Contacts of the helix formed by residues 500 - 515 (chain A) in PDB entry 1N0U
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 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A VAL* 3.9 8.5 - - + +
497A ASN* 2.6 46.7 + - - +
499A ASN* 1.3 72.7 - - - +
501A LEU* 1.3 64.2 + - - +
502A PRO* 3.2 4.0 - - - -
503A LYS* 2.8 40.9 + - - +
504A LEU 3.1 9.0 + - - -
552A VAL* 3.1 38.1 - - + +
553A PRO* 4.7 2.1 - - - +
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU* 5.7 4.0 - - + -
495A VAL* 3.5 30.8 - - + +
498A ALA* 3.1 27.5 + - + +
500A ASP* 1.3 75.3 - - - +
502A PRO* 1.3 71.7 - - + +
504A LEU* 2.9 8.6 + - + +
505A VAL* 2.9 34.1 + - + +
528A HIS* 5.3 11.2 - - + +
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Residues in contact with PRO 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 ALA 4.6 0.4 - - - +
499A ASN 3.2 18.4 - - - +
500A ASP 3.3 1.6 - - - -
501A LEU* 1.3 95.4 - - + +
503A LYS* 1.3 59.6 + - + +
505A VAL* 4.0 6.8 - - + +
506A GLU* 3.1 28.9 + - - +
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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
----------------------------------------------------------
499A ASN 5.6 1.8 - - - +
500A ASP* 2.8 35.6 + - - +
502A PRO* 1.3 74.1 - - + +
504A LEU* 1.3 54.3 + - - +
506A GLU* 3.4 4.9 + - - +
507A GLY* 2.7 31.9 + - - -
549A HIS 4.5 0.5 - - - +
550A ALA* 3.8 14.3 - - - +
552A VAL* 3.4 31.5 - - + +
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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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493A VAL* 3.9 33.4 - - + +
494A GLU* 4.1 2.5 - - - -
495A VAL* 3.4 44.9 - - + +
500A ASP 3.1 4.0 + - - -
501A LEU* 2.9 9.7 + - + +
503A LYS* 1.3 75.3 - - - +
505A VAL* 1.3 67.6 + - + +
507A GLY* 2.9 2.4 + - - -
508A LEU* 2.8 48.4 + - + +
528A HIS* 4.5 14.1 - - + -
545A LEU* 4.2 11.0 - - + -
550A ALA* 4.0 7.1 - - + +
552A VAL* 5.6 0.8 - - + +
554A LEU* 4.2 9.9 - - + -
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Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 2.9 26.7 + - + +
502A PRO* 4.0 6.3 - - + +
504A LEU* 1.3 77.7 - - + +
506A GLU* 1.3 62.8 + - - +
508A LEU* 3.4 18.7 + - + +
509A LYS* 3.4 33.8 + - - +
528A HIS* 4.1 26.7 - - + +
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Residues in contact with GLU 506 (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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502A PRO 3.1 20.1 + - - +
503A LYS* 3.7 7.0 - - - +
505A VAL* 1.3 74.2 - - - +
507A GLY* 1.3 67.5 + - - +
509A LYS* 3.1 22.1 + - - +
510A ARG* 3.1 56.9 + - - +
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Residues in contact with GLY 507 (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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503A LYS 2.7 17.0 + - - -
504A LEU 2.9 4.2 + - - -
506A GLU* 1.3 74.6 - - - +
508A LEU* 1.3 51.4 + - - +
510A ARG* 3.0 4.9 + - - +
511A LEU* 2.7 36.0 + - - +
545A LEU* 3.7 7.2 - - - -
549A HIS* 3.3 32.6 + - - +
550A ALA* 3.9 2.9 - - - -
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 5.5 0.2 - - + -
504A LEU* 2.8 28.0 + - + +
505A VAL* 3.6 13.9 - - + +
507A GLY* 1.3 75.6 - - - +
509A LYS* 1.3 58.0 + - + +
511A LEU* 3.6 5.4 - - + +
512A SER* 2.9 35.0 + - - -
520A THR* 4.0 22.5 + - + +
528A HIS* 3.6 36.8 - - + +
529A ILE 5.9 0.4 - - - +
530A VAL* 3.7 29.8 - - + -
545A LEU* 3.7 20.2 - - + -
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Residues in contact with LYS 509 (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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505A VAL* 3.5 28.9 - - - +
506A GLU* 3.1 25.0 + - - +
508A LEU* 1.3 78.9 - - + +
510A ARG* 1.3 62.9 + - - +
512A SER* 3.3 6.5 + - - -
513A LYS* 2.9 38.4 + - - +
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Residues in contact with ARG 510 (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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506A GLU* 3.1 42.3 + - - +
507A GLY* 3.0 7.7 + - - +
509A LYS* 1.3 76.5 - - - +
511A LEU* 1.3 62.7 + - - +
513A LYS* 3.2 10.7 + - + +
514A SER* 3.0 24.3 + - - -
548A ASP 4.8 4.2 + - - -
549A HIS* 3.6 40.9 + - - +
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Residues in contact with LEU 511 (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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507A GLY 2.7 19.9 + - - +
508A LEU* 3.6 4.7 - - + +
510A ARG* 1.3 73.1 - - - +
512A SER* 1.3 62.4 + - - +
514A SER* 2.8 20.8 + - - +
515A ASP* 3.0 14.0 + - + +
518A VAL* 3.9 24.2 - - + -
520A THR* 4.3 9.9 - - + -
530A VAL* 4.2 16.8 - - + -
541A CYS* 4.1 37.9 - - + +
544A ASP* 5.4 0.7 - - + -
545A LEU* 4.4 16.2 - - + -
549A HIS* 3.7 28.6 + - + +
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Residues in contact with SER 512 (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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508A LEU 2.9 21.0 + - - -
509A LYS* 3.6 6.9 - - - -
511A LEU* 1.3 77.6 - - - +
513A LYS* 1.3 61.9 + - - +
515A ASP 2.8 21.1 - - - +
516A PRO* 4.8 0.9 - - - +
518A VAL* 3.7 15.7 + - - +
520A THR* 3.2 26.2 + - - +
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Residues in contact with LYS 513 (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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509A LYS* 2.9 29.5 + - - +
510A ARG* 3.2 8.9 + - + +
512A SER* 1.3 76.4 - - - +
514A SER* 1.3 61.2 + - - +
515A ASP 3.6 0.7 + - - -
516A PRO* 5.4 1.6 - - - +
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ARG 3.0 12.7 + - - -
511A LEU* 2.8 19.1 + - - +
513A LYS* 1.3 75.9 - - - +
515A ASP* 1.3 60.8 + - - +
516A PRO* 4.0 5.6 - - - +
549A HIS* 3.3 23.9 + - - -
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Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LEU* 3.0 11.9 + - + +
512A SER 2.8 19.6 + - - +
513A LYS 3.4 0.4 - - - -
514A SER* 1.3 83.0 - - - +
516A PRO* 1.3 64.4 - - - +
517A CYS* 2.7 35.0 + - - +
518A VAL* 3.1 33.3 + - + +
537A HIS* 2.9 27.5 - - - -
541A CYS* 3.8 5.9 - - - -
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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