Contacts of the helix formed by residues 522 - 532 (chain D) in PDB entry 4DHJ
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 522 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520D SER 4.5 6.7 - - - +
521D ASP* 1.3 78.7 - - - +
523D ILE* 1.3 64.2 + - - +
524D GLU* 3.1 20.6 - - - +
525D ASN* 2.7 45.6 + - - +
526D VAL* 3.3 13.9 + - - +
552D ASP 4.0 3.4 - - - -
553D GLY* 4.9 7.9 - - - +
554D ARG 3.4 11.2 - - - +
555D THR* 4.1 8.5 - - + +
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Residues in contact with ILE 523 (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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522D THR* 1.3 73.7 - - - +
524D GLU* 1.3 60.8 + - - +
526D VAL* 3.3 8.9 + - + +
527D LYS* 3.2 38.3 + - - +
543D LEU* 4.4 10.0 - - + +
550D LEU* 3.7 48.7 - - + +
551D GLU 3.1 23.8 - - - +
552D ASP* 3.5 5.7 + - - +
554D ARG 2.8 17.0 + - - +
555D THR 4.6 2.7 - - - +
556D LEU* 3.8 28.5 - - + -
559D TYR* 4.1 13.7 - - + -
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Residues in contact with GLU 524 (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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522D THR* 3.1 22.7 + - - +
523D ILE* 1.3 74.5 - - - +
525D ASN* 1.3 58.5 + - - +
526D VAL 3.0 1.8 - - - -
527D LYS* 2.8 28.7 + - + +
528D ALA* 2.8 16.1 + - - +
552D ASP* 3.5 36.9 + - - +
553D GLY* 4.3 6.1 + - - -
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Residues in contact with ASN 525 (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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520D SER 5.1 0.2 - - - +
521D ASP* 4.1 21.6 - - + +
522D THR* 2.7 49.9 + - - +
524D GLU* 1.3 77.5 - - - +
526D VAL* 1.3 57.5 + - - +
528D ALA* 3.8 7.8 + - - +
529D LYS* 3.1 35.6 + - - +
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Residues in contact with VAL 526 (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 ILE* 4.7 3.1 - - + -
505D VAL* 5.3 0.7 - - + -
515D LEU* 3.7 21.8 - - + -
517D VAL* 4.7 5.8 - - + -
521D ASP* 4.6 7.2 - - + -
522D THR 3.3 15.9 + - - +
523D ILE* 3.5 8.3 - - + +
524D GLU 3.0 0.8 - - - -
525D ASN* 1.3 75.8 - - - +
527D LYS* 1.3 59.6 + - - +
528D ALA 3.3 0.4 - - - -
529D LYS* 3.2 6.9 + - + +
530D ILE* 3.1 31.7 + - + +
543D LEU* 3.8 22.0 - - + -
556D LEU* 4.0 31.9 - - + -
567D LEU* 4.6 11.2 - - + -
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Residues in contact with LYS 527 (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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523D ILE* 3.2 25.5 + - - +
524D GLU* 2.8 11.6 + - + +
526D VAL* 1.3 75.3 - - - +
528D ALA* 1.3 61.8 + - - +
530D ILE* 3.3 20.4 - - - +
531D GLN* 3.5 11.8 + - - +
538D PRO* 3.8 27.4 + - + +
541D GLN* 3.5 47.3 + - + +
542D ARG* 5.2 0.8 - - - +
543D LEU* 4.3 16.6 - - + +
550D LEU 4.6 5.8 + - - -
552D ASP* 2.5 37.2 + - - +
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Residues in contact with ALA 528 (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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524D GLU 2.8 13.7 + - - +
525D ASN* 4.0 9.4 - - - +
527D LYS* 1.3 75.3 - - - +
529D LYS* 1.3 56.4 + - - +
530D ILE 3.1 1.6 - - - -
531D GLN* 3.0 12.1 + - + +
532D ASP* 2.7 42.0 + - - +
538D PRO* 5.1 3.5 - - + +
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Residues in contact with LYS 529 (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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515D LEU* 3.8 19.3 - - + +
516D GLU 3.4 25.8 + - - +
517D VAL* 4.2 10.7 - - + +
521D ASP* 3.3 29.7 + - - +
525D ASN* 3.1 27.2 + - - +
526D VAL* 3.2 9.8 + - - +
528D ALA* 1.3 75.6 - - - +
530D ILE* 1.3 58.3 + - - +
532D ASP* 4.4 9.0 - - + +
533D LYS* 3.7 18.5 + - - +
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Residues in contact with ILE 530 (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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505D VAL* 4.7 9.9 - - + -
513D ILE* 4.1 17.0 - - + -
515D LEU* 3.8 28.3 - - + -
526D VAL* 3.1 16.7 + - + +
527D LYS* 3.3 19.3 - - - +
529D LYS* 1.3 77.1 - - - +
531D GLN* 1.3 55.6 + - - +
532D ASP 3.4 1.1 - - - -
533D LYS* 3.6 4.2 - - - +
534D GLU* 2.6 38.5 + - + +
535D GLY 3.6 0.2 + - - -
536D ILE* 4.6 4.2 + - + +
541D GLN* 3.5 34.3 - - + +
543D LEU* 4.8 12.3 - - + -
569D LEU* 4.0 15.9 - - + -
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Residues in contact with GLN 531 (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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527D LYS 3.5 13.7 + - - +
528D ALA* 3.0 19.8 + - + +
530D ILE* 1.3 77.8 - - - +
532D ASP* 1.3 69.6 + - - +
533D LYS 3.3 0.9 - - - -
535D GLY* 3.2 26.1 + - - +
536D ILE 3.2 24.6 - - - +
537D PRO* 4.9 0.3 - - - +
538D PRO* 3.2 30.7 - - + +
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Residues in contact with ASP 532 (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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528D ALA* 2.7 29.6 + - - +
529D LYS* 4.6 7.3 - - - +
531D GLN* 1.3 89.5 + - - +
533D LYS* 1.3 64.3 + - + +
535D GLY 4.9 0.2 + - - -
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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