Contacts of the helix formed by residues 349 - 358 (chain C) in PDB entry 3OX4
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 349 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C TYR* 3.0 25.2 + - - +
346C LYS* 2.7 40.8 + - - +
348C GLU* 1.3 81.1 - - - +
350C VAL* 1.3 65.9 + - - +
351C PRO* 3.3 4.3 - - - -
352C LEU* 3.1 25.6 + - + +
353C LEU* 3.2 19.7 + - + +
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Residues in contact with VAL 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 LYS 3.6 1.2 + - - +
347C LYS* 3.1 26.7 - - + +
349C ASP* 1.3 76.8 - - - +
351C PRO* 1.3 64.7 - - + +
353C LEU* 3.1 10.0 + - + +
354C ALA* 3.0 28.8 + - - +
376C GLU* 3.5 30.5 - - + +
379C PHE* 3.8 10.3 - - + -
380C LEU* 3.5 36.8 - - + -
383C PHE* 4.2 17.5 - - + -
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Residues in contact with PRO 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LYS 4.2 3.8 - - - +
348C GLU* 4.5 4.3 - - - +
349C ASP* 3.4 7.6 - - - +
350C VAL* 1.3 97.1 - - + +
352C LEU* 1.3 56.7 + - - +
353C LEU 3.4 0.2 - - - -
355C ASP* 3.2 7.4 - - - +
372C GLN* 2.6 24.8 + - - +
376C GLU* 3.0 28.9 - - - +
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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
----------------------------------------------------------
272C TYR* 4.8 19.7 - - + +
349C ASP* 3.1 19.9 + - + +
351C PRO* 1.3 78.3 - - - +
353C LEU* 1.3 64.6 + - + +
355C ASP* 4.1 4.5 - - + +
356C HIS* 3.1 67.5 + - + +
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Residues in contact with LEU 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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268C GLN* 3.4 43.2 - - + +
269C LEU* 3.3 24.0 - - + -
272C TYR* 4.9 10.5 - - + -
273C TYR* 4.0 22.2 - - + +
345C ALA* 5.2 4.7 - - + -
346C LYS 5.2 1.3 - - - +
349C ASP* 3.3 21.8 - - + +
350C VAL* 3.1 11.1 + - + +
352C LEU* 1.3 78.7 - - + +
354C ALA* 1.3 54.7 + - - +
356C HIS* 3.3 1.3 + - - -
357C ALA* 2.7 34.0 + - - +
379C PHE* 3.7 24.5 - - + -
383C PHE* 5.7 2.9 - - + -
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Residues in contact with ALA 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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350C VAL 3.0 7.7 + - - +
353C LEU* 1.3 75.1 - - - +
355C ASP* 1.3 66.5 + - - +
357C ALA* 2.8 15.2 + - - +
358C LEU* 3.0 20.1 + - - +
372C GLN* 3.6 4.5 - - - +
375C VAL* 3.8 22.2 - - + -
376C GLU* 3.4 33.4 - - + +
379C PHE* 3.4 14.3 - - + -
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Residues in contact with ASP 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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351C PRO 3.2 10.0 + - - +
352C LEU* 4.1 5.5 - - + +
354C ALA* 1.3 75.9 - - - +
356C HIS* 1.3 69.6 + - + +
358C LEU* 4.0 5.9 + - - +
359C LYS* 3.0 52.5 + - - +
372C GLN* 2.7 41.9 - - - +
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Residues in contact with HIS 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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159C VAL* 4.7 6.7 - - + +
268C GLN* 2.9 27.7 + - - +
272C TYR* 3.1 43.7 - + - -
352C LEU* 3.1 42.3 + - + +
353C LEU 3.3 1.6 + - - +
354C ALA 3.1 0.2 - - - -
355C ASP* 1.3 93.0 + - + +
357C ALA* 1.3 65.6 + - - +
359C LYS* 3.0 33.4 + - + +
360C ASP* 3.1 9.7 + - - -
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Residues in contact with ALA 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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264C ALA* 3.4 37.3 - - + +
265C MET* 4.3 15.7 - - + -
268C GLN* 3.9 2.2 - - + -
353C LEU 2.7 16.1 + - - +
354C ALA* 2.8 15.8 + - - +
356C HIS* 1.3 73.2 - - - +
358C LEU* 1.3 54.9 + - + +
359C LYS 2.9 4.0 - - - -
360C ASP* 2.7 30.3 + - - +
363C ALA* 3.8 1.6 - - - +
375C VAL* 4.6 6.3 - - + -
379C PHE* 4.5 0.9 - - + -
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Residues in contact with LEU 358 (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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261C TYR* 3.8 20.0 - - + +
354C ALA 3.0 15.9 + - - +
355C ASP* 4.2 6.5 - - - +
357C ALA* 1.3 76.5 - - - +
359C LYS* 1.3 59.2 + - + +
360C ASP 3.3 1.3 + - - +
363C ALA* 3.9 15.1 - - + +
370C GLY 3.8 13.7 - - - +
371C ASP* 3.8 3.1 - - - -
372C GLN* 3.2 42.8 - - + +
375C VAL* 3.5 23.8 - - + -
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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