU* 4.2 5.8 - - + -
424B LYS* 4.1 12.3 - - - -
428B PHE* 3.7 30.3 - - + -
431B TRP* 3.7 25.1 - - + -
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Residues in contact with ASN 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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201B TYR 3.7 19.6 + - - -
202B GLU* 3.9 4.1 - - - +
203B HIS* 3.5 17.7 + - - -
372B LYS* 3.0 32.0 + - - +
373B TYR* 4.9 0.9 - - - -
375B LEU* 1.3 76.9 - - - +
377B ASN* 1.3 75.0 + - - +
378B HIS* 3.9 4.7 + - - -
395B LYS* 3.4 20.6 + - - +
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Residues in contact with ASN 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.4 24.8 - - - +
373B TYR* 2.7 73.2 + - + +
374B ILE 3.2 5.5 - - - +
376B ASN* 1.3 89.4 + - - +
378B HIS* 1.3 57.7 + - - +
379B GLY 3.6 2.7 - - - -
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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