Contacts of the helix formed by residues 400 - 406 (chain F) in PDB entry 3PRJ
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 400 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F TYR* 3.7 11.4 - - + +
398F SER* 3.3 5.6 - - - -
399F LYS* 1.3 80.4 - - + +
401F PRO* 1.3 73.1 - - + +
402F TYR* 3.1 39.5 + - - +
403F GLU* 3.3 31.5 + - - +
404F ALA 3.5 7.4 + - - -
427F ARG* 5.1 0.9 + - - -
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Residues in contact with PRO 401 (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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334F LEU* 4.1 11.7 - - + -
367F TYR* 3.5 40.6 - - + +
400F ASP* 1.3 90.7 - - + +
402F TYR* 1.3 68.3 + - + +
404F ALA* 3.1 15.6 + - + +
405F CYS* 3.1 22.0 + - - -
419F MET* 4.2 5.8 - - + -
420F PHE* 5.2 0.4 - - + -
423F LEU* 3.9 39.9 - - + -
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Residues in contact with TYR 402 (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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400F ASP* 3.1 21.8 + - - +
401F PRO* 1.3 84.4 - - + +
403F GLU* 1.3 66.0 + - - +
405F CYS* 3.3 4.5 + - - +
406F ASP* 3.1 26.3 + - - +
423F LEU* 3.6 16.3 - - + +
424F ASP* 2.9 37.2 + - + +
427F ARG* 3.5 54.1 - - + +
428F ILE* 3.9 33.4 - - + -
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Residues in contact with GLU 403 (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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330F LYS* 3.0 20.1 + - - -
365F HIS* 4.7 1.1 + - - -
397F ILE 5.1 0.3 - - - +
398F SER* 3.9 10.7 + - - +
399F LYS* 3.2 38.9 + - - +
400F ASP* 3.3 20.6 + - - +
402F TYR* 1.3 79.0 - - - +
404F ALA* 1.3 59.2 + - - +
406F ASP* 3.4 13.1 + - - +
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Residues in contact with ALA 404 (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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330F LYS* 3.1 15.8 + - - +
332F ALA* 3.4 18.4 - - + +
334F LEU* 4.6 7.2 - - + -
365F HIS* 3.6 27.9 - - - +
367F TYR* 4.6 2.2 - - + -
398F SER* 3.3 24.2 + - - +
400F ASP 3.5 1.0 + - - +
401F PRO* 3.1 16.2 + - + +
403F GLU* 1.3 80.0 - - - +
405F CYS* 1.3 58.0 + - - +
408F ALA* 3.9 5.2 - - - +
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Residues in contact with CYS 405 (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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332F ALA* 4.0 9.2 - - - -
334F LEU* 4.6 10.3 - - - -
401F PRO* 3.1 19.7 + - - +
402F TYR 3.3 3.8 + - - +
403F GLU 3.3 0.2 - - - -
404F ALA* 1.3 75.2 - - - +
406F ASP* 1.3 64.2 + - - +
407F GLY 3.1 4.9 + - - -
408F ALA* 3.1 16.7 + - - +
411F VAL* 3.8 28.3 - - + -
428F ILE* 3.6 39.5 - - + -
431F LYS 4.0 0.9 - - - +
432F MET* 3.3 15.2 - - - +
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Residues in contact with ASP 406 (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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330F LYS* 3.0 24.4 + - - +
402F TYR 3.1 13.3 + - - +
403F GLU* 3.4 17.3 - - - +
404F ALA 3.3 1.4 - - - -
405F CYS* 1.3 74.7 - - - +
407F GLY* 1.3 62.6 + - - +
431F LYS* 3.9 30.9 - - - +
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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