Contacts of the helix formed by residues 574 - 584 (chain D) in PDB entry 5JA4
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 HIS 574 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D CYS 3.9 9.0 - - - -
538D ILE 3.3 15.6 + - - -
539D GLU 3.7 5.3 - - - -
540D GLY* 3.2 38.5 + - - -
569D ALA* 4.1 5.4 - - - +
572D TYR* 3.5 30.9 - - + +
573D GLY* 1.3 70.3 + - - -
575D LEU* 1.3 65.0 + - - +
576D GLU 3.3 2.9 - - - +
577D ILE* 3.1 19.3 + - + +
578D VAL* 3.0 24.0 + - + +
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Residues in contact with LEU 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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573D GLY 3.4 2.3 - - - -
574D HIS* 1.3 76.4 - - - +
576D GLU* 1.3 71.9 + - + +
578D VAL* 3.1 7.3 - - - +
579D ARG* 3.1 25.7 + - + +
612D GLU* 4.0 34.5 - - + +
613D VAL* 3.7 15.5 - - + -
616D LEU* 3.5 29.2 - - + -
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Residues in contact with GLU 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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542D LEU* 3.2 39.4 - - + +
574D HIS* 3.3 0.6 - - - +
575D LEU* 1.3 87.4 - - + +
577D ILE* 1.3 64.7 + - + +
579D ARG* 4.0 11.4 - - + +
580D PHE* 3.8 10.2 + - - +
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Residues in contact with ILE 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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537D CYS* 3.8 18.6 - - + -
540D GLY* 3.5 32.1 - - - +
541D GLN 3.6 3.6 - - - +
542D LEU* 3.5 34.5 - - + +
545D VAL* 3.8 11.0 - - + -
569D ALA* 4.8 1.3 - - + -
574D HIS* 3.1 30.7 + - + +
576D GLU* 1.3 78.4 - - + +
578D VAL* 1.3 64.8 + - + +
579D ARG 3.1 2.4 + - - -
580D PHE* 3.2 6.1 + - - +
581D LEU* 3.1 41.6 + - + +
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Residues in contact with VAL 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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566D LEU* 4.7 3.1 - - + -
569D ALA* 3.4 39.3 - - + +
570D CYS* 3.8 6.3 - - - +
574D HIS 3.0 15.4 + - - +
575D LEU 3.1 18.6 - - - +
577D ILE* 1.3 75.1 - - - +
579D ARG* 1.3 58.2 + - - +
581D LEU* 3.7 9.9 - - - -
582D LEU* 2.9 40.9 + - + +
613D VAL* 4.1 20.2 - - + -
616D LEU* 3.6 22.9 - - + -
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Residues in contact with ARG 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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575D LEU* 3.1 17.6 + - + +
576D GLU* 4.2 13.5 - - + +
577D ILE 3.1 0.8 - - - -
578D VAL* 1.3 75.8 - - - +
580D PHE* 1.3 67.0 + - - +
581D LEU 3.3 0.2 + - - -
582D LEU* 4.2 5.2 - - - +
583D ASP* 3.4 32.7 + - - +
616D LEU* 3.9 35.5 + - + +
619D GLU* 3.2 27.1 + - - +
620D ARG* 5.2 10.9 - - - +
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Residues in contact with PHE 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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542D LEU* 4.3 7.9 - - + -
545D VAL* 3.6 19.3 - - + -
546D GLN* 3.5 50.3 - - + -
549D VAL* 3.3 38.8 - - + -
550D ARG* 6.2 0.7 - - + -
576D GLU 3.8 10.7 + - - +
577D ILE 3.2 9.5 + - - +
579D ARG* 1.3 79.3 - - - +
581D LEU* 1.3 55.1 + - + +
583D ASP* 3.1 9.7 - - - +
584D HIS* 2.7 47.5 + + - -
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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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533D LEU* 4.9 10.3 - - + -
537D CYS* 3.9 10.5 - - + -
545D VAL* 3.6 29.4 - - + -
549D VAL* 4.4 12.6 - - + -
565D PRO* 4.6 5.2 - - + +
566D LEU* 4.8 10.3 - - + -
569D ALA* 3.4 32.3 - - + -
577D ILE* 3.1 31.8 + - + +
578D VAL* 3.7 4.9 - - - +
579D ARG 3.2 0.2 - - - -
580D PHE* 1.3 76.3 - - + +
582D LEU* 1.3 54.5 + - + +
583D ASP 2.9 5.7 + - - -
584D HIS* 2.7 35.5 + - - +
586D ALA 4.1 2.5 - - - +
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Residues in contact with LEU 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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566D LEU* 3.4 39.3 - - + -
578D VAL* 2.9 22.0 + - + +
579D ARG* 4.2 6.5 - - - +
581D LEU* 1.3 68.7 - - - +
583D ASP* 1.3 67.3 + - - +
584D HIS 3.5 5.1 - - - +
586D ALA* 4.2 7.5 - - - +
588D VAL* 3.5 49.5 - - + +
616D LEU* 3.5 31.6 - - + -
617D LEU* 4.1 16.8 - - + -
619D GLU 6.1 0.2 - - - +
620D ARG* 5.0 12.3 - - + +
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Residues in contact with ASP 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 ARG* 3.4 24.8 + - - +
580D PHE* 3.1 16.8 - - - +
581D LEU 2.9 0.4 - - - -
582D LEU* 1.3 82.3 - - - +
584D HIS* 1.3 72.9 + - + +
585D GLY 5.1 0.3 - - - -
586D ALA* 4.8 2.9 - - - +
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Residues in contact with HIS 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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549D VAL* 3.6 30.6 - - + +
580D PHE* 2.7 47.7 + + - -
581D LEU* 2.7 19.4 + - - +
582D LEU 3.5 0.7 - - - +
583D ASP* 1.3 88.9 - - + +
585D GLY* 1.3 63.8 + - - +
586D ALA* 3.1 12.3 - - - +
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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