Contacts of the helix formed by residues 490 - 504 (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 SER 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A GLN* 3.5 4.4 + - - +
488A GLU 3.6 1.2 + - - -
489A TRP* 1.3 87.0 - - - +
491A TRP* 1.3 66.8 + - - +
492A LYS* 3.7 6.5 + - - +
493A ASN* 3.2 29.1 + - - -
494A LEU* 3.1 23.6 + - - +
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Residues in contact with TRP 491 (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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489A TRP* 3.6 23.3 - + - +
490A SER* 1.3 73.2 - - - +
492A LYS* 1.3 63.4 + - - +
494A LEU* 3.4 2.1 + - - +
495A ASN* 3.0 35.7 + - - +
535A ASP* 3.1 46.7 - - + -
536A ASN* 2.9 32.0 + - - +
539A ILE* 3.8 36.5 - - + +
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Residues in contact with LYS 492 (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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361A GLU* 5.5 5.5 + - - -
490A SER* 3.2 7.5 + - - +
491A TRP* 1.3 80.5 - - - +
493A ASN* 1.3 68.4 + - - +
495A ASN* 3.5 8.5 + - - +
496A THR* 2.9 27.9 + - - +
499A TRP* 5.4 0.9 - - - -
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Residues in contact with ASN 493 (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 SER 5.3 5.9 + - - -
479A LYS* 6.2 2.9 - - - +
483A GLN* 3.4 18.6 - - - +
488A GLU* 3.7 16.5 - - + +
490A SER* 3.2 17.5 + - - +
491A TRP 3.4 0.2 - - - -
492A LYS* 1.3 83.6 - - - +
494A LEU* 1.3 61.3 + - - +
496A THR* 2.9 10.2 + - - -
497A LEU* 2.9 29.6 + - - +
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Residues in contact with LEU 494 (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 GLN* 3.6 24.3 - - + +
489A TRP* 3.5 28.5 - - + -
490A SER 3.1 18.0 + - - +
491A TRP 3.9 3.1 - - - +
493A ASN* 1.3 76.6 - - - +
495A ASN* 1.3 62.3 + - - +
497A LEU* 3.5 8.1 + - + +
498A CYS* 3.3 31.5 + - - -
524A LEU* 4.4 16.6 - - + -
527A LEU* 4.6 6.1 - - + -
539A ILE* 4.2 11.4 - - + -
540A ILE* 3.8 24.9 - - + -
543A ASN* 3.2 16.0 - - + +
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Residues in contact with ASN 495 (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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491A TRP* 3.0 28.2 + - - +
492A LYS* 3.7 7.3 - - - +
494A LEU* 1.3 76.4 - - - +
496A THR* 1.3 58.0 + - - +
498A CYS* 3.5 0.5 + - - -
499A TRP* 2.8 64.3 + - + +
539A ILE* 4.0 24.3 - - - +
543A ASN* 3.1 31.6 + - - +
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Residues in contact with THR 496 (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 3.5 10.8 - - - +
422A SER 3.5 19.1 + - - +
423A ARG* 4.2 0.7 - - - -
424A MET* 3.5 38.0 + - - +
492A LYS* 2.9 18.4 + - - +
493A ASN* 2.9 13.2 + - - -
495A ASN* 1.3 76.7 - - - +
497A LEU* 1.3 64.0 + - - +
499A TRP* 3.6 15.4 - - - +
500A ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 497 (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* 3.9 22.6 + - + +
476A MET* 4.0 13.0 - - + +
479A LYS* 3.5 31.6 - - + +
480A LEU* 3.3 43.5 - - + +
483A GLN* 4.6 10.1 - - + -
493A ASN 2.9 14.3 + - - +
494A LEU* 3.9 12.8 - - + +
495A ASN 3.4 0.2 - - - -
496A THR* 1.3 76.4 - - - +
498A CYS* 1.3 60.5 + - - +
500A ALA* 3.5 2.1 + - - +
501A ILE* 3.0 45.9 + - + +
524A LEU* 5.9 0.2 - - + -
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Residues in contact with CYS 498 (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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494A LEU* 3.3 28.9 + - - -
