Contacts of the helix formed by residues 469 - 486 (chain A) in PDB entry 1EJ9
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 GLU 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A SER* 3.7 6.2 + - - +
468A LYS* 1.3 78.6 - - - +
470A MET* 1.3 64.6 - - - +
471A LYS* 3.8 30.1 + - + +
472A VAL* 3.1 40.3 + - + +
473A ARG* 3.4 3.3 + - - +
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Residues in contact with MET 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LYS 3.2 6.8 + - - +
469A GLU* 1.3 70.1 - - - +
471A LYS* 1.3 56.2 + - - +
473A ARG* 2.8 15.0 + - - +
474A GLN* 2.8 49.1 + - + +
553A LEU* 3.5 35.7 - - + +
554A PHE* 3.3 39.5 - - + -
566A ASP* 5.2 3.6 - - - +
567A ARG* 5.3 7.2 - - + -
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Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A GLU* 3.8 28.7 + - + +
470A MET* 1.3 77.8 - - - +
472A VAL* 1.3 66.4 + - + +
473A ARG 3.1 0.2 + - - -
474A GLN* 3.1 15.0 + - - +
475A ARG* 2.9 32.9 + - + +
567A ARG* 4.0 23.0 - - + +
568A LEU* 4.9 0.9 - - + +
572A ILE* 4.1 33.7 - - + +
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Residues in contact with VAL 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP* 3.7 16.7 - - + +
467A SER* 3.4 23.8 - - - +
469A GLU* 3.1 41.9 + - + +
471A LYS* 1.3 79.4 - - + +
473A ARG* 1.3 57.2 + - - +
475A ARG* 3.6 39.7 + - - +
476A ALA* 3.0 26.3 + - - +
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Residues in contact with ARG 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP 3.6 12.1 - - - +
465A TRP* 2.8 28.6 + - - +
466A LYS* 2.8 32.1 + - - +
467A SER* 2.5 26.6 + - - +
468A LYS 5.0 1.2 + - - -
469A GLU 3.9 7.0 - - - +
470A MET* 2.8 19.4 + - - +
472A VAL* 1.3 77.0 - - - +
474A GLN* 1.3 64.3 + - - +
476A ALA* 3.1 3.1 + - - +
477A VAL* 2.9 27.5 + - - +
550A ASN* 2.7 36.0 + - - +
553A LEU* 5.3 10.8 - - - +
554A PHE* 3.9 15.7 - - + -
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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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470A MET* 2.8 30.8 + - - +
471A LYS* 3.7 5.9 - - - +
473A ARG* 1.3 70.7 - - - +
475A ARG* 1.3 64.5 + - - +
478A ALA* 2.8 26.5 + - - +
554A PHE* 3.5 27.8 - - + +
558A LYS* 4.8 0.2 - - - +
564A LEU 3.4 15.6 + - - -
565A PHE* 3.5 20.5 - - + +
566A ASP* 2.5 48.0 + - - +
567A ARG* 2.9 21.6 - - - +
568A LEU* 3.4 11.5 - - + +
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Residues in contact with ARG 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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460A GLN* 4.7 1.2 + - - -
464A ASP* 3.7 12.7 + - - -
471A LYS* 2.9 24.3 + - + +
472A VAL* 3.6 39.5 + - - +
474A GLN* 1.3 78.7 - - - +
476A ALA* 1.3 59.4 + - - +
478A ALA* 3.1 3.1 + - - +
479A LEU* 2.9 29.6 + - + +
568A LEU* 3.6 17.6 - - + +
572A ILE* 4.8 14.3 - - + +
573A LEU* 4.3 23.9 - - + +
576A HIS* 2.9 58.3 + - - +
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Residues in contact with ALA 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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461A TYR* 3.7 16.9 - - + +
464A ASP* 3.5 26.0 - - + +
465A TRP* 3.3 26.4 + - + +
472A VAL 3.0 16.7 + - - +
473A ARG 3.1 2.2 + - - +
475A ARG* 1.3 83.4 - - - +
477A VAL* 1.3 56.1 + - - +
479A LEU* 3.4 5.6 + - - +
480A TYR* 2.9 21.8 + - - +
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A TRP* 3.8 20.4 - - + +
473A ARG* 2.9 22.6 + - - +
476A ALA* 1.3 69.2 - - - +
478A ALA* 1.3 73.4 + - - +
480A TYR* 3.0 17.4 - - - +
481A PHE* 3.1 24.9 + - + -
547A VAL* 4.1 16.6 - - + -
550A ASN* 4.3 14.4 - - + +
551A LEU* 4.1 7.0 - - + -
554A PHE* 3.7 16.4 - - + -
565A PHE* 3.5 26.9 - - + -
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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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474A GLN 2.8 19.8 + - - +
475A ARG 3.1 4.7 - - - +
477A VAL* 1.3 76.6 - - - +
479A LEU* 1.3 57.8 + - - +
481A PHE* 2.9 21.8 + - - +
482A ILE* 3.0 13.7 + - + +
