Contacts of the helix formed by residues 506 - 518 (chain D) in PDB entry 1Z6T
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 SER 506 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502D ALA 4.1 8.8 + - - -
503D LEU 3.3 22.4 - - - -
504D MET 2.9 7.9 + - - +
505D PHE* 1.3 75.5 - - - +
507D LEU* 1.3 63.8 + - - +
508D ASP* 3.6 12.6 + - - +
509D TRP* 3.5 14.2 + - - +
510D ILE* 3.1 24.6 + - - +
544D PHE* 3.4 7.5 - - - -
579D GLN* 3.5 5.4 - - - -
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Residues in contact with LEU 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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506D SER* 1.3 71.2 - - - +
508D ASP* 1.3 57.8 + - - +
510D ILE* 3.8 4.6 - - + +
511D LYS* 2.9 31.1 + - - +
544D PHE* 4.4 7.8 - - + -
547D PHE* 4.2 10.5 - - + -
563D ILE* 3.9 27.9 - - + +
564D VAL* 4.6 8.5 - - + -
567D GLY* 5.4 0.4 - - - -
576D VAL* 4.0 25.4 - - + +
579D GLN* 3.1 24.5 + - + +
580D ALA* 3.6 37.9 - - + +
583D GLN* 4.1 19.3 - - - +
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Residues in contact with ASP 508 (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 HIS* 5.7 11.0 - - + +
506D SER* 3.2 10.5 + - - +
507D LEU* 1.3 78.6 - - - +
509D TRP* 1.3 56.2 + - - +
511D LYS* 3.7 7.6 - - - +
512D ALA* 3.0 30.0 + - - +
583D GLN* 4.0 19.4 + - - +
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Residues in contact with TRP 509 (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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470D PRO* 3.9 35.0 - - + -
473D LEU* 4.8 4.7 - - + -
483D TRP 4.6 1.8 - - - -
484D TYR* 3.4 45.1 - + - -
487D LEU* 4.6 10.3 - - + -
488D ALA* 6.0 2.6 - - + +
503D LEU* 3.2 56.5 - - + +
504D MET* 4.1 16.2 - - - +
506D SER* 3.3 10.5 + - - +
508D ASP* 1.3 76.1 - - - +
510D ILE* 1.3 63.6 + - + +
512D ALA* 4.5 4.0 - - + +
513D LYS* 2.9 51.8 + - + +
522D LEU* 3.9 25.6 - - + +
525D GLU* 5.2 1.9 + - - -
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Residues in contact with ILE 510 (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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504D MET 4.5 6.3 - - - +
506D SER 3.1 16.3 + - - +
507D LEU* 3.8 6.5 - - - +
508D ASP 3.4 0.2 - - - -
509D TRP* 1.3 77.2 - - + +
511D LYS* 1.3 53.3 + - - +
514D THR* 2.5 48.5 + - + +
522D LEU* 4.0 20.9 - - + -
526D PHE* 4.9 0.9 - - + -
544D PHE* 3.4 38.1 - - + -
547D PHE* 4.2 21.1 - - + -
548D LEU* 3.7 35.2 - - + -
555D LEU* 4.9 4.3 - - + -
563D ILE* 4.7 9.0 - - + -
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Residues in contact with LYS 511 (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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268C SER* 4.8 10.6 + - - -
271C ASP* 4.7 11.8 + - - -
507D LEU 2.9 17.2 + - - +
508D ASP* 3.7 7.9 - - - +
510D ILE* 1.3 76.7 - - - +
512D ALA* 1.3 63.8 + - - +
515D GLU* 3.1 58.8 + - - +
561D PRO 5.7 3.4 - - - -
563D ILE* 3.2 34.5 - - + +
583D GLN* 6.1 3.2 - - - +
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Residues in contact with ALA 512 (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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470D PRO 5.6 2.2 - - - +
471D HIS* 6.0 4.0 - - - -
484D TYR* 3.4 24.6 + - + +
508D ASP 3.0 19.3 + - - +