495A ASN 4.1 0.2 - - - +
497A LEU* 1.3 79.5 - - - +
499A TRP* 1.3 67.4 + - + +
501A ILE* 3.7 9.7 - - - +
502A GLY* 3.0 18.0 + - - -
524A LEU* 4.3 9.9 - - - -
543A ASN* 3.5 35.9 - - + +
546A TYR* 3.6 13.4 - - + -
547A ILE* 3.7 27.6 - - + +
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Residues in contact with TRP 499 (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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424A MET* 3.6 32.3 - - + +
425A ALA* 3.7 7.0 - - - -
426A LYS* 3.7 37.9 - - + -
427A PRO* 3.9 28.1 - - + +
454A TYR* 4.8 2.1 - - + -
492A LYS 5.4 0.4 - - - -
495A ASN* 2.8 51.3 + - + +
496A THR* 3.6 17.9 - - - +
498A CYS* 1.3 78.4 - - + +
500A ALA* 1.3 61.8 + - - +
502A GLY* 3.3 2.4 + - - -
503A SER* 3.0 23.6 + - - -
543A ASN* 5.2 2.9 + - - -
546A TYR* 4.1 23.1 + + - -
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Residues in contact with ALA 500 (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* 4.0 32.1 - - + +
424A MET* 3.8 15.8 - - + +
461A LEU* 4.0 1.7 - - + +
476A MET* 3.8 16.2 - - + +
496A THR 3.0 16.5 + - - +
497A LEU 3.7 5.4 - - - +
499A TRP* 1.3 74.9 - - - +
501A ILE* 1.3 64.3 + - - +
503A SER* 2.5 25.3 + - - -
504A ILE* 3.6 5.0 + - - +
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Residues in contact with ILE 501 (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* 3.6 32.5 - - + +
480A LEU* 4.7 6.1 - - + -
497A LEU* 3.0 43.9 + - + +
498A CYS* 3.7 10.5 - - - +
499A TRP 3.4 0.2 - - - -
500A ALA* 1.3 74.5 - - - +
502A GLY* 1.3 58.9 + - - +
504A ILE* 3.2 10.2 - - - +
516A PHE* 3.7 25.4 - - + -
517A LEU* 5.1 0.2 - - + -
520A VAL* 3.9 25.6 - - + -
524A LEU* 6.0 0.2 - - + -
547A ILE* 4.4 24.9 - - + -
551A TYR* 2.7 30.0 + - + +
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Residues in contact with GLY 502 (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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498A CYS 3.0 14.8 + - - -
499A TRP 3.8 3.6 - - - -
500A ALA 3.2 0.2 - - - -
501A ILE* 1.3 75.7 - - - +
503A SER* 1.3 63.5 + - - +
504A ILE 3.2 2.0 + - - -
505A SER* 3.3 13.0 + - - -
546A TYR* 4.3 5.2 - - - -
547A ILE* 5.6 2.2 - - - -
550A GLN* 3.0 43.2 + - - -
551A TYR* 4.4 6.1 - - - -
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Residues in contact with SER 503 (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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424A MET* 3.8 10.3 - - - +
454A TYR* 3.7 22.6 + - - -
458A ARG* 3.0 48.1 - - - +
461A LEU* 4.0 5.9 - - - +
462A VAL* 3.9 5.2 - - - +
499A TRP 3.0 12.5 + - - -
500A ALA* 2.5 28.2 + - - -
502A GLY* 1.3 77.2 - - - +
504A ILE* 1.3 59.1 + - - +
505A SER 3.4 1.6 + - - +
550A GLN* 4.9 1.1 - - - +
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Residues in contact with ILE 504 (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 LEU* 3.5 44.6 - - + +
462A VAL* 4.0 8.5 - - + -
465A THR* 4.0 11.2 - - + +
472A THR* 4.1 11.0 - - + -
476A MET* 3.7 26.9 - - + -
500A ALA 3.8 1.6 - - - +
501A ILE 3.2 16.4 - - - +
503A SER* 1.3 79.1 - - - +
505A SER* 1.3 67.8 + - - +
506A GLY 3.1 0.2 + - - -
507A ALA* 2.8 29.5 + - + +
508A MET* 4.3 23.3 + - + +
516A PHE* 4.6 4.0 - - + -
551A TYR* 3.7 6.1 - - - +
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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