Contacts of the helix formed by residues 350 - 358 (chain A) in PDB entry 4OIV
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 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A LYS* 4.6 11.9 + - - +
348A HIS 3.6 5.9 + - - +
349A SER* 1.3 74.8 + - - +
351A LEU* 1.3 64.0 + - - +
352A LEU 3.3 2.0 - - - -
353A GLU* 3.4 24.9 + - + +
354A GLU* 3.0 42.3 + - + +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LEU 4.7 3.8 - - - +
345A PRO* 5.2 11.0 - - + -
349A SER* 3.0 18.3 + - - +
350A ASP* 1.3 77.3 - - - +
352A LEU* 1.3 64.8 + - - +
354A GLU* 3.2 16.4 + - + +
355A ARG* 2.9 69.4 + - + +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU* 3.4 31.2 - - + -
294A MET* 4.2 19.7 - - + -
339A ILE* 4.3 18.8 - - + +
340A PHE* 4.0 39.3 - - + +
343A LYS* 6.1 2.5 - - - -
344A LEU 5.2 10.1 + - - +
349A SER 4.8 3.8 + - - +
350A ASP 3.3 0.6 - - - -
351A LEU* 1.3 81.5 - - - +
353A GLU* 1.3 63.0 + - - +
355A ARG* 3.3 4.6 + - + +
356A ILE* 2.9 29.1 + - + +
501A XX9 4.4 15.5 - - + -
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A PHE* 3.7 32.8 - - + -
343A LYS* 5.4 3.4 - - - -
350A ASP* 3.4 27.5 + - + +
351A LEU 3.3 0.2 - - - -
352A LEU* 1.3 78.4 - - - +
354A GLU* 1.3 65.6 + - + +
356A ILE* 3.4 2.1 + - - +
357A ARG* 2.7 65.8 + - - +
370A PHE* 4.0 12.9 - - + -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ASP* 3.0 35.3 + - + +
351A LEU* 3.6 22.0 + - + +
353A GLU* 1.3 81.0 - - + +
355A ARG* 1.3 62.2 + - + +
357A ARG* 3.4 8.6 + - - +
358A ASN* 3.1 25.1 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ASN* 2.9 43.1 - - + +
290A ILE* 3.8 42.0 - - - +
291A LEU* 4.1 13.0 - - + -
294A MET* 4.4 11.9 - - - +
351A LEU* 2.9 53.1 + - + +
352A LEU* 3.6 8.5 - - - +
354A GLU* 1.3 76.3 - - - +
356A ILE* 1.3 64.4 + - - +
358A ASN 3.1 13.2 + - - +
359A SER* 3.2 15.1 - - - -
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU* 3.8 25.6 - - + -
340A PHE* 4.2 14.1 - - + -
352A LEU* 2.9 35.0 + - + +
353A GLU 3.7 4.3 - - - +
355A ARG* 1.3 76.7 - - - +
357A ARG* 1.4 57.7 + - - +
358A ASN 3.1 0.2 - - - -
359A SER* 2.9 19.2 + - - +
361A ILE* 4.7 4.6 - - + +
366A ILE* 3.6 32.6 - - + +
370A PHE* 3.6 35.0 - - + -
373A TYR* 4.9 0.7 - - + -
501A XX9 4.0 30.5 - - + -
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Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLU* 2.7 55.6 + - - +
354A GLU* 3.8 7.9 - - - +
355A ARG 3.4 0.2 - - - -
356A ILE* 1.4 72.7 - - - +
358A ASN* 1.3 57.7 + - - +
359A SER 3.7 1.0 + - - -
361A ILE 5.7 0.6 - - - +
363A ASP* 6.0 0.2 + - - -
366A ILE* 4.7 10.3 - - + +
370A PHE* 3.4 32.9 - - + +
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Residues in contact with ASN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A SER* 4.4 6.7 - - - +
284A ALA* 3.3 29.3 - - - +
287A ASN* 3.1 25.5 + - - +
354A GLU 3.1 13.2 + - - +
355A ARG 3.1 6.7 + - - -
357A ARG* 1.3 80.9 - - - +
359A SER* 1.3 56.1 - - - +
360A GLY 3.6 1.6 - - - +
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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