Contacts of the helix formed by residues 477 - 485 (chain A) in PDB entry 4PJW
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 ALA 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A PHE* 3.6 13.0 - - + -
476A HIS* 1.3 71.4 - - - +
478A ALA* 1.3 65.2 + - - +
479A TYR 3.1 3.1 - - - -
480A LEU* 4.0 6.7 - - + -
481A VAL* 2.9 30.4 + - + +
523A GLU* 2.8 26.6 + - + -
524A ILE* 3.9 26.0 - - + -
527A CYS* 3.5 11.2 - - - -
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A HIS* 3.5 25.0 + - + +
477A ALA* 1.3 78.2 - - - +
479A TYR* 1.3 65.4 + - + +
481A VAL* 4.1 1.6 - - - +
482A ASP* 3.4 23.7 + - - +
527A CYS* 3.3 15.3 - - - -
530A ARG* 3.5 24.2 - - - +
531A GLN* 4.3 2.9 - - - +
538A PRO* 3.6 17.1 - - + +
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Residues in contact with TYR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A VAL 3.5 2.6 - - - +
418A TYR* 4.7 3.1 - - + -
419A SER 5.3 0.9 - - - -
420A ALA* 6.5 0.7 - - - -
474A HIS* 3.8 27.4 - + + +
476A HIS* 3.6 33.2 + + - -
477A ALA 3.1 0.4 - - - -
478A ALA* 1.3 82.0 - - + +
480A LEU* 1.3 58.9 + - - +
481A VAL 3.2 1.1 - - - -
483A SER* 2.7 34.5 + - - -
538A PRO* 3.8 17.9 - - + +
539A VAL* 2.5 45.2 + - - +
540A GLY* 5.3 1.1 - - - -
541A ARG* 3.3 42.3 + - + +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A VAL* 3.8 23.8 - - + -
418A TYR* 3.8 25.1 - - + +
432A LEU* 4.5 2.2 - - + -
464A LEU* 3.8 23.8 - - + -
467A PHE* 3.8 20.9 - - + -
468A PHE* 3.7 37.5 - - + -
477A ALA* 3.4 12.7 + - + +
479A TYR* 1.3 78.3 - - - +
481A VAL* 1.3 65.5 + - + +
483A SER* 3.2 12.6 + - - -
484A MSE 3.3 23.0 + - + +
524A ILE* 4.9 4.0 - - + -
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 5.4 1.8 - - + -
477A ALA* 2.9 29.5 + - + +
478A ALA 4.1 2.0 - - - +
480A LEU* 1.3 82.4 - - + +
482A ASP* 1.3 61.9 + - - +
484A MSE 3.0 18.5 + - - +
485A TRP* 3.1 24.5 + - + -
492A LEU* 3.8 8.7 - - + +
524A ILE* 4.2 19.7 - - + +
527A CYS* 3.7 19.7 - - + -
528A THR* 4.1 26.2 - - + +
531A GLN* 4.0 12.3 - - - +
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Residues in contact with ASP 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ARG* 2.8 51.3 + - - -
478A ALA 3.4 14.6 + - - +
479A TYR 4.0 0.2 - - - +
480A LEU 3.4 0.6 - - - -
481A VAL* 1.3 80.3 - - - +
483A SER* 1.3 62.1 + - - +
485A TRP* 3.2 8.6 + - - +
531A GLN* 2.8 37.7 + - - +
537A PRO* 3.8 3.4 - - - +
538A PRO* 3.6 16.6 - - + -
541A ARG* 2.9 35.9 + - - +
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Residues in contact with SER 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A VAL* 2.8 40.7 + - - -
425A ALA* 3.5 15.4 - - - +
426A VAL* 3.9 28.1 - - - +
429A GLY* 4.1 8.4 - - - -
479A TYR 2.7 18.7 + - - -
480A LEU 3.2 2.9 + - - -
481A VAL 3.2 0.6 - - - -
482A ASP* 1.3 78.3 - - - +
484A MSE 1.3 60.9 + - - +
485A TRP 3.7 0.2 + - - -
486A ASP 4.7 1.9 + - - -
487A CYS* 4.4 5.0 - - - -
541A ARG* 2.9 11.9 + - - +
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Residues in contact with MSE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A VAL* 5.4 0.7 - - - -
429A GLY* 3.6 28.0 - - - +
432A LEU* 3.4 31.9 - - + -
433A TYR* 4.7 9.6 - - + +
437A PHE* 3.7 34.3 - - + -
464A LEU* 4.3 12.8 - - + -
480A LEU* 3.4 24.0 - - + +
481A VAL* 3.0 9.4 + - - +
483A SER* 1.3 74.8 - - - +
485A TRP* 1.3 65.1 + - - +
486A ASP 3.2 2.8 + - - -
487A CYS* 3.3 8.9 + - - -
488A ALA* 3.0 33.9 + - + +
491A LEU* 6.2 0.4 - - + -
492A LEU* 3.8 17.0 - - + +
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Residues in contact with TRP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ARG* 4.0 7.4 - - - +
481A VAL* 3.1 12.2 + - + +
482A ASP 3.2 18.2 + - - +
484A MSE 1.3 77.8 - - - +
486A ASP* 1.3 69.4 + - - +
489A THR* 3.4 31.4 + - - -
492A LEU* 3.8 27.1 - - + -
493A LYS* 4.2 22.8 - - + +
528A THR* 3.4 39.0 - - - -
531A GLN* 3.6 44.7 + - + +
532A ALA* 3.7 16.2 - - + -
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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