Contacts of the helix formed by residues 493 - 504 (chain A) in PDB entry 3N51
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 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A PHE* 3.8 3.1 - - - -
456A GLY 3.3 17.7 - - - +
457A LYS* 4.4 13.2 - - + +
492A VAL* 1.3 75.0 - - - +
494A PHE* 1.3 64.5 + - - +
495A ASP* 3.5 9.1 + - - +
496A GLU* 2.9 48.6 + - - +
497A PHE* 3.0 22.0 + - - +
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Residues in contact with PHE 494 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A ARG 4.3 5.4 - - - -
443A LEU* 3.9 25.6 - - + -
444A GLU* 3.6 48.5 - - + -
447A PHE* 3.5 42.2 - + + -
448A ARG* 3.7 28.7 - - - +
456A GLY 4.1 1.0 + - - -
493A ASP* 1.3 75.8 - - - +
495A ASP* 1.3 62.5 + - + +
497A PHE* 3.2 4.7 + + - +
498A GLN* 2.9 52.6 + - + +
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Residues in contact with ASP 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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493A ASP* 3.4 9.4 + - - +
494A PHE* 1.3 86.3 - - + +
496A GLU* 1.3 58.3 + - + +
498A GLN* 3.4 15.8 + - - +
499A GLN* 2.5 61.4 + - - +
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Residues in contact with GLU 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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457A LYS* 5.6 2.4 + - - -
481A LEU* 5.6 0.7 - - + -
484A VAL* 4.2 18.6 - - + +
485A ASP* 3.7 23.0 - - + +
488A ASN* 6.0 0.7 - - - +
491A GLU 3.9 4.5 - - - +
492A VAL* 3.2 21.5 - - + +
493A ASP* 2.9 47.6 + - - +
495A ASP* 1.3 72.9 - - - +
497A PHE* 1.3 60.8 + - - +
499A GLN* 3.1 15.2 + - - +
500A MET* 2.8 33.8 + - - +
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Residues in contact with PHE 497 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A LEU* 4.0 26.2 - - + -
343A ALA* 4.4 6.1 - - + -
443A LEU* 4.1 11.2 - - + -
447A PHE* 4.0 20.4 - + + -
458A ILE* 4.7 4.5 - - + -
463A LEU* 3.7 32.3 - - + -
466A ILE* 4.3 20.2 - - + -
467A PHE* 3.8 20.4 - + - -
492A VAL* 4.1 9.5 - - + +
493A ASP 3.0 14.3 + - - +
494A PHE* 3.3 11.2 - + - +
496A GLU* 1.3 76.1 - - - +
498A GLN* 1.3 57.7 + - - +
500A MET* 3.0 11.6 + - - +
501A LEU* 3.0 57.0 + - + +
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Residues in contact with GLN 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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346A TYR* 2.8 38.2 + - + +
440A ARG* 4.4 12.8 - - - +
443A LEU* 4.5 8.8 - - + +
494A PHE* 2.9 46.9 + - + +
495A ASP* 3.6 17.3 + - - +
496A GLU 3.3 0.2 - - - -
497A PHE* 1.3 75.7 - - - +
499A GLN* 1.3 63.0 + - + +
501A LEU* 3.4 10.2 + - - +
502A LEU* 3.0 28.5 + - + +
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Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A VAL* 3.6 34.8 - - + +
495A ASP* 2.5 52.3 + - - +
496A GLU* 3.1 15.0 + - - +
498A GLN* 1.3 74.4 - - + +
500A MET* 1.3 64.9 + - - +
502A LEU* 3.2 14.1 + - + +
503A LYS* 3.1 27.1 + - - +
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Residues in contact with MET 500 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A LEU* 4.5 9.0 - - + -
467A PHE* 3.7 24.5 - - + -
477A TRP* 3.3 47.6 - - + +
480A VAL* 3.5 19.8 - - + +
481A LEU* 3.8 31.0 - - + -
484A VAL* 4.0 4.9 - - + +
492A VAL* 4.2 14.6 - - - -
496A GLU 2.8 17.4 + - - +
497A PHE* 3.0 13.7 + - - +
499A GLN* 1.3 74.4 - - - +
501A LEU* 1.3 62.6 + - - +
503A LYS* 3.0 4.2 + - - -
504A LEU* 2.9 27.7 + - + +
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A ALA* 3.8 23.1 - - + +
346A TYR* 3.7 29.4 - - + -
347A MET* 3.5 19.7 - - + +
443A LEU* 3.8 30.1 - - + -
467A PHE* 3.9 31.2 - - + -
497A PHE* 3.0 29.7 + - + +
498A GLN* 3.7 5.6 - - - +
499A GLN 3.4 0.2 - - - -
500A MET* 1.3 75.6 - - - +
502A LEU* 1.3 63.9 + - - +
504A LEU* 3.2 12.2 + - + -
505A CYS* 3.4 16.4 + - - -
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Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A TYR* 3.4 26.9 - - + +
350A LYS* 3.7 40.6 - - + -
498A GLN* 3.0 24.0 + - + +
499A GLN* 3.6 15.0 - - + +
500A MET 3.2 0.2 - - - -
501A LEU* 1.3 75.0 - - - +
503A LYS* 1.3 60.6 + - + +
505A CYS* 3.3 10.0 + - - -
507A ASN* 2.9 44.4 + - + +
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Residues in contact with LYS 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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480A VAL* 3.5 32.9 - - + +
483A GLU* 3.8 35.6 + - - +
484A VAL* 3.8 31.2 - - + +
499A GLN* 3.1 12.5 + - - +
500A MET 3.0 2.3 + - - +
502A LEU* 1.3 76.3 - - + +
504A LEU* 1.3 60.6 + - - +
505A CYS 3.2 1.6 + - - -
506A GLY* 3.6 8.9 + - - -
507A ASN* 3.9 24.8 + - - +
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Residues in contact with LEU 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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347A MET* 3.8 14.0 - - - +
467A PHE* 3.7 34.5 - - + -
472A VAL* 3.8 22.0 - - + -
476A THR* 3.5 31.9 - - + -
477A TRP* 4.4 8.7 - - + -
480A VAL* 4.1 14.8 - - + -
500A MET* 2.9 23.9 + - + +
501A LEU* 3.2 10.4 + - + +
503A LYS* 1.3 77.3 - - - +
505A CYS* 1.3 57.6 + - - +
506A GLY 3.6 0.7 - - - -
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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