Contacts of the helix formed by residues 572 - 585 (chain D) in PDB entry 5VOT
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 GLY 572 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541D PHE* 3.5 11.3 - - - -
571D PHE* 1.3 76.0 - - - +
573D ILE* 1.3 54.3 + - - +
574D PHE 3.2 2.7 - - - -
575D ASN* 3.3 11.3 + - - -
576D SER* 2.6 41.2 + - - -
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Residues in contact with ILE 573 (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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537D SER* 5.1 4.9 - - - +
538D VAL* 5.2 3.8 - - + -
541D PHE* 3.1 52.7 - - + -
572D GLY* 1.3 71.4 - - - +
574D PHE* 1.3 63.3 + - + +
576D SER* 3.4 2.7 + - - -
577D LEU* 2.9 31.6 + - + +
195E VAL* 3.8 28.3 - - + -
199E HIS* 5.9 5.8 - - + -
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Residues in contact with PHE 574 (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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594C ARG 4.0 13.7 - - - -
596C LEU* 3.5 42.4 - - + -
599C ARG* 4.2 15.9 - - + -
572D GLY* 3.2 0.4 - - - -
573D ILE* 1.3 85.9 - - + +
575D ASN* 1.3 71.4 + - - +
577D LEU* 3.2 13.5 + - + +
578D TRP* 2.9 33.8 + + + +
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Residues in contact with ASN 575 (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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594C ARG* 5.0 16.6 + - - +
570D GLU 5.6 0.2 - - - -
571D PHE 4.2 10.5 - - - +
572D GLY* 3.3 13.6 + - - +
574D PHE* 1.3 88.1 - - - +
576D SER* 1.3 57.9 + - - +
578D TRP* 3.3 15.3 + - + +
579D PHE* 2.9 27.0 + - - +
591D ILE* 5.5 10.3 - - + +
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Residues in contact with SER 576 (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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537D SER* 4.9 4.5 - - - -
540D LEU* 4.8 15.2 - - - +
541D PHE* 3.8 21.7 - - - +
544D SER* 5.6 0.2 - - - -
570D GLU 3.1 22.9 + - - -
571D PHE 4.8 0.2 + - - -
572D GLY 2.6 30.5 + - - -
573D ILE* 3.7 6.5 - - - -
575D ASN* 1.3 73.7 - - - +
577D LEU* 1.3 63.2 + - - +
579D PHE* 3.0 13.3 + - - +
580D SER* 2.9 22.0 + - - -
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Residues in contact with LEU 577 (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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533D TYR* 2.9 41.9 + - + +
534D ILE* 4.8 9.4 - - + -
537D SER* 3.3 30.7 - - - +
573D ILE* 2.9 21.4 + - + +
574D PHE* 3.6 12.3 - - + +
576D SER* 1.3 75.8 - - - +
578D TRP* 1.3 57.7 + - - +
580D SER* 2.8 25.1 + - - -
581D LEU 3.0 0.5 + - - -
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Residues in contact with TRP 578 (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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589C CYS* 5.6 4.7 - - + -
592C SER* 3.7 29.6 - - - -
593C PRO* 4.4 21.1 - - + -
599C ARG* 3.4 40.7 + - + +
606C TRP* 3.4 39.8 - + - -
574D PHE* 2.9 19.8 + + + +
575D ASN* 3.5 18.6 - - + +
577D LEU* 1.3 77.0 - - - +
579D PHE* 1.3 62.1 + - + +
580D SER 3.2 0.2 + - - -
581D LEU* 3.3 9.7 + - + +
582D GLY* 2.9 31.6 + - - -
588D GLY 5.3 3.1 - - - -
589D CYS* 3.6 33.4 - - + -
590D ASP 5.6 0.2 - - - -
591D ILE* 5.7 2.2 - - + -
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Residues in contact with PHE 579 (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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540D LEU* 4.1 25.6 - - + -
575D ASN 2.9 13.6 + - - +
