Contacts of the helix formed by residues 477 - 486 (chain A) in PDB entry 3JUE
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 GLY 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A VAL* 4.4 4.3 - - - -
415A ASP 4.7 0.2 - - - -
417A ASN* 3.3 19.5 - - - -
436A GLY 3.0 18.6 + - - -
473A MET 3.6 2.9 + - - -
476A LEU* 1.3 81.5 - - - +
478A ASN* 1.3 62.2 + - - -
479A VAL 3.3 2.5 - - - -
480A ILE 3.2 3.8 + - - -
481A ILE* 2.9 29.3 + - - +
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Residues in contact with ASN 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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415A ASP 4.1 0.2 + - - -
416A GLY* 3.0 17.7 - - - +
417A ASN* 2.9 14.3 + - - -
419A GLN 2.8 26.4 - - - +
421A CYS* 3.4 22.3 + - + +
437A VAL* 3.1 31.8 - - - +
438A THR* 2.9 22.9 + - - +
477A GLY* 1.3 68.4 - - - -
479A VAL* 1.3 61.4 + - + +
482A ASN* 2.8 42.8 + - - +
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 3.7 47.3 + - + +
416A GLY* 3.9 11.0 - - - -
477A GLY 3.3 0.8 - - - -
478A ASN* 1.3 77.8 - - + +
480A ILE* 1.3 70.0 + - + +
482A ASN* 3.9 3.9 - - - +
483A GLN* 3.0 42.0 + - + +
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Residues in contact with ILE 480 (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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475A GLU 4.6 5.8 - - - +
476A LEU* 3.8 35.9 + - + +
477A GLY 3.2 8.5 + - - +
479A VAL* 1.3 82.0 - - + +
481A ILE* 1.3 69.4 + - + +
483A GLN* 3.1 38.6 + - - +
484A ILE* 3.5 12.5 + - + +
586A PRO* 4.1 34.3 - - + -
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Residues in contact with ILE 481 (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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421A CYS* 4.7 5.6 - - - -
435A LEU* 3.3 30.1 - - + +
436A GLY 4.3 3.1 - - - +
437A VAL* 3.6 26.2 - - + -
476A LEU* 4.2 13.7 - - + -
477A GLY 2.9 19.3 + - - +
478A ASN 4.3 0.4 - - - +
480A ILE* 1.3 78.5 - - + +
482A ASN* 1.3 51.3 + - - +
484A ILE* 3.1 10.6 + - + +
485A TYR* 2.7 57.6 + - + -
513A LYS* 5.7 0.2 - - - -
514A TYR* 4.9 7.6 - - + -
589A ALA* 3.9 27.8 - - + -
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Residues in contact with ASN 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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421A CYS* 3.3 31.1 + - - +
424A ARG* 6.0 1.8 - - - +
478A ASN* 2.8 29.9 + - - +
479A VAL* 4.0 3.6 - - - +
481A ILE* 1.3 68.4 - - - +
483A GLN* 1.3 64.8 + - - +
484A ILE 3.0 1.8 - - - -
485A TYR* 4.2 1.6 - - - +
486A GLU* 2.9 43.4 + - + +
487A ALA* 4.3 0.2 - - - -
496A LYS* 3.5 8.7 - - - +
513A LYS* 2.8 29.9 + - - -
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Residues in contact with GLN 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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479A VAL* 3.0 34.5 + - + +
480A ILE* 3.1 29.1 + - - +
482A ASN* 1.3 74.8 - - - +
484A ILE* 1.3 59.4 + - + +
487A ALA* 3.2 24.0 - - - +
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Residues in contact with ILE 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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480A ILE* 3.9 17.7 - - + +
481A ILE* 3.1 14.0 + - + +
482A ASN 3.0 0.4 - - - -
483A GLN* 1.3 79.5 - - + +
485A TYR* 1.3 71.5 + - + +
486A GLU 3.3 1.4 + - - -
487A ALA* 3.3 16.9 + - - +
520A LEU* 4.0 13.9 - - + +
521A THR 4.9 0.5 + - - -
586A PRO* 3.7 12.8 - - + +
589A ALA* 3.8 12.6 - - + -
590A ASP* 3.5 49.4 - - + +
593A ALA* 3.7 30.1 - - + -
594A HIS* 4.9 2.1 + - - +
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Residues in contact with TYR 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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435A LEU* 3.8 28.2 - - + +
481A ILE* 2.7 41.7 + - + +
484A ILE* 1.3 78.5 - - + +
486A GLU* 1.3 59.9 + - + +
487A ALA 3.5 0.7 - - - -
513A LYS* 3.5 43.5 - - + +
514A TYR* 3.8 20.2 - + - -
517A LYS* 3.9 22.3 + - + -
519A PHE* 3.3 25.6 + - - +
520A LEU* 3.9 11.9 - - + +
589A ALA* 4.9 3.7 + - + -
592A LEU* 5.0 0.5 - - - +
593A ALA* 3.4 36.2 + - + +
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Residues in contact with GLU 486 (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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482A ASN* 2.9 26.0 + - + +
485A TYR* 1.3 82.4 - - - +
487A ALA* 1.3 64.2 + - - +
488A ARG 3.2 4.4 + - - -
489A VAL* 3.3 33.4 + - + +
490A GLU 4.8 0.3 + - - -
496A LYS* 2.7 36.1 + - - +
509A TRP* 3.0 26.8 + - + -
513A LYS* 2.7 34.9 + - + -
519A PHE* 4.0 1.8 - - + -
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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