Contacts of the helix formed by residues 472 - 487 (chain A) in PDB entry 1JSC
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 LYS 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A TYR* 4.7 5.8 - - + -
463A MET 4.8 6.1 - - - +
464A GLU 5.5 0.2 - - - +
465A GLU* 3.0 32.2 - - + +
470A LYS 3.5 1.1 + - - +
471A ILE* 1.3 73.2 - - - +
473A PRO* 1.3 73.0 - - + +
474A GLN* 3.9 11.7 - - - +
475A THR* 3.1 23.8 + - - +
476A VAL* 3.4 8.1 + - - +
645A VAL* 4.0 0.9 - - - -
646A ASP* 4.7 4.9 - - + -
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Residues in contact with PRO 473 (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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471A ILE 3.9 0.2 - - - +
472A LYS* 1.3 81.4 - - + +
474A GLN* 1.3 78.4 + - - +
476A VAL* 2.9 18.3 + - + +
477A ILE* 3.1 16.8 + - - +
503A TRP* 3.3 44.4 - - + -
575A LEU* 4.2 13.9 - - + +
645A VAL* 3.5 37.0 - - + -
646A ASP* 4.6 7.2 - - + +
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Residues in contact with GLN 474 (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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462A TYR* 3.6 35.1 - - + +
472A LYS* 3.9 10.9 - - - +
473A PRO* 1.3 90.7 - - - +
475A THR* 1.3 55.7 + - - +
477A ILE* 3.2 8.2 + - - +
478A LYS* 2.9 35.4 + - - +
503A TRP* 3.2 33.8 + - + -
507A HIS* 3.1 39.6 - - + +
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Residues in contact with THR 475 (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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462A TYR* 2.8 32.7 + - - +
465A GLU* 2.5 32.8 + - - +
472A LYS 3.1 4.4 + - - -
473A PRO 3.0 0.6 - - - -
474A GLN* 1.3 76.2 - - - +
476A VAL* 1.3 66.7 + - - +
478A LYS* 3.4 3.3 + - + +
479A LYS* 3.0 52.2 + - + +
625A LEU* 4.6 6.5 - - + -
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Residues in contact with VAL 476 (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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471A ILE* 3.7 19.7 - - + -
472A LYS 3.6 14.1 - - - +
473A PRO* 2.9 13.5 + - + +
475A THR* 1.3 75.9 - - - +
477A ILE* 1.3 59.3 + - + +
479A LYS* 3.8 1.9 - - - +
480A LEU* 2.8 29.2 + - + +
573A LEU* 4.2 15.3 - - + -
575A LEU* 4.0 21.1 - - + -
625A LEU* 4.4 13.7 - - + -
629A LEU* 4.2 14.8 - - + +
643A VAL* 4.0 26.2 - - + -
645A VAL* 4.2 0.7 - - + -
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Residues in contact with ILE 477 (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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473A PRO 3.1 13.3 + - - +
474A GLN* 3.6 7.0 - - - +
476A VAL* 1.3 76.6 - - + +
478A LYS* 1.3 65.8 + - - +
480A LEU* 3.4 4.7 + - - +
481A SER* 2.9 26.7 + - - -
500A HIS 4.4 2.7 - - - +
503A TRP* 3.5 38.6 - - + +
504A ALA* 3.6 16.6 - - - +
507A HIS* 4.0 23.3 - - + -
508A TRP* 4.0 19.0 - - + +
547A ILE* 4.5 13.2 - - + -
573A LEU* 5.5 2.2 - - + -
575A LEU* 4.3 21.8 - - + -
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Residues in contact with LYS 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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460A TYR 5.3 5.5 + - - -
461A ALA* 5.9 1.6 - - - +
462A TYR* 3.1 39.8 - - + +
474A GLN 2.9 18.0 + - - +
475A THR* 3.9 3.6 - - - +
477A ILE* 1.3 76.0 - - - +
479A LYS* 1.3 63.9 + - + +
481A SER* 3.4 4.7 - - - -
482A LYS* 3.4 18.0 + - - +
507A HIS* 3.7 42.6 + - + +
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Residues in contact with LYS 479 (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 THR* 3.0 33.5 + - + +
476A VAL 3.8 0.9 - - - +
478A LYS* 1.3 75.6 - - + +
480A LEU* 1.3 66.4 + - - +
