Contacts of the helix formed by residues 498 - 507 (chain F) in PDB entry 4CYM
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 498 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468F HIS* 3.7 2.7 - - - -
489F VAL 4.6 2.0 - - - -
490F ASN* 3.8 38.8 - - - +
491F ALA 3.4 3.4 - - - +
492F THR* 4.3 1.6 - - + -
496F GLY 3.8 0.6 + - - -
497F ALA* 1.3 73.2 - - - +
499F PRO* 1.3 74.2 - - - +
500F LEU* 3.5 12.5 + - - +
501F HIS* 2.7 45.4 + - - +
502F LEU* 3.1 11.4 + - - +
521F SER 4.8 2.2 + - - +
524F VAL* 4.1 26.0 - - + -
532F PRO* 4.2 1.4 - - - +
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Residues in contact with PRO 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465F THR* 4.8 0.7 - - - +
467F LEU* 3.9 36.8 - - + +
468F HIS* 3.5 27.3 - - + +
471F ALA* 3.8 12.3 - - + +
488F MET 5.1 0.9 - - - +
489F VAL 3.5 19.1 - - - +
491F ALA 3.4 13.9 - - - +
498F THR* 1.3 86.2 - - - +
500F LEU* 1.3 57.6 + - - +
502F LEU* 3.0 6.9 + - + +
503F ALA* 2.9 28.2 + - - +
515F LEU* 3.8 13.5 - - + -
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Residues in contact with LEU 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489F VAL 5.3 0.8 + - - +
498F THR* 3.1 11.3 + - - +
499F PRO* 1.3 79.7 - - - +
501F HIS* 1.3 62.1 + - - +
503F ALA* 3.4 0.9 + - - +
504F CYS* 3.0 27.9 + - - +
512F THR* 3.8 41.5 - - - +
515F LEU* 3.6 16.2 - - + +
516F LEU* 4.0 18.6 - - + -
520F ALA* 4.2 12.7 - - + +
521F SER 3.6 22.9 - - - +
522F ALA* 3.9 10.5 - - - -
532F PRO* 3.7 18.8 - - + -
548F LEU* 4.3 4.0 - - + -
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Residues in contact with HIS 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496F GLY 4.1 7.0 - - - -
497F ALA* 4.0 11.4 - - + -
498F THR* 2.7 48.4 + - - +
500F LEU* 1.3 72.4 - - - +
502F LEU* 1.3 65.2 + - + +
504F CYS* 3.4 0.9 + - - +
505F GLN* 3.1 23.6 + - - +
524F VAL* 3.0 37.1 + - + -
526F ASP* 3.9 11.8 + - + -
530F ASN 2.6 28.3 + - - -
531F THR 3.5 3.0 - - - -
532F PRO* 3.6 24.8 - - + +
535F LEU* 3.6 27.8 - - + +
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Residues in contact with LEU 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464F HIS* 4.6 10.3 - - + +
468F HIS* 3.5 51.1 - - + +
471F ALA* 4.7 1.3 - - + -
472F VAL* 4.2 28.1 - - + +
493F ASP* 5.2 3.6 - - - +
497F ALA* 4.5 15.0 - - + -
498F THR 3.7 8.5 - - - +
499F PRO* 3.0 8.1 + - + +
501F HIS* 1.3 75.6 - - + +
503F ALA* 1.3 67.1 + - - +
505F GLN* 3.2 21.2 + - - +
506F LYS* 3.0 25.5 + - - +
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Residues in contact with ALA 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471F ALA* 4.7 7.5 - - + +
499F PRO 2.9 14.6 + - - +
500F LEU 3.8 4.0 - - - +
502F LEU* 1.3 77.4 - - - +
504F CYS* 1.3 57.4 + - - +
506F LYS* 3.2 4.7 + - - +
507F GLY 2.8 25.6 + - - -
508F TYR* 3.2 13.5 + - + +
511F VAL* 3.5 32.5 - - + -
512F THR* 4.0 17.5 - - + +
515F LEU* 4.2 4.5 - - + -
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Residues in contact with CYS 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500F LEU* 3.0 23.6 + - - +
501F HIS 4.1 2.0 - - - +
503F ALA* 1.3 76.5 - - - +
505F GLN* 1.3 63.0 + - - +
507F GLY* 3.6 5.5 + - - +
512F THR* 3.8 26.0 - - - -
532F PRO* 3.4 27.6 - - + +
535F LEU* 4.9 0.4 - - + -
536F ALA* 3.6 23.8 - - + +
541F HIS* 3.9 6.9 + - - +
544F CYS* 4.5 10.5 - - - -
548F LEU* 3.7 26.9 - - - -
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Residues in contact with GLN 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501F HIS 3.1 15.5 + - - +
502F LEU* 3.5 22.8 + - - +
504F CYS* 1.3 76.7 - - - +
506F LYS* 1.3 60.0 + - + +
535F LEU* 4.3 24.6 - - + +
539F TYR* 3.2 44.7 + - + -
541F HIS* 3.0 24.4 - - - -
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Residues in contact with LYS 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472F VAL* 3.4 31.6 - - + +
502F LEU 3.0 15.8 + - - +
503F ALA* 3.8 3.6 - - - +
505F GLN* 1.3 80.9 - - + +
507F GLY* 1.3 57.9 + - - +
508F TYR* 3.0 55.9 - - + -
541F HIS* 3.4 7.6 + - - -
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Residues in contact with GLY 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503F ALA 2.8 9.9 + - - -
504F CYS 3.6 0.6 + - - -
505F GLN 3.2 3.4 - - - -
506F LYS* 1.3 78.9 - - - +
508F TYR* 1.3 59.5 + - - -
509F GLN 3.3 6.4 + - - -
541F HIS* 2.7 31.0 - - - -
543F ASP* 3.9 10.0 - - - +
544F CYS* 3.5 12.0 - - - -
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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