504A CYS* 3.6 20.7 - - - -
505A CYS* 5.1 5.4 - - - -
565A PHE* 3.8 14.8 - - + -
568A LEU* 3.7 17.5 - - + -
573A LEU* 5.0 7.0 - - + -
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 4.1 18.8 - - + -
461A TYR* 3.9 20.2 - - + -
475A ARG* 2.9 14.1 + - + +
476A ALA* 3.8 9.4 - - - +
478A ALA* 1.3 72.9 - - - +
480A TYR* 1.3 60.2 + - - +
482A ILE* 3.7 19.7 - - + +
483A ASP* 2.8 33.1 + - - +
573A LEU* 4.6 9.8 - - + +
576A HIS* 5.4 8.7 - - + +
577A LEU* 3.5 29.4 - - + -
580A LEU* 5.2 2.5 - - + -
589A PHE* 3.4 33.4 - - + -
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Residues in contact with TYR 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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461A TYR* 3.9 19.5 - - - -
462A ARG* 4.5 12.6 - - - -
465A TRP* 3.5 28.5 - + + -
476A ALA 2.9 13.8 + - - +
477A VAL* 3.0 11.0 + - - +
479A LEU* 1.3 77.5 - - - +
481A PHE* 1.3 74.5 + + - +
483A ASP* 3.5 1.6 - - - +
484A LYS* 2.6 81.8 + - + +
543A VAL* 3.7 19.6 - - + -
544A GLU* 3.6 19.5 + - + +
547A VAL* 3.5 29.4 - - + -
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Residues in contact with PHE 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 VAL* 3.5 30.5 - - + -
478A ALA 2.9 5.5 + - - +
480A TYR* 1.3 104.4 - + - +
482A ILE* 1.3 61.3 + - - +
484A LYS 4.3 0.2 - - - +
485A LEU* 2.6 51.2 + - + +
486A ALA 3.2 1.0 + - - -
487A LEU* 3.6 25.1 + - + -
504A CYS* 4.0 10.1 - - - -
507A LEU* 4.8 3.1 - - + -
512A ILE* 6.0 0.7 - - + -
525A VAL* 5.2 0.7 - - + -
527A PHE* 3.8 25.1 - + - -
543A VAL* 4.5 7.6 - - + -
547A VAL* 4.3 2.5 - - + -
551A LEU* 4.1 23.1 - - + -
564A LEU* 5.3 2.2 - - + -
565A PHE* 3.7 20.2 - + - -
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Residues in contact with ILE 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 ALA* 3.0 15.1 + - + +
479A LEU* 3.8 13.5 - - + +
481A PHE* 1.3 78.4 - - - +
483A ASP* 1.3 67.4 + - - +
486A ALA* 2.9 23.8 + - - -
487A LEU 3.2 28.7 - - - +
488A ARG 4.5 2.5 - - - +
489A ALA* 5.0 1.6 - - - +
504A CYS* 4.0 23.8 - - + -
505A CYS* 5.3 0.7 - - - -
573A LEU* 3.9 28.3 - - + -
586A ALA* 4.0 17.5 - - + +
589A PHE* 3.6 36.2 - - + +
590A ARG* 6.1 0.7 - - + -
593A ASN* 4.9 0.2 - - - +
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Residues in contact with ASP 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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454A VAL* 4.2 2.3 - - - +
458A ARG* 2.8 45.4 + - - +
461A TYR* 2.6 28.8 + - + +
479A LEU 2.8 23.9 + - - +
480A TYR 3.5 2.9 - - - +
482A ILE* 1.3 77.9 - - - +
484A LYS* 1.3 58.2 + - - +
486A ALA 4.1 0.2 + - - -
589A PHE* 3.8 33.1 - - + +
592A TYR* 4.6 3.3 - - - -
593A ASN* 3.1 23.7 - - - +
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Residues in contact with LYS 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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461A TYR* 5.6 0.9 - - - +
480A TYR* 2.6 61.6 + - + +
481A PHE* 4.7 0.4 - - - -
483A ASP* 1.3 75.9 - - + +
485A LEU* 1.3 72.6 + - + +
541A VAL* 3.7 18.0 - - + +
542A PRO* 2.8 29.5 + - - +
543A VAL* 4.2 0.2 - - - +
593A ASN* 4.9 2.5 - - - +
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Residues in contact with LEU 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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481A PHE* 2.6 32.6 + - + +
484A LYS* 1.3 95.7 - - + +
486A ALA* 1.3 68.1 + - - +
487A LEU* 3.9 21.8 - - + +
527A PHE* 3.5 39.3 - - + -
537A TYR* 4.1 15.5 + - - +
539A ASN* 4.2 9.2 - - - +
541A VAL* 4.1 26.7 - - + -
593A ASN* 5.6 0.2 - - - -
629A LEU* 3.8 10.1 - - - +
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ILE* 2.9 16.5 + - - -
483A ASP 4.1 1.3 + - - -
484A LYS 3.6 1.2 - - - -
485A LEU* 1.3 83.3 - - - +
487A LEU* 1.3 67.0 + - - +
488A ARG* 3.7 0.7 + - - +
589A PHE 6.1 0.2 - - - -
590A ARG* 3.2 40.0 + - + +
593A ASN* 4.9 6.7 - - - +
629A LEU* 3.6 36.1 - - + +
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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