481A SER 3.1 1.8 - - - -
482A LYS* 2.9 17.8 + - - +
483A VAL* 3.0 16.3 + - + +
622A GLN* 5.2 3.6 + - - +
625A LEU* 3.9 28.9 - - + +
626A ASP* 3.4 36.6 + - - +
629A LEU* 3.6 15.7 - - + -
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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
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476A VAL 2.8 21.9 + - - +
477A ILE* 3.9 4.3 - - - +
479A LYS* 1.3 72.8 - - - +
481A SER* 1.3 54.3 + - - +
483A VAL* 3.3 4.2 + - + -
484A ALA* 2.8 36.9 + - - +
508A TRP* 3.9 15.0 - - + -
545A ILE* 4.1 28.3 - - + -
547A ILE* 4.8 2.9 - - + -
573A LEU* 3.9 28.0 - - + -
629A LEU* 3.9 25.7 - - + +
632A PHE* 4.3 10.3 - - + -
633A VAL* 3.6 30.1 - - + -
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Residues in contact with SER 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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477A ILE 2.9 18.9 + - - -
478A LYS* 3.4 7.9 - - - -
480A LEU* 1.3 77.5 - - - +
482A LYS* 1.3 56.2 + - - +
484A ALA* 3.7 1.4 - - - +
485A ASN* 2.9 30.9 + - - +
507A HIS 4.7 0.7 - - - -
508A TRP* 3.6 36.5 + - - -
509A THR* 3.5 27.9 + - - -
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Residues in contact with LYS 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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478A LYS 3.4 8.8 + - - +
479A LYS* 2.9 12.0 + - - +
481A SER* 1.3 80.2 - - - +
483A VAL* 1.3 63.8 + - + +
485A ASN* 3.2 9.2 + - + +
486A ASP* 2.9 68.0 + - - +
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Residues in contact with VAL 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 LYS* 3.0 18.1 + - + +
480A LEU* 3.7 9.6 - - + +
482A LYS* 1.3 76.9 - - + +
484A ALA* 1.3 65.2 + - - +
486A ASP* 3.3 20.3 + - - +
487A THR* 3.5 11.9 - - + +
626A ASP* 5.4 1.6 - - - +
629A LEU* 4.1 26.9 - - + +
630A LYS* 4.2 29.8 - - + +
633A VAL* 3.9 28.0 - - + -
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Residues in contact with ALA 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 LEU* 2.8 22.0 + - + +
481A SER 3.7 3.8 - - - +
483A VAL* 1.3 72.6 - - - +
485A ASN* 1.3 61.8 + - - +
487A THR* 2.6 30.2 + - - -
488A GLY 4.1 0.3 + - - -
489A ARG 5.0 0.2 - - - +
491A VAL* 4.2 21.1 - - + +
508A TRP* 3.9 22.9 - - + -
543A LEU* 4.4 9.6 - - + -
545A ILE* 4.3 11.9 - - + -
633A VAL* 4.7 2.2 - - - +
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Residues in contact with ASN 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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344A GLU* 5.2 4.9 + - - +
481A SER 2.9 18.9 + - - +
482A LYS* 3.4 8.9 - - - +
484A ALA* 1.3 78.9 - - - +
486A ASP* 1.3 64.6 + - - +
488A GLY* 3.0 21.8 + - - -
489A ARG 5.9 0.7 - - - -
491A VAL* 5.1 3.1 - - - +
511A ARG* 4.8 17.7 + - - +
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Residues in contact with ASP 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 LYS* 2.9 59.2 + - - +
483A VAL* 3.6 12.8 - - - +
484A ALA 3.2 0.8 - - - -
485A ASN* 1.3 84.7 + - - +
487A THR* 1.3 61.1 + - + +
488A GLY* 3.2 1.0 + - - -
630A LYS* 5.7 2.3 + - - -
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Residues in contact with THR 487 (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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483A VAL* 3.5 12.3 - - + +
484A ALA 2.6 21.3 + - - +
486A ASP* 1.3 79.5 - - + +
488A GLY* 1.3 59.4 + - - +
489A ARG* 3.0 39.4 + - - +
491A VAL* 4.8 0.2 - - - +
543A LEU* 4.3 5.1 - - + +
633A VAL* 3.6 25.8 - - + -
634A SER* 6.1 0.2 - - - +
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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