Contacts of the helix formed by residues 366 - 375 (chain F) in PDB entry 4R8A
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 366 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365F CYS* 1.3 92.9 - - - +
367F VAL* 1.3 65.8 + - - +
368F GLU* 4.2 9.5 + - - +
369F TRP* 3.1 34.9 + - - +
370F ALA* 3.4 10.7 + - - +
384F TYR* 5.3 0.5 - - - -
6G C 5.1 6.3 - - - -
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Residues in contact with VAL 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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366F SER* 1.3 72.2 - - - +
368F GLU* 1.3 73.7 + - - +
370F ALA* 3.1 16.3 + - - +
371F VAL* 3.2 13.4 + - + +
523F VAL* 4.0 12.6 - - + -
525F GLY* 3.8 36.8 - - - +
526F PRO* 4.7 7.9 - - + -
553F VAL* 4.3 22.2 - - + -
6G C 3.7 20.8 + - - +
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Residues in contact with GLU 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F SER* 3.4 7.2 - - - +
367F VAL* 1.3 85.1 + - - +
369F TRP* 1.3 61.8 + - - +
370F ALA 3.3 0.5 + - - -
371F VAL* 3.4 5.4 + - - +
372F ARG* 3.4 20.1 + - - +
384F TYR* 3.5 33.0 + - + +
507F ASP* 3.2 40.2 - - + +
508F LEU* 4.2 6.4 - - + +
523F VAL* 3.5 24.3 - - + +
524F LYS* 5.2 1.2 - - - -
528F ASP* 5.3 0.7 - - - +
5G A 3.4 37.3 + - - +
6G C 4.6 1.7 + - - -
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Residues in contact with TRP 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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365F CYS* 4.0 15.5 - - - -
366F SER* 3.1 25.8 + - - +
367F VAL 3.3 0.6 - - - -
368F GLU* 1.3 80.1 - - - +
370F ALA* 1.3 62.4 + - - +
372F ARG* 3.6 42.5 + - - +
373F GLU* 3.3 19.2 + - - +
384F TYR* 3.7 39.5 - + + -
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Residues in contact with ALA 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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365F CYS* 4.6 6.0 - - - -
366F SER 3.4 9.9 + - - +
367F VAL* 3.1 12.2 + - + +
369F TRP* 1.3 78.0 - - - +
371F VAL* 1.3 60.6 + - + +
373F GLU* 3.1 11.3 + - - +
374F HIS* 2.9 28.8 + - - +
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Residues in contact with VAL 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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356F LEU* 4.4 5.6 - - + -
367F VAL* 3.2 15.2 + - + +
368F GLU 3.8 5.6 - - - +
370F ALA* 1.3 77.1 - - + +
372F ARG* 1.3 58.2 + - - +
374F HIS* 3.1 6.1 + - - +
375F LEU* 2.8 50.0 + - + +
508F LEU* 4.0 8.3 - - + -
521F VAL* 5.6 0.2 - - + -
523F VAL* 3.7 37.5 - - + -
551F CYS* 4.3 11.7 - - + -
553F VAL* 4.1 22.0 - - + -
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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 GLU 3.4 10.1 + - - +
369F TRP* 3.7 40.8 + - + +
370F ALA 3.2 0.6 - - - -
371F VAL* 1.3 78.9 - - - +
373F GLU* 1.3 87.4 + - - +
375F LEU 3.5 1.9 + - - -
376F GLU* 3.4 21.4 + - - +
382F VAL* 3.4 50.7 + - + +
383F HIS* 4.2 13.0 - - - +
384F TYR* 4.4 0.9 - - - +
508F LEU* 4.1 14.5 - - + +
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Residues in contact with GLU 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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369F TRP 3.3 10.7 + - - +
370F ALA* 3.1 12.9 + - - +
372F ARG* 1.3 97.7 + - - +
374F HIS* 1.3 60.2 + - + +
376F GLU* 2.9 46.1 - - - +
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Residues in contact with HIS 374 (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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356F LEU* 4.3 32.1 - - + +
370F ALA 2.9 12.9 + - - +
371F VAL* 3.1 11.6 + - - +
373F GLU* 1.3 75.2 - - + +
375F LEU* 1.3 61.9 + - + +
376F GLU* 3.0 21.0 + - - +
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Residues in contact with LEU 375 (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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354F LEU* 5.2 12.1 - - + -
356F LEU* 4.7 10.1 - - + -
371F VAL* 2.8 43.9 + - + +
372F ARG 3.5 1.3 + - - +
373F GLU 3.5 0.2 - - - -
374F HIS* 1.3 80.5 - - + +
376F GLU* 1.3 63.0 + - - +
377F GLU* 3.6 6.0 + - - +
380F CYS* 4.1 9.9 - - - -
382F VAL* 3.3 34.4 - - + +
508F LEU* 5.0 3.4 - - + -
510F GLN* 3.2 29.1 - - - +
521F VAL* 4.7 14.8 - - + -
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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