Contacts of the helix formed by residues 675 - 684 (chain A) in PDB entry 1ZJK
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 TYR 675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A HIS* 3.7 33.7 - + - -
531A ASN* 2.6 43.5 + - - -
533A ILE* 3.9 26.0 - - + -
615A ASN* 3.2 27.1 + - + +
670A THR* 3.6 23.3 - - + -
671A LYS 3.2 28.0 - - - -
672A VAL 2.9 9.8 + - - +
674A ASN* 1.3 88.1 - - + +
676A ILE* 1.3 58.2 + - - +
677A PRO* 3.4 3.4 - - - -
678A TRP* 3.1 11.2 + - + -
679A ILE* 2.9 31.9 + - + +
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Residues in contact with ILE 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A LEU* 4.2 22.4 - - + -
554A PRO* 3.8 43.3 - - + +
672A VAL* 4.0 7.4 - - + +
673A ILE* 3.5 22.7 - - + +
674A ASN 3.6 0.2 - - - -
675A TYR* 1.3 77.6 - - - +
677A PRO* 1.3 66.9 - - + +
679A ILE* 3.3 5.7 + - + +
680A GLU* 2.8 51.4 + - + +
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Residues in contact with PRO 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A ILE 4.8 1.8 - - - +
674A ASN 4.2 8.5 - - - +
675A TYR* 3.5 5.8 - - - -
676A ILE* 1.3 94.0 - - + +
678A TRP* 1.3 59.3 + - - +
680A GLU* 4.0 10.8 - - + +
681A ASN* 3.0 31.4 + - - +
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Residues in contact with TRP 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A PHE 3.4 21.5 - - - -
519A ILE 3.9 3.8 - - - -
520A HIS* 3.4 53.8 - + + +
521A GLU* 3.1 26.7 + - - -
533A ILE* 4.1 27.6 - - + -
535A LEU* 3.8 26.2 - - + -
675A TYR* 3.1 16.5 + - + +
677A PRO* 1.3 79.6 - - - +
679A ILE* 1.3 75.5 + - + +
681A ASN* 3.6 6.3 + - + +
682A ILE* 3.4 45.1 + - + +
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Residues in contact with ILE 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU* 4.5 5.4 - - + -
479A LEU* 4.1 13.2 - - + -
533A ILE* 4.1 18.8 - - + -
535A LEU* 4.1 10.5 - - + -
553A LEU* 4.0 33.4 - - + -
672A VAL* 4.4 9.9 - - + -
675A TYR* 2.9 25.8 + - + +
676A ILE* 3.7 7.0 - - + +
678A TRP* 1.3 95.4 - - + +
680A GLU* 1.3 66.6 + - - +
682A ILE* 3.2 4.0 + - - +
683A ILE* 3.1 45.9 + - + +
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Residues in contact with GLU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A TYR* 6.2 0.2 - - - +
553A LEU* 5.8 5.6 - - + -
676A ILE* 2.8 40.9 + - + +
677A PRO* 4.0 8.3 - - + +
679A ILE* 1.3 74.3 - - + +
681A ASN* 1.3 63.4 + - - +
683A ILE* 4.0 4.3 - - - +
684A SER* 3.1 28.6 + - - -
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Residues in contact with ASN 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A PRO 3.0 19.9 + - - +
678A TRP* 3.8 7.2 - - + +
679A ILE 3.2 0.2 - - - -
680A GLU* 1.3 77.9 - - - +
682A ILE* 1.3 67.5 + - - +
684A SER* 3.3 17.5 + - - -
685A ASP* 4.0 7.1 + - - +
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Residues in contact with ILE 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A TRP* 3.5 30.5 - - + -
518A PHE* 4.2 32.8 - - + -
535A LEU* 3.8 8.7 - - + -
678A TRP* 3.4 57.4 + - + +
679A ILE 3.2 6.3 + - - +
681A ASN* 1.3 81.4 - - - +
683A ILE* 1.3 66.1 + - - +
684A SER 3.2 1.6 - - - -
685A ASP* 3.2 13.8 + - - +
686A PHE* 3.4 15.5 - - + -
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Residues in contact with ILE 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU* 4.2 11.0 - - + -
474A TYR* 3.8 40.4 - - + +
477A TRP* 3.6 47.6 + - + +
535A LEU* 4.5 5.2 - - + -
553A LEU* 5.2 0.2 - - + -
679A ILE* 3.1 38.5 + - + +
680A GLU* 4.4 3.8 - - - +
682A ILE* 1.3 76.0 - - - +
684A SER* 1.3 61.5 + - - +
685A ASP 3.3 0.2 - - - -
686A PHE* 3.5 18.8 + - - +
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Residues in contact with SER 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A GLU 3.1 17.0 + - - -
681A ASN* 3.3 16.5 + - - -
682A ILE 3.2 0.4 - - - -
683A ILE* 1.3 74.4 - - - +
685A ASP* 1.3 57.8 + - - +
686A PHE 3.2 10.9 + - - +
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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