Contacts of the helix formed by residues 468 - 485 (chain A) in PDB entry 3NC0
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 ASP 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A SER* 3.5 10.6 + - - -
388A THR* 6.0 1.3 - - - -
417A ARG* 3.4 18.0 + - - +
464A LEU 3.2 4.3 + - - -
465A THR 3.5 2.5 - - - -
466A HIS 3.2 1.4 + - - -
467A LEU* 1.3 83.5 - - - +
469A TYR* 1.3 61.4 + - - +
470A VAL* 3.4 15.1 + - - +
471A ASP* 3.2 41.5 + - - +
472A THR* 3.5 8.8 + - - -
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Residues in contact with TYR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 4.3 19.1 - - - -
465A THR* 3.0 38.7 + - + +
466A HIS 5.9 0.2 - - - -
468A ASP* 1.3 70.8 - - - +
470A VAL* 1.3 88.6 + - + +
471A ASP 3.2 0.2 - - - -
472A THR* 3.1 3.7 + - - -
473A GLU* 2.9 33.8 + - - +
507A ALA 5.5 1.6 - - - +
508A MET* 4.4 28.5 - - + +
509A HIS 6.3 0.7 - - - -
512A ASP* 3.1 41.5 + - + -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 5.3 2.2 - - - +
468A ASP* 3.3 11.0 - - - +
469A TYR* 1.3 105.8 - - + +
471A ASP* 1.3 63.7 + - - +
473A GLU* 3.3 6.5 + - - +
474A ILE* 3.0 44.9 + - + +
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A SER* 2.9 27.5 + - - -
417A ARG* 2.7 29.1 + - - +
468A ASP* 3.2 30.5 + - - +
469A TYR 3.2 0.4 - - - -
470A VAL* 1.3 79.7 - - - +
472A THR* 1.3 62.8 + - - +
474A ILE* 3.1 12.9 + - - +
475A ILE* 2.9 39.7 + - - +
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Residues in contact with THR 472 (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 ARG* 3.5 19.6 - - + +
421A VAL* 5.4 1.3 - - + -
461A LEU* 4.6 8.5 - - + -
465A THR* 2.9 37.4 + - - +
468A ASP 3.5 2.2 + - - -
469A TYR* 3.1 10.2 + - - -
471A ASP* 1.3 79.7 - - - +
473A GLU* 1.3 57.6 + - - +
475A ILE* 3.2 8.5 + - - +
476A MET* 3.0 58.1 + - + +
504A ILE* 4.1 9.0 - - + -
508A MET* 5.4 1.1 - - + -
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Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A TYR* 2.9 26.7 + - - +
470A VAL* 3.8 5.8 - - - +
472A THR* 1.3 79.0 - - - +
474A ILE* 1.3 55.4 + - + +
476A MET* 3.6 1.9 + - - +
477A THR* 2.6 45.5 + - - +
508A MET* 4.4 13.8 - - + +
512A ASP* 5.2 2.9 - - - +
515A ARG* 4.9 4.3 - - - +
516A PHE* 3.7 49.6 + - + +
519A THR* 5.9 1.6 - - - -
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Residues in contact with ILE 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 VAL* 3.0 36.8 + - + +
471A ASP* 3.6 13.5 - - - +
473A GLU* 1.3 77.0 - - + +
475A ILE* 1.3 68.7 + - + +
477A THR* 3.1 7.2 + - - -
478A LYS* 3.0 27.0 + - + +
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Residues in contact with ILE 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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414A SER* 4.1 21.1 - - - +
417A ARG* 4.5 7.4 - - + -
418A LEU* 3.6 41.7 - - + +
421A VAL* 4.2 20.0 - - + -
471A ASP* 2.9 44.1 + - - +
472A THR* 3.4 9.4 - - - +
474A ILE* 1.3 78.6 - - + +
476A MET* 1.3 59.0 + - + +
478A LYS* 3.3 5.0 + - - +
479A LYS* 3.0 28.6 + - + +
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Residues in contact with MET 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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421A VAL* 4.1 22.0 - - + -
461A LEU* 3.9 15.3 - - + -
472A THR* 3.0 39.6 + - + +
473A GLU 4.0 4.3 - - - +
475A ILE* 1.3 75.3 - - - +
477A THR* 1.3 59.7 + - - +
479A LYS* 3.8 1.5 - - - +
480A LEU* 3.0 31.1 + - - +
497A LEU* 4.0 13.6 - - + +
500A ALA* 3.8 23.1 - - + +
501A ILE* 3.6 26.4 - - + +
504A ILE* 3.7 19.7 - - + -
516A PHE* 3.8 23.1 - - + -
