Contacts of the helix formed by residues 348 - 357 (chain C) in PDB entry 5D0A
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 TYR 348 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317C LEU* 3.5 42.9 - - + +
318C PRO* 3.7 24.8 - - + +
321C THR* 3.4 32.3 - - + -
340C ILE* 3.6 24.2 - - + -
345C ASP* 3.2 20.9 + - - +
346C PRO 3.1 1.4 - - - -
347C ALA* 1.3 83.7 - - + +
349C ALA* 1.3 64.7 + - - +
350C GLU 3.4 1.6 - - - -
351C GLU* 3.3 13.5 + - + +
352C LEU* 3.1 22.7 + - - +
375C LEU* 4.0 2.7 - - + -
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Residues in contact with ALA 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C PRO* 3.0 19.6 + - + +
348C TYR* 1.3 77.1 - - - +
350C GLU* 1.3 63.7 + - - +
352C LEU* 3.2 8.5 + - - +
353C GLU* 3.0 27.3 + - + +
372C ILE* 4.9 4.1 - - + +
375C LEU* 3.5 27.1 - - + +
376C LYS* 4.9 16.6 - - - +
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Residues in contact with GLU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C PRO 4.6 0.2 + - - -
347C ALA 4.5 6.8 + - - +
348C TYR 3.4 0.4 - - - -
349C ALA* 1.3 79.3 - - - +
351C GLU* 1.3 57.7 + - - +
353C GLU* 2.9 31.9 + - + +
354C LYS* 3.0 42.7 + - - +
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Residues in contact with GLU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C THR* 4.0 18.8 - - + +
324C MET* 4.4 4.0 - - + -
325C HIS* 2.7 35.2 + - - +
347C ALA 5.1 0.8 + - - +
348C TYR* 3.3 18.9 + - + +
350C GLU* 1.3 75.7 - - - +
352C LEU* 1.3 62.3 + - - +
354C LYS* 3.9 21.1 - - - +
355C ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C MET* 3.5 28.0 - - + -
337C ALA* 3.9 19.5 - - + +
340C ILE* 3.9 25.4 - - + -
341C GLY 4.3 2.0 - - - +
348C TYR 3.1 13.9 + - - +
349C ALA* 3.2 7.6 + - - +
351C GLU* 1.3 75.0 - - - +
353C GLU* 1.3 63.1 + - - +
355C ALA* 3.2 2.4 + - - -
356C LEU* 2.9 20.1 + - - +
368C ILE* 3.3 16.0 - - + +
371C GLY* 3.7 33.9 - - - +
372C ILE* 3.7 15.3 - - + +
375C LEU* 4.0 16.2 - - + -
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Residues in contact with GLU 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C ALA* 3.0 23.1 + - + +
350C GLU* 2.9 21.1 + - + +
352C LEU* 1.3 74.8 - - - +
354C LYS* 1.3 63.3 + - + +
356C LEU* 3.2 22.5 + - - +
357C GLU* 3.5 14.1 + - - +
372C ILE* 3.6 36.5 - - - +
376C LYS* 3.9 16.3 + - - -
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C HIS* 5.2 0.7 - - + -
350C GLU* 3.0 43.7 + - - +
351C GLU* 3.8 26.2 - - - +
353C GLU* 1.3 77.6 - - + +
355C ALA* 1.3 63.6 + - - +
357C GLU* 3.3 11.7 + - - +
358C LYS* 3.3 28.8 - - + +
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Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C MET* 3.7 26.0 - - + -
325C HIS* 3.7 26.6 - - + +
351C GLU 2.9 18.1 + - - +
352C LEU 3.6 4.3 - - - +
354C LYS* 1.3 74.6 - - - +
356C LEU* 1.3 60.8 + - - +
358C LYS* 2.9 4.8 + - - +
359C GLU* 2.8 32.3 + - + +
368C ILE* 4.0 9.0 - - + -
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Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.3 2.2 - - - +
55A GLU* 3.9 18.4 - - + +
352C LEU 2.9 12.5 + - - +
353C GLU* 3.2 18.4 - - - +
355C ALA* 1.3 76.9 - - - +
357C GLU* 1.3 75.2 + - - +
358C LYS 3.3 0.9 + - - -
359C GLU 3.8 6.2 + - - +
365C LYS* 3.7 59.5 + - + +
368C ILE* 3.9 13.6 - - + +
369C GLU* 3.9 28.0 - - + +
372C ILE* 4.0 14.1 - - + -
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Residues in contact with GLU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 4.6 11.5 - - - +
353C GLU 3.5 12.7 + - - +
354C LYS* 3.3 10.2 + - - +
355C ALA 3.2 1.0 - - - -
356C LEU* 1.3 94.5 - - - +
358C LYS* 1.3 62.9 + - + +
359C GLU 5.0 0.4 - - - -
360C LYS* 4.1 13.8 + - - -
365C LYS* 5.8 3.0 + - - +
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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