Contacts of the helix formed by residues 362 - 373 (chain F) in PDB entry 4OIO
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 SER 362 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360F LYS 4.1 0.2 + - - -
361F LEU* 1.3 75.5 - - - +
363F GLU* 1.3 65.8 + - - +
364F ARG* 3.1 7.7 + - - +
365F GLU* 3.1 38.9 + - - +
366F ALA* 3.0 21.8 + - - +
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Residues in contact with GLU 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F LEU 3.9 0.6 + - - -
362F SER* 1.3 73.7 - - - +
364F ARG* 1.3 61.3 + - + +
366F ALA* 4.1 6.3 - - - +
367F MET* 3.1 29.9 + - - +
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Residues in contact with ARG 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362F SER* 3.1 7.1 + - - +
363F GLU* 1.3 82.9 - - + +
365F GLU* 1.3 57.6 + - - +
367F MET* 3.1 0.5 + - - +
368F VAL* 2.7 42.4 + - + +
390F PHE* 3.5 38.1 - - + +
392F VAL* 4.5 14.5 - - - +
396F ARG* 3.8 20.6 - - - +
400F ILE* 3.6 33.8 - - + +
403F LYS* 5.5 6.3 - - - +
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Residues in contact with GLU 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361F LEU* 3.3 22.0 - - + +
362F SER* 3.1 35.5 + - - +
364F ARG* 1.3 78.5 - - + +
366F ALA* 1.3 58.6 + - - +
368F VAL* 3.4 1.9 + - - +
369F LEU* 2.9 30.7 + - - +
400F ILE* 4.2 22.4 - - + +
403F LYS* 3.2 33.3 + - - +
404F ALA* 3.7 26.8 - - + +
407F LYS* 4.6 12.7 - - - +
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Residues in contact with ALA 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F LEU* 3.5 41.0 - - + +
361F LEU* 4.0 8.6 - - + +
362F SER 3.0 13.7 + - - +
363F GLU* 4.1 6.7 - - - +
365F GLU* 1.3 77.0 - - - +
367F MET* 1.3 52.9 + - + +
369F LEU* 3.3 1.7 + - - +
370F LYS* 2.7 48.4 + - - +
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Residues in contact with MET 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F GLU 3.1 24.3 + - - +
364F ARG* 3.1 4.8 + - - +
366F ALA* 1.3 75.0 - - + +
368F VAL* 1.3 60.0 + - - +
370F LYS* 4.4 21.1 - - + +
371F LEU* 2.9 47.6 + - + +
376F ILE* 4.9 5.2 - - - -
389F PHE* 4.8 9.6 - - + -
390F PHE* 3.6 23.6 - - + -
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Residues in contact with VAL 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364F ARG* 2.7 26.1 + - + +
365F GLU 3.8 3.6 - - - +
367F MET* 1.3 71.6 - - - +
369F LEU* 1.3 64.0 + - - +
371F LEU* 3.3 2.3 + - - +
372F ARG* 3.2 28.7 + - - +
386F VAL* 3.9 16.7 - - + +
390F PHE* 3.7 20.9 - - + -
397F ILE* 3.7 29.8 - - + +
400F ILE* 4.0 15.0 - - + -
401F GLU* 4.1 31.0 - - + +
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Residues in contact with LEU 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C LEU* 4.2 19.9 - - + +
358F LEU* 4.4 9.4 - - + -
361F LEU* 4.1 4.3 - - + -
365F GLU 2.9 13.6 + - - +
366F ALA 3.8 3.1 - - - +
368F VAL* 1.3 78.7 - - + +
370F LYS* 1.3 58.8 + - - +
372F ARG* 4.7 2.7 - - + -
373F LYS* 3.1 40.2 + - + +
401F GLU* 3.6 42.2 - - + +
404F ALA* 3.8 24.9 - - + -
405F LEU* 4.3 10.3 - - + +
408F LEU* 3.5 31.4 - - + -
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Residues in contact with LYS 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F GLU* 2.9 41.0 + - - -
358F LEU* 3.6 28.0 - - + -
366F ALA* 2.7 32.9 + - + +
367F MET* 4.0 19.7 - - + +
369F LEU* 1.3 70.4 - - - +
371F LEU* 1.3 67.7 + - - +
374F GLY 3.5 1.4 + - - -
375F LEU* 3.1 48.6 + - + -
376F ILE* 3.5 21.6 + - + -
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Residues in contact with LEU 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F MET* 2.9 32.0 + - + +
368F VAL* 3.3 5.4 + - - +
370F LYS* 1.3 80.8 - - - +
372F ARG* 1.3 59.2 + - - +
374F GLY* 3.6 6.9 + - - -
376F ILE* 3.7 22.7 - - + +
377F ASP* 5.8 1.6 - - + -
380F GLU* 3.9 0.2 - - - -
381F HIS* 3.0 51.8 + - + +
385F GLU 5.5 0.4 - - - +
386F VAL* 4.2 29.8 - - + -
389F PHE* 3.6 34.3 - - + -
390F PHE* 4.7 0.7 - - + -
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Residues in contact with ARG 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368F VAL* 3.2 24.9 + - - +
369F LEU* 4.6 5.4 - - + +
371F LEU* 1.3 75.3 - - - +
373F LYS* 1.3 68.2 + - + +
374F GLY 3.4 1.6 - - - -
380F GLU* 3.1 23.9 + - - +
381F HIS 3.1 42.1 + - - +
382F THR* 4.1 1.4 - - - +
383F LEU* 3.0 50.4 - - - +
386F VAL* 4.3 9.4 - - + -
397F ILE* 4.9 1.6 - - - -
401F GLU* 3.0 45.6 + - - +
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Residues in contact with LYS 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769C PRO* 3.5 17.7 - - - +
772C ARG* 3.5 30.8 + - + +
773C LEU* 3.7 38.6 - - + +
776C SER* 2.4 37.3 + - - +
369F LEU* 3.1 29.9 + - + +
372F ARG* 1.3 86.0 + - + +
374F GLY* 1.3 62.1 + - - +
375F LEU* 3.4 7.9 + - + +
380F GLU* 5.7 1.0 + - - -
401F GLU* 4.6 16.1 + - - -
405F LEU* 5.7 3.3 - - - +
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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