Contacts of the helix formed by residues 354 - 365 (chain B) in PDB entry 3E88
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 354 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B ASN* 2.7 22.4 + - - +
353B GLN* 1.3 75.1 - - + +
355B HIS* 1.3 62.4 + - - +
356B GLU* 3.4 24.4 + - - +
357B ARG* 3.2 23.9 + - + +
358B LEU* 2.9 26.3 + - - +
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Residues in contact with HIS 355 (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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314B PRO* 3.3 40.1 - - + +
315B GLU* 4.9 5.4 + - - -
352B ASN 4.8 1.3 - - - -
353B GLN 3.5 11.0 + - - -
354B ASP* 1.3 72.2 + - - +
356B GLU* 1.3 58.9 + - + +
358B LEU* 4.0 14.4 - - + -
359B PHE* 2.7 62.6 + + + -
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Residues in contact with GLU 356 (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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354B ASP* 3.4 19.2 + - - +
355B HIS* 1.3 78.0 - - - +
357B ARG* 1.3 71.0 + - + +
359B PHE* 4.2 6.7 - - - +
360B GLU* 3.3 22.2 + - - +
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Residues in contact with ARG 357 (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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352B ASN* 3.5 26.2 - - - +
354B ASP* 3.2 32.5 + - + +
355B HIS 3.2 0.4 - - - -
356B GLU* 1.3 84.5 + - - +
358B LEU* 1.3 58.6 + - - +
360B GLU* 2.9 45.6 + - - +
361B LEU* 3.1 30.4 + - + +
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Residues in contact with LEU 358 (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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314B PRO* 4.1 3.8 - - + -
315B GLU* 3.8 38.8 - - + +
350B PHE* 3.8 34.5 - - + +
351B TYR* 4.0 6.7 - - - -
352B ASN* 3.7 21.9 - - - +
354B ASP 2.9 15.1 + - - +
355B HIS* 3.1 23.1 + - + +
357B ARG* 1.3 74.5 - - - +
359B PHE* 1.3 63.2 + - + +
361B LEU* 3.1 5.4 + - + +
362B ILE* 3.0 40.4 + - + +
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Residues in contact with PHE 359 (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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310B PHE* 4.5 12.1 - + - -
314B PRO* 3.8 24.0 - - + -
317B LEU* 3.6 28.9 - - + -
322B LEU* 3.4 35.7 - - + +
355B HIS* 2.7 50.6 + + + +
356B GLU* 4.3 5.6 - - - +
358B LEU* 1.3 74.7 - - + +
360B GLU* 1.3 64.2 + - - +
362B ILE* 3.6 5.5 + - + -
363B LEU* 3.2 32.2 + - + +
10D PHE* 5.6 1.6 - + - -
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Residues in contact with GLU 360 (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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356B GLU 3.3 15.2 + - - +
357B ARG* 2.9 37.0 + - - +
358B LEU 3.2 0.4 - - - -
359B PHE* 1.3 74.3 - - - +
361B LEU* 1.3 62.3 + - + +
363B LEU* 4.7 3.6 - - - +
364B MET* 2.9 57.8 + - + +
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Residues in contact with LEU 361 (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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350B PHE* 3.5 19.3 - - + -
351B TYR* 3.7 38.4 - - - +
352B ASN* 4.7 4.5 - - + +
357B ARG 3.1 18.0 + - - +
358B LEU* 3.1 10.1 + - - +
360B GLU* 1.3 79.5 - - + +
362B ILE* 1.3 59.0 + - - +
364B MET* 5.2 0.2 - - - -
365B GLU* 2.9 63.6 + - + +
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Residues in contact with ILE 362 (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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314B PRO 3.6 21.8 - - - +
315B GLU 4.4 6.7 - - - +
317B LEU* 3.4 29.2 - - + +
319B PRO* 3.6 32.1 - - + +
322B LEU* 3.8 19.3 - - + -
334B TRP* 3.9 8.9 - - + -
350B PHE* 4.2 21.3 - - + -
358B LEU* 3.0 32.1 + - + +
359B PHE* 4.1 5.8 - - + -
360B GLU 3.4 0.2 - - - -
361B LEU* 1.3 74.3 - - - +
363B LEU* 1.3 55.4 + - - +
387B LYS* 2.7 25.1 + - - -
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Residues in contact with LEU 363 (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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319B PRO* 3.3 35.2 - - + +
322B LEU* 3.7 28.3 - - + +
323B GLU* 3.9 22.0 - - + +
359B PHE* 3.2 22.0 + - + +
360B GLU* 4.0 3.6 - - - +
362B ILE* 1.3 81.9 - - - +
364B MET* 1.3 82.7 + - + +
387B LYS* 3.3 18.2 - - - +
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Residues in contact with MET 364 (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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360B GLU* 2.9 40.2 + - + +
361B LEU* 5.2 0.2 - - - -
363B LEU* 1.3 100.7 - - + +
365B GLU* 1.3 64.6 + - + +
366B GLU* 3.9 1.9 + - - +
387B LYS* 4.2 4.2 - - - -
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Residues in contact with GLU 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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350B PHE* 3.3 14.4 - - + -
361B LEU* 2.9 52.2 + - + +
364B MET* 1.3 74.1 - - + +
366B GLU* 1.3 86.2 + - - +
367B ILE 3.8 0.5 + - - -
387B LYS* 2.8 29.3 + - - -
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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