Contacts of the helix formed by residues 350 - 355 (chain A) in PDB entry 5T0H
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 GLY 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLY 2.8 25.1 - - - +
179A GLY* 4.7 7.4 - - - -
180A CYS* 6.3 1.1 - - - -
347A ASP* 4.0 13.8 - - - +
349A GLU* 1.3 77.2 - - - +
351A ARG* 1.3 55.8 + - - +
352A THR 3.1 0.4 - - - -
353A HIS* 2.9 17.4 + - - -
354A ILE* 2.9 18.9 + - - +
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Residues in contact with ARG 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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346A PRO* 3.4 18.6 - - + +
347A ASP 2.6 45.5 + - - +
348A LEU* 3.4 21.3 + - - +
349A GLU 2.8 2.5 + - - +
350A GLY* 1.3 76.6 - - - +
352A THR* 1.3 51.1 + - - +
354A ILE* 3.2 11.6 + - + +
355A PHE* 2.5 50.3 + - + -
374A ALA* 4.4 11.4 + - + -
377A CYS* 3.0 31.1 + - - -
378A PRO* 3.7 3.6 - - - +
379A ASN* 3.0 27.9 - - - +
380A SER* 3.0 24.7 + - - +
381A THR 4.9 3.4 - - - +
385A ILE* 4.2 13.7 - - + -
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Residues in contact with THR 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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349A GLU* 2.6 29.6 + - + +
351A ARG* 1.3 74.0 - - - +
353A HIS* 1.3 73.3 + - + +
355A PHE* 3.2 9.8 - - - +
356A LYS* 2.6 43.5 + - + +
370A PHE* 3.7 27.6 - - - +
371A GLU 5.2 0.3 + - - -
374A ALA* 5.0 10.1 - - - +
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Residues in contact with HIS 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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177A VAL 5.0 2.7 - - - +
178A GLY* 3.2 25.3 - - - +
179A GLY* 3.5 20.2 + - - +
349A GLU* 4.5 5.8 - - + -
350A GLY* 2.9 19.2 + - - -
352A THR* 1.3 93.0 - - + +
354A ILE* 1.3 53.6 + - - +
355A PHE 3.1 1.8 - - - -
356A LYS* 3.1 19.1 - - + +
357A ILE* 2.6 34.3 + - - +
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Residues in contact with ILE 354 (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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178A GLY* 3.2 28.9 - - - +
180A CYS* 6.1 4.0 - - - -
345A LEU 5.8 4.3 - - - +
346A PRO* 6.1 1.3 - - + -
350A GLY 2.9 10.0 + - - +
351A ARG* 3.3 11.4 - - + +
353A HIS* 1.3 74.8 - - - +
355A PHE* 1.3 61.5 + - - +
357A ILE* 3.1 31.6 - - + +
358A HIS* 3.5 7.3 + - - -
381A THR 3.6 22.0 - - - +
382A GLY* 3.9 23.6 - - - +
385A ILE* 3.7 22.6 - - + +
386A ARG* 4.8 4.5 - - + +
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Residues in contact with PHE 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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351A ARG* 2.5 24.9 + - + +
352A THR* 3.2 8.5 - - - +
354A ILE* 1.3 80.0 - - - +
356A LYS* 1.3 57.7 + - - +
357A ILE 3.4 1.1 - - - -
358A HIS* 3.8 13.3 + - - +
359A ALA 3.8 4.5 + - - -
370A PHE* 4.2 30.4 - + + -
373A LEU* 3.6 34.1 - - + -
374A ALA* 4.0 17.0 - - + -
377A CYS* 3.9 25.1 - - + -
385A ILE* 3.3 48.0 - - + -
388A VAL* 4.6 2.9 - - + -
389A CYS* 3.5 25.0 - - - -
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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