Contacts of the helix formed by residues 498 - 507 (chain D) in PDB entry 4CZ2
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468D HIS* 3.7 1.6 - - - -
489D VAL 4.9 1.3 - - - +
490D ASN* 3.8 26.7 + - - +
491D ALA 3.5 12.2 + - - -
492D THR* 4.4 0.7 - - - +
496D GLY 3.9 0.6 + - - -
497D ALA* 1.3 75.9 - - - +
499D PRO* 1.3 68.2 - - + +
500D LEU* 3.2 34.3 - - + +
501D HIS* 3.1 37.5 + - + +
502D LEU* 3.3 9.2 + - - +
521D SER 4.5 9.9 - - - +
524D VAL* 4.1 13.9 - - - +
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Residues in contact with PRO 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D THR* 4.9 1.1 - - - +
467D LEU* 3.9 37.5 - - + +
468D HIS* 3.5 25.6 - - + +
471D ALA* 3.5 13.8 - - + +
488D MET 5.0 0.9 - - - +
489D VAL 3.4 23.6 - - - +
491D ALA 3.3 16.4 - - - +
498D THR* 1.3 82.2 - - - +
500D LEU* 1.3 61.8 + - - +
502D LEU* 3.0 6.6 + - + +
503D ALA* 3.0 20.3 + - - +
515D LEU* 3.6 11.4 - - + -
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Residues in contact with LEU 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D VAL 5.3 0.4 + - - -
498D THR* 3.2 15.3 - - + +
499D PRO* 1.3 79.1 - - - +
501D HIS* 1.3 53.9 + - - +
503D ALA* 3.6 1.3 + - - +
504D CYS* 2.9 31.3 + - - +
512D THR* 3.7 44.6 - - + +
515D LEU* 3.3 19.3 - - + +
516D LEU* 4.1 17.5 - - + -
520D ALA* 4.3 10.1 - - + -
521D SER 3.6 22.9 - - - +
522D ALA* 3.9 10.5 - - - -
532D PRO* 3.6 20.9 - - + -
548D LEU* 4.2 4.5 - - + -
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Residues in contact with HIS 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D GLY 4.2 1.0 + - - -
497D ALA* 4.1 10.7 - - + +
498D THR* 3.1 52.1 + - + +
500D LEU* 1.3 76.0 - - - +
502D LEU* 1.3 64.5 + - + +
504D CYS 3.3 0.9 + - - -
505D GLN* 3.1 25.5 + - - +
524D VAL* 3.1 29.0 + - - +
526D ASP* 3.9 19.1 + - + +
530D ASN 2.9 29.2 - - - -
532D PRO* 3.6 22.4 - - + +
535D LEU* 3.5 30.3 - - + +
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Residues in contact with LEU 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D HIS* 4.8 11.7 - - + -
468D HIS* 3.5 45.8 - - + +
471D ALA* 4.4 4.7 - - + -
472D VAL* 4.3 25.8 - - + -
493D ASP* 5.3 2.7 - - - +
497D ALA* 4.5 15.7 - - + -
498D THR 3.6 10.8 - - - +
499D PRO* 3.0 7.5 + - + +
501D HIS* 1.3 76.0 - - + +
503D ALA* 1.3 65.5 + - - +
505D GLN* 3.1 17.8 + - - +
506D LYS* 3.0 28.0 + - - +
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Residues in contact with ALA 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D ALA* 4.4 4.1 + - - +
499D PRO 3.0 11.2 + - - +
500D LEU 3.7 7.9 - - - +
502D LEU* 1.3 74.0 - - - +
504D CYS* 1.3 56.9 + - - +
506D LYS 3.7 0.2 + - - -
507D GLY* 3.0 22.0 + - - -
508D TYR* 3.0 23.6 + - - +
511D VAL* 3.6 32.1 - - + -
512D THR* 3.7 21.6 + - - +
515D LEU* 4.3 2.2 - - + -
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Residues in contact with CYS 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D LEU* 2.9 23.7 + - - +
501D HIS 3.3 4.2 + - - +
502D LEU 3.3 0.4 - - - -
503D ALA* 1.3 72.0 - - - +
505D GLN* 1.3 58.3 + - - +
507D GLY* 3.8 6.9 + - - +
512D THR* 3.6 27.1 - - - -
532D PRO* 3.5 26.5 - - + +
535D LEU* 4.0 1.3 - - + +
536D ALA* 3.4 26.1 - - + +
541D HIS* 4.4 3.8 - - - +
544D CYS* 4.4 10.1 - - - -
548D LEU* 3.7 30.5 - - - -
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Residues in contact with GLN 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D HIS 3.1 14.9 + - - +
502D LEU* 3.1 17.2 + - - +
504D CYS* 1.3 77.6 - - - +
506D LYS* 1.3 72.3 + - + +
507D GLY 3.1 4.8 + - - -
535D LEU* 3.7 31.9 - - + +
539D TYR* 3.3 49.3 + - + -
541D HIS* 3.4 14.9 + - - -
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Residues in contact with LYS 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D VAL* 3.8 35.1 + - + +
502D LEU 3.0 11.8 + - - +
505D GLN* 1.3 86.9 - - + +
507D GLY* 1.3 61.0 + - - +
508D TYR* 3.1 40.2 + - + +
541D HIS* 3.4 9.7 - - - -
506E LYS* 4.7 10.8 + - - +
507E GLY 5.0 8.5 + - - -
508E TYR* 4.1 15.1 + - - -
541E HIS* 5.4 10.1 - - + -
543E ASP* 5.2 6.5 + - - -
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Residues in contact with GLY 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503D ALA 3.0 9.3 + - - -
504D CYS 3.8 1.1 - - - -
505D GLN 3.1 6.3 - - - +
506D LYS* 1.3 76.9 - - - +
508D TYR* 1.3 57.2 + - - -
509D GLN 3.1 7.6 + - - -
541D HIS* 2.7 30.5 + - - -
543D ASP* 3.5 11.4 - - - +
544D CYS* 3.5 13.1 - - - -
506E LYS* 5.2 3.3 + - - -
508E TYR* 4.1 6.9 + - - -
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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