509D TRP* 3.9 8.1 - - + +
511D LYS* 1.3 78.3 - - - +
513D LYS* 1.3 63.8 + - - +
515D GLU* 3.6 5.6 + - - +
516D LEU* 3.5 21.5 + - - +
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Residues in contact with LYS 513 (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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484D TYR* 2.8 51.7 + - + +
485D ASN* 5.5 0.7 - - - -
509D TRP* 2.9 37.3 + - + +
512D ALA* 1.3 78.4 - - - +
514D THR* 1.3 57.9 + - - +
516D LEU* 3.2 4.2 + - - +
517D VAL* 3.0 50.9 + - + +
518D GLY 5.1 1.1 - - - +
521D HIS* 3.1 28.7 - - - -
522D LEU* 3.8 24.5 - - + +
525D GLU* 2.7 28.3 + - - -
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Residues in contact with THR 514 (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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218D LEU* 5.2 0.2 - - - +
510D ILE* 2.5 44.1 + - + +
511D LYS* 3.4 6.1 + - - -
513D LYS* 1.3 72.7 - - - +
515D GLU* 1.3 62.4 + - - +
516D LEU 4.1 0.2 - - - -
518D GLY 2.9 37.9 + - - +
519D PRO* 4.0 7.6 - - + -
522D LEU* 3.7 20.4 - - + -
548D LEU* 4.5 1.1 - - + -
555D LEU* 3.9 30.5 - - + +
556D GLY* 3.0 18.6 + - - -
563D ILE* 4.4 2.3 - - - +
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Residues in contact with GLU 515 (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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268C SER* 5.6 1.6 + - - -
215D ARG* 6.1 1.0 - - - +
511D LYS* 3.1 58.6 + - + +
512D ALA* 4.0 6.0 - - - +
513D LYS 3.3 0.2 - - - -
514D THR* 1.3 80.2 + - - +
516D LEU* 1.3 60.8 + - + +
556D GLY* 4.2 4.3 - - - +
560D PHE* 3.2 72.6 - - + +
561D PRO* 4.9 3.5 - - + +
563D ILE* 5.3 2.9 - - + +
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Residues in contact with LEU 516 (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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216D LEU* 3.5 29.7 + - + +
218D LEU* 5.0 2.6 - - - +
475D PRO* 3.9 26.7 - - + -
480D CYS* 4.5 5.4 - - - -
481D MET* 4.4 16.2 - - + -
484D TYR* 3.4 44.2 - - + +
512D ALA 3.5 6.6 + - - +
513D LYS* 3.2 8.2 + - - +
514D THR 3.2 0.4 - - - -
515D GLU* 1.3 82.6 - - + +
517D VAL* 1.3 65.6 + - + +
518D GLY 3.8 0.4 - - - -
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Residues in contact with VAL 517 (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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196D LEU* 5.2 2.4 - - - +
200D GLN* 3.1 39.0 + - - +
216D LEU* 4.1 6.1 - - + -
218D LEU* 3.7 14.5 - - - +
481D MET* 3.7 30.3 - - + -
484D TYR* 5.6 2.7 - - + -
485D ASN* 5.2 4.3 - - - +
513D LYS* 3.0 48.2 + - + +
516D LEU* 1.3 83.5 - - + +
518D GLY* 1.3 66.2 + - - +
520D ALA* 5.1 1.4 + - - +
521D HIS* 5.5 6.4 + - + -
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Residues in contact with GLY 518 (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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218D LEU* 3.8 13.6 - - - +
513D LYS* 4.4 0.9 - - - +
514D THR* 2.9 35.5 + - - +
516D LEU 3.8 0.4 - - - -
517D VAL* 1.3 90.1 - - - +
519D PRO* 1.3 73.0 - - - +
520D ALA 3.6 1.1 + - - -
521D HIS* 5.0 1.9 + - - +
522D LEU* 5.0 4.5 + - - +
555D LEU 4.1 4.0 - - - -
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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