576D SER* 3.0 12.1 + - - +
578D TRP* 1.3 81.7 - - + +
580D SER* 1.3 53.2 + - - +
582D GLY* 5.2 0.4 - - - -
583D ALA* 2.6 54.4 + - + +
589D CYS* 3.7 32.5 - - + -
591D ILE* 3.7 25.6 - - + -
592D SER* 4.9 0.7 - - - -
593D PRO* 4.3 24.2 - - + -
602D GLY* 5.0 12.3 - - - -
605D TRP* 5.4 4.7 - + - -
606D TRP* 4.5 22.9 - + - -
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Residues in contact with SER 580 (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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533D TYR* 3.4 20.2 - - - -
536D VAL* 5.7 2.4 - - - +
537D SER* 2.6 38.7 + - - -
540D LEU* 5.1 4.3 - - - +
576D SER 2.9 12.8 + - - -
577D LEU* 2.8 14.0 + - - -
579D PHE* 1.3 77.4 - - - +
581D LEU* 1.3 64.0 + - - -
583D ALA* 3.1 6.1 + - - +
584D PHE* 2.9 20.4 + - - +
605D TRP* 3.8 9.0 + - - +
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Residues in contact with LEU 581 (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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599C ARG 5.6 1.6 - - - +
603C GLY* 4.2 25.1 - - - +
606C TRP* 5.0 7.4 - - + -
607C PHE* 3.6 39.9 - - + -
533D TYR* 2.8 30.5 + - + +
577D LEU 3.0 3.6 + - - +
578D TRP* 4.1 11.0 - - + +
580D SER* 1.3 72.3 - - - +
582D GLY* 1.3 67.2 + - - +
584D PHE* 2.8 24.3 + - + +
585D MET* 3.1 15.4 + - + +
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Residues in contact with GLY 582 (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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606C TRP* 4.5 27.4 - - - -
578D TRP* 2.9 21.6 + - - -
579D PHE* 5.2 0.7 - - - -
581D LEU* 1.3 74.4 - - - +
583D ALA* 1.3 56.5 + - - +
585D MET* 3.1 8.2 + - - +
587D GLN* 2.7 31.0 - - - +
588D GLY 4.6 8.7 - - - -
589D CYS* 5.6 2.7 - - - -
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Residues in contact with ALA 583 (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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579D PHE* 2.6 44.4 + - + +
580D SER 3.3 5.2 - - - +
581D LEU 3.1 0.2 - - - -
582D GLY* 1.3 76.4 - - - +
584D PHE* 1.3 62.9 + - - +
585D MET 3.1 7.8 - - - +
587D GLN 4.1 3.8 - - - +
588D GLY* 5.8 2.0 - - - -
589D CYS* 5.5 1.5 - - - +
605D TRP* 3.7 22.9 - - + +
606D TRP* 4.5 14.4 + - - +
609D THR* 4.2 8.1 + - - +
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Residues in contact with PHE 584 (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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607C PHE* 5.6 7.2 - + - -
610C LEU* 5.2 9.2 - - + -
526D TRP* 5.7 9.2 - + - -
529D ILE* 4.6 20.4 - - + -
533D TYR* 5.1 4.9 - + + -
580D SER 2.9 10.6 + - - +
581D LEU* 2.8 21.5 + - + +
583D ALA* 1.3 78.6 - - - +
585D MET* 1.3 71.8 + - + +
605D TRP* 4.0 23.9 - + + +
608D PHE* 5.0 5.2 - + - -
609D THR* 3.2 39.0 - - - +
612D ILE* 4.3 19.5 - - + -
613D ILE* 3.5 33.6 - - + +
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Residues in contact with MET 585 (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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606C TRP* 3.9 34.5 - - + +
607C PHE* 5.6 4.9 - - + +
609C THR* 6.1 0.9 - - + -
610C LEU* 5.7 10.3 - - + -
581D LEU* 3.1 14.6 + - + +
582D GLY* 3.1 3.4 - - - +
583D ALA 3.1 5.7 - - - +
584D PHE* 1.3 94.1 - - + +
586D ARG* 1.3 67.8 + - - +
587D GLN 2.9 15.7 + - - +
609D THR* 5.3 0.3 - - - +
613D ILE* 5.9 1.3 - - - -
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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