Contacts of the helix formed by residues 354 - 359 (chain O) in PDB entry 5C7O
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 VAL 354 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352O GLU 4.6 0.4 - - - +
353O VAL* 1.3 81.9 - - - +
355O SER* 1.3 68.0 + - - +
356O THR* 3.9 0.9 - - - +
357O ASP* 2.9 25.5 + - - +
358O PHE* 3.7 6.1 - - - -
385O TRP* 4.1 7.2 - - - -
269P ARG* 4.0 16.8 - - + -
272P ARG* 3.4 48.9 - - + +
277P ASN* 3.3 24.0 - - - +
278P ILE 3.7 9.6 - - - +
279P ILE* 3.9 23.8 - - + -
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Residues in contact with SER 355 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309O THR* 4.8 2.9 - - - +
311O ASP 5.1 2.1 + - - -
312O VAL* 3.3 33.3 - - - +
354O VAL* 1.3 74.1 - - - +
356O THR* 1.3 65.1 + - - +
358O PHE* 3.0 13.0 + - - +
385O TRP* 3.5 28.8 - - - -
276P GLN 4.0 4.0 + - - -
277P ASN* 3.4 7.6 - - - -
278P ILE* 3.0 39.2 + - - +
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Residues in contact with THR 356 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312O VAL* 5.0 0.4 - - - -
354O VAL* 3.9 0.2 - - - +
355O SER* 1.3 80.4 + - - +
357O ASP* 1.3 62.2 + - - +
358O PHE 3.0 2.3 + - - -
359O LEU* 3.2 40.1 + - + +
272P ARG* 3.7 16.5 + - - -
276P GLN* 3.6 30.5 - - + +
277P ASN* 2.6 27.7 + - - +
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Residues in contact with ASP 357 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353O VAL* 3.4 20.6 - - + +
354O VAL* 2.9 29.3 + - - +
356O THR* 1.3 76.3 - - - +
358O PHE* 1.3 66.5 + - + +
359O LEU 3.5 1.7 - - - +
361O ASP* 5.2 1.9 - - - +
272P ARG* 2.8 44.8 + - - -
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Residues in contact with PHE 358 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312O VAL* 4.0 14.1 - - + -
349O THR* 4.6 3.6 - - + -
353O VAL* 3.6 39.5 - - + -
354O VAL 3.7 10.5 - - - -
355O SER 3.0 9.8 + - - +
357O ASP* 1.3 84.0 - - + +
359O LEU* 1.3 64.4 + - - +
360O GLY 3.1 0.5 + - - -
361O ASP* 3.0 34.2 + - + +
366O ILE* 3.5 45.5 - - + -
385O TRP* 3.3 44.6 - + + -
387O ASP* 3.4 14.7 - - - +
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Residues in contact with LEU 359 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O THR* 3.8 39.3 - - + +
124O HIS* 4.5 3.1 - - + +
310O PRO* 6.4 0.9 - - + -
311O ASP* 3.8 12.3 - - + +
312O VAL* 3.8 21.4 - - + +
356O THR* 3.2 38.3 + - + +
357O ASP 3.5 2.1 - - - +
358O PHE* 1.3 75.5 - - - +
360O GLY* 1.3 60.4 + - - +
361O ASP 3.5 0.3 + - - -
387O ASP* 3.5 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