Contacts of the helix formed by residues 374 - 381 (chain B) in PDB entry 1ASZ
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 ALA 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B PRO 2.9 26.6 + - - +
371B LYS* 3.5 8.2 + - - +
372B ARG 3.6 0.8 + - - -
373B PHE* 1.3 75.7 - - - +
375B HIS* 1.3 65.5 + - - +
377B ILE* 3.4 9.8 + - - +
378B GLU* 3.3 24.0 + - + +
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Residues in contact with HIS 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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134B ALA* 4.8 9.8 + - + -
183B THR* 5.4 9.9 - - + +
372B ARG 5.4 0.2 + - - -
373B PHE 3.2 0.8 - - - -
374B ALA* 1.3 78.9 - - - +
376B GLU* 1.3 82.3 + - - +
378B GLU* 3.0 18.7 + - - +
379B LEU* 3.1 50.2 + - + +
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Residues in contact with GLU 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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246B ALA* 3.2 44.9 - - + +
249B ARG* 3.5 30.0 + - + +
250B ILE* 4.4 3.1 - - + -
372B ARG 4.2 4.3 - - - +
373B PHE* 3.5 43.7 - - + +
375B HIS* 1.3 96.0 - - - +
377B ILE* 1.3 62.9 + - - +
379B LEU* 3.2 11.1 + - - -
380B VAL* 3.3 7.8 - - - +
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Residues in contact with ILE 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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250B ILE* 3.6 23.8 - - + +
369B LEU* 3.8 28.9 - - + +
370B PRO* 4.4 5.6 - - + -
373B PHE* 3.0 16.5 + - + +
374B ALA* 3.5 12.6 - - - +
376B GLU* 1.3 76.2 - - - +
378B GLU* 1.3 60.0 + - - +
380B VAL* 2.7 30.5 + - - +
381B ARG* 3.0 34.9 + - - +
536B TYR* 4.3 19.1 - - + +
537B LEU* 4.7 13.7 - - + -
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Residues in contact with GLU 378 (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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374B ALA 3.3 11.2 + - - +
375B HIS* 3.0 11.8 + - - +
377B ILE* 1.3 80.1 - - + +
379B LEU* 1.3 61.7 + - + +
381B ARG* 3.1 45.7 + - - +
382B LYS* 2.7 59.3 + - - +
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Residues in contact with LEU 379 (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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134B ALA* 3.6 26.0 - - + +
183B THR* 5.2 7.2 - - + -
242B VAL* 3.1 37.5 - - + +
243B THR* 3.3 17.2 - - + +
246B ALA* 4.1 9.0 - - + -
375B HIS* 3.1 63.7 + - + +
376B GLU* 3.6 8.5 - - - +
377B ILE 2.9 1.4 + - - -
378B GLU* 1.3 80.2 - - + +
380B VAL* 1.3 61.8 + - + +
382B LYS* 3.4 17.8 + - - +
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Residues in contact with VAL 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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243B THR* 4.0 16.4 - - - +
246B ALA* 4.2 2.7 - - + +
247B ILE* 3.8 37.7 - - + +
250B ILE* 5.1 0.7 - - + -
376B GLU 3.3 15.7 - - - +
377B ILE* 2.7 9.3 + - - +
379B LEU* 1.3 74.8 - - - +
381B ARG* 1.3 59.2 + - - +
382B LYS 3.1 1.8 - - - -
383B GLN* 3.0 3.5 + - - -
384B TYR* 2.8 56.1 + - + +
537B LEU* 4.6 15.3 - - + +
539B LEU* 4.2 11.9 - - + -
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Residues in contact with ARG 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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377B ILE* 3.0 22.7 + - - +
378B GLU* 3.1 49.8 + - - +
380B VAL* 1.3 76.6 - - - +
382B LYS* 1.3 62.9 + - + +
383B GLN 3.0 5.2 + - - -
384B TYR 3.9 5.8 - - - -
385B PRO* 3.2 28.7 - - + +
386B VAL* 3.4 29.6 + - - +
387B GLU 3.4 6.5 + - - -
388B GLU* 3.2 58.6 + - - +
389B PHE 4.7 0.6 - - - +
475B ARG* 5.5 0.2 - - - +
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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