Contacts of the helix formed by residues 417 - 419 (chain A) in PDB entry 4PK7
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 VAL 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A TYR* 3.1 21.5 - - - +
415A HIS 3.1 0.2 - - - -
416A LEU* 1.3 79.7 - - - +
418A TYR* 1.3 58.2 + - + +
419A SER 3.3 0.4 - - - -
425A ALA* 3.6 5.5 - - - +
428A ALA* 4.0 18.2 - - + +
429A GLY* 4.1 11.0 - - - +
432A LEU* 4.2 18.8 - - + -
467A PHE* 4.8 1.3 - - + -
479A TYR 3.8 2.4 - - - +
480A LEU* 3.8 31.9 - - + -
483A SER* 2.7 42.4 + - - +
484A MET* 5.4 0.4 - - + -
541A ARG* 2.8 16.6 + - - -
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Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A TYR 4.7 7.6 - - - -
415A HIS* 3.2 22.1 + + - +
416A LEU 3.1 0.8 - - - -
417A VAL* 1.3 80.1 - - + +
419A SER* 1.3 61.5 + - - +
420A ALA 3.9 0.9 + - - -
467A PHE* 4.0 9.6 - + - -
468A PHE* 4.0 5.8 - + - -
471A SER* 2.5 37.9 + - - -
473A LEU* 4.3 20.9 - - + -
474A HIS* 3.3 63.1 + + + +
476A HIS 5.0 0.2 - - - -
479A TYR* 4.7 1.3 - - + -
480A LEU* 3.7 47.9 - - + +
541A ARG* 4.0 4.0 - - - +
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Residues in contact with SER 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A TYR* 4.7 6.1 - - - -
416A LEU* 3.0 26.9 + - - -
417A VAL 3.3 2.0 + - - -
418A TYR* 1.3 78.8 - - - +
420A ALA* 1.3 67.3 + - - +
421A HIS* 3.1 14.2 + - - +
424A VAL* 3.2 26.3 - - - +
425A ALA* 4.5 0.7 - - - -
479A TYR* 5.3 1.2 - - - -
541A ARG* 3.0 23.4 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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