520A VAL* 6.3 1.1 - - - -
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLU* 2.6 32.3 + - - +
474A ILE* 3.1 8.2 + - - -
476A MET* 1.3 77.4 - - - +
478A LYS* 1.3 59.4 + - - +
480A LEU* 3.6 7.1 + - - +
481A GLN* 3.0 30.4 + - + +
516A PHE* 5.1 3.1 - - - -
519A THR* 5.7 11.0 - - + +
520A VAL* 6.0 1.9 - - - +
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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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474A ILE* 3.0 18.7 + - + +
475A ILE* 3.8 5.2 - - - +
477A THR* 1.3 75.4 - - - +
479A LYS* 1.3 60.7 + - + +
481A GLN* 3.3 5.9 + - + +
482A ASN* 2.9 49.3 + - - +
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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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418A LEU* 3.9 19.7 - - + -
421A VAL* 4.2 10.8 - - + +
422A SER* 3.3 30.4 + - - +
475A ILE 3.0 18.6 + - - +
476A MET* 3.8 0.7 - - - +
478A LYS* 1.3 77.9 - - + +
480A LEU* 1.3 62.1 + - - +
482A ASN* 3.3 8.2 + - - +
483A GLN* 3.2 24.3 + - - +
488A GLU* 3.6 25.4 + - - +
493A ASN* 6.2 3.0 - - - +
497A LEU* 3.5 32.5 - - + -
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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 MET 3.0 20.4 + - - +
477A THR* 3.9 7.0 - - - +
479A LYS* 1.3 77.3 - - - +
481A GLN* 1.3 66.8 + - - +
483A GLN* 3.3 7.4 + - + +
484A VAL* 3.2 34.5 + - + +
497A LEU* 3.3 13.9 - - + -
501A ILE* 4.7 6.3 - - + -
520A VAL* 3.4 50.0 - - + +
523A ASP* 4.0 18.8 - - + +
524A LEU* 4.0 19.7 - - + -
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Residues in contact with GLN 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 THR* 3.0 23.2 + - + +
478A LYS* 3.7 7.9 - - + +
479A LYS 3.2 0.2 - - - -
480A LEU* 1.3 79.4 - - - +
482A ASN* 1.3 57.4 + - - +
484A VAL* 2.9 25.6 + - - +
485A ASN* 2.9 37.8 + - - +
486A GLY 3.3 4.4 + - - +
523A ASP* 4.5 12.8 - - - +
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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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478A LYS* 2.9 40.3 + - - +
479A LYS* 3.3 4.3 + - - +
481A GLN* 1.3 76.0 - - - +
483A GLN* 1.3 55.1 + - - +
486A GLY* 3.5 19.0 - - - +
487A THR 2.5 27.6 + - - -
488A GLU* 2.8 47.0 + - + +
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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 LYS 3.2 14.1 + - - +
480A LEU* 3.5 9.2 - - + +
481A GLN 3.1 0.4 - - - -
482A ASN* 1.3 80.2 - - - +
484A VAL* 1.3 63.2 + - - +
487A THR* 4.1 3.1 - - - -
488A GLU* 3.0 26.7 - - + +
489A TRP* 3.4 55.8 - - - +
490A SER 3.5 4.8 + - - +
493A ASN* 3.4 17.2 - - - +
494A LEU* 3.6 28.7 - - + +
497A LEU* 4.6 12.8 - - + -
524A LEU* 6.3 1.1 - - + -
527A LEU* 4.1 18.6 - - + +
531A LYS* 4.6 1.7 + - - -
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Residues in contact with VAL 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* 3.2 29.8 + - + +
481A GLN* 2.9 26.8 + - - +
483A GLN* 1.3 79.2 - - - +
485A ASN* 1.3 64.6 + - + +
487A THR* 4.3 3.3 + - - -
523A ASP* 4.0 22.2 - - + +
527A LEU* 3.8 20.0 - - + +
530A GLN* 3.1 37.8 + - - +
531A LYS* 5.4 0.5 + - - -
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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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481A GLN* 2.9 17.4 + - - +
483A GLN 3.5 0.2 - - - -
484A VAL* 1.3 83.6 - - + +
486A GLY* 1.3 57.0 + - - +
487A THR* 2.6 26.6 + - - -
530A GLN* 5.8 0.3 + - - -
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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