Contacts of the helix formed by residues 494 - 507 (chain A) in PDB entry 4N20
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 THR 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A SER* 1.3 71.3 - - - +
495A SER* 1.3 68.2 + - - +
497A CYS* 3.1 2.8 + - - +
498A TYR* 3.0 30.9 + - - -
541A ASN* 2.9 57.3 + - - +
542A LEU* 5.0 0.2 - - - -
544A PHE* 4.4 2.9 - - + -
545A GLN* 2.7 15.3 + - - +
548A LEU* 4.2 8.5 - - + +
571A ALA 3.2 14.4 - - - +
573A PHE* 3.7 26.9 - - + -
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 3.7 4.3 - - - -
494A THR* 1.3 79.9 + - - +
496A ALA* 1.3 56.5 + - - +
498A TYR* 3.4 5.7 + - - +
499A LYS* 3.0 28.6 + - - +
545A GLN* 3.0 24.4 + - - -
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Residues in contact with ALA 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 3.0 28.0 + - - +
495A SER* 1.3 74.6 - - - +
497A CYS* 1.3 64.9 + - - +
499A LYS* 3.5 6.6 + - - +
500A LEU* 3.1 23.9 + - - +
568A ASP* 4.7 10.5 - - + +
569A LEU 4.6 0.7 - - - -
570A PRO* 4.1 18.8 - - + +
617A HIS* 5.0 9.6 + - + +
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Residues in contact with CYS 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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493A SER 3.5 2.4 + - - -
494A THR 3.1 5.2 + - - +
496A ALA* 1.3 76.5 - - - +
498A TYR* 1.3 62.2 + - + +
500A LEU* 3.3 4.6 + - - +
501A PHE* 2.9 68.4 + - - -
570A PRO* 3.7 7.4 - - + +
571A ALA 3.2 28.7 - - - +
572A LEU* 4.3 8.3 - - + -
585A PHE* 3.8 24.7 - - - -
614A LEU* 4.4 4.0 - - - -
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Residues in contact with TYR 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 THR* 3.0 29.4 + - - +
495A SER* 4.0 5.4 - - - +
497A CYS* 1.3 78.0 - - - +
499A LYS* 1.3 55.2 + - - +
501A PHE* 3.8 5.0 - + - +
502A ARG* 2.9 65.1 + - - +
531A ILE* 4.6 10.7 + - + +
532A LEU* 3.7 24.5 - - + -
537A LEU* 3.4 36.7 + - - +
538A VAL* 3.6 31.6 + - + +
541A ASN* 3.6 18.2 + - + -
572A LEU* 3.4 28.0 - - + +
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Residues in contact with LYS 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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495A SER 3.0 17.6 + - - +
496A ALA* 3.7 7.9 - - - +
498A TYR* 1.3 77.3 - - - +
500A LEU* 1.3 57.3 + - - +
502A ARG* 3.8 10.5 - - + +
503A GLU* 3.0 56.5 + - + +
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Residues in contact with LEU 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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496A ALA 3.1 18.6 + - - +
497A CYS 3.6 3.1 - - - +
499A LYS* 1.3 77.6 - - - +
501A PHE* 1.3 63.4 + - + +
503A GLU* 3.2 8.6 + - + +
504A LYS* 3.0 55.1 + - + +
570A PRO* 4.7 2.2 - - + -
613A CYS* 3.8 28.5 - - + +
614A LEU* 3.7 30.3 - - + -
617A HIS* 3.9 33.2 - - + +
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Residues in contact with PHE 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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497A CYS* 2.9 43.7 + - - +
498A TYR* 4.0 4.7 - + - +
500A LEU* 1.3 83.1 - - + +
502A ARG* 1.3 58.5 + - - +
504A LYS* 3.4 3.2 + - - +
505A GLN* 2.9 29.8 + - - +
514A MET* 4.2 6.1 - - - -
528A ILE* 3.5 28.5 - - + +
531A ILE* 3.9 41.7 - - + -
532A LEU* 3.9 13.2 - - + -
572A LEU* 4.5 5.2 - - + -
585A PHE* 4.7 1.3 - + - -
606A PRO* 3.7 33.9 - - + -
613A CYS* 4.2 6.1 - - - -
614A LEU* 4.1 19.3 - - + -
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Residues in contact with ARG 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 TYR* 2.9 55.7 + - - +
499A LYS* 3.8 9.1 - - + +
501A PHE* 1.3 77.3 - - - +
503A GLU* 1.3 57.1 + - + +
505A GLN* 3.5 7.1 + - - +
506A LYS* 3.0 28.2 + - - +
532A LEU* 3.9 26.6 + - + +
538A VAL* 4.2 21.6 - - - +
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Residues in contact with GLU 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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499A LYS* 3.0 44.8 + - + +
500A LEU* 3.2 11.4 + - + +
502A ARG* 1.3 77.5 - - - +
504A LYS* 1.3 62.5 - - + +
506A LYS* 3.1 11.0 + - - +
507A ASP* 2.9 44.7 + - - +
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Residues in contact with LYS 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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500A LEU* 3.0 42.0 + - + +
501A PHE 3.9 0.4 - - - +
503A GLU* 1.3 78.6 - - - +
505A GLN* 1.3 59.0 + - - +
507A ASP* 3.2 22.3 + - - +
508A GLY 3.3 0.3 + - - -
509A HIS* 2.9 39.1 + - + +
528A ILE* 3.8 21.5 - - + -
608A VAL* 4.4 20.5 - - + +
613A CYS* 4.4 22.9 - - + -
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Residues in contact with GLN 505 (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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501A PHE 2.9 17.6 + - - +
502A ARG* 3.6 8.5 - - - +
504A LYS* 1.3 74.3 - - - +
506A LYS* 1.3 64.1 + - - +
508A GLY* 3.0 14.4 + - - -
509A HIS 3.9 0.3 + - - -
510A GLY* 3.8 12.6 + - - +
528A ILE* 4.1 5.5 - - + +
529A ASN* 2.8 36.0 + - - +
532A LEU* 3.3 30.5 - - + +
533A SER* 5.5 2.0 + - - -
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Residues in contact with LYS 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ARG 3.0 14.4 + - - +
503A GLU* 3.1 16.4 + - - +
505A GLN* 1.3 77.2 + - - +
507A ASP* 1.3 62.5 + - - +
508A GLY* 3.2 4.5 + - - -
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Residues in contact with ASP 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLU* 2.9 30.8 + - - +
504A LYS* 3.5 25.4 + - - +
505A GLN 3.1 0.4 - - - -
506A LYS* 1.3 83.6 - - - +
508A GLY* 1.3 57.2 + - - +
509A HIS* 3.5 23.2 + - + +
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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