Contacts of the helix formed by residues 587 - 600 (chain A) in PDB entry 1CJY
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 PHE 587 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A PRO* 3.5 9.1 + - + +
586A PRO* 1.3 95.8 - - + +
588A LYS* 1.3 67.6 + - - +
589A GLU* 3.4 7.2 - - - -
590A LEU* 3.9 20.4 - - + -
591A LEU* 2.9 43.4 + - + +
607A ILE* 5.0 2.7 - - + -
611A VAL* 3.5 28.3 - - + -
612A PHE* 3.5 27.8 - + + -
621A TYR* 3.7 35.2 - + - -
623A PHE* 4.0 16.2 - + - -
639A HIS* 3.9 17.0 - + - -
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Residues in contact with LYS 588 (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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585A PRO 4.8 3.3 + - - +
586A PRO* 6.1 0.2 - - + -
587A PHE* 1.3 79.8 - - - +
589A GLU* 1.3 70.5 + - - +
591A LEU* 3.8 6.6 - - - +
592A LEU* 3.1 59.2 + - + +
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Residues in contact with GLU 589 (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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554A PHE* 4.2 4.5 - - - +
555A ASN* 4.3 13.9 - - + +
556A LEU* 3.2 23.1 - - + +
575A ASP* 2.5 33.3 - - - +
577A SER* 3.7 19.1 + - - +
586A PRO* 2.9 23.2 - - - +
587A PHE* 3.6 2.3 + - - -
588A LYS* 1.3 83.1 + - + +
590A LEU* 1.3 76.2 + - - +
592A LEU* 2.9 15.2 + - - +
593A ALA* 2.9 22.2 + - - +
639A HIS* 3.5 7.6 - - - -
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Residues in contact with LEU 590 (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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556A LEU* 3.8 10.8 - - + -
558A TYR* 5.0 6.1 - - - +
587A PHE* 3.4 24.4 + - + +
589A GLU* 1.3 91.3 - - - +
591A LEU* 1.3 58.2 + - + +
593A ALA* 3.0 5.2 + - - +
594A GLU* 2.8 24.6 + - - +
604A PHE* 3.8 14.8 - - + -
607A ILE* 3.4 34.5 - - + -
623A PHE* 4.0 18.2 - - + -
637A ILE* 5.3 2.2 - - + -
639A HIS* 3.3 38.8 - - + +
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Residues in contact with LEU 591 (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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587A PHE* 2.9 34.2 + - + +
588A LYS* 3.8 5.8 - - - +
590A LEU* 1.3 77.6 - - - +
592A LEU* 1.3 57.3 + - + +
594A GLU* 3.2 26.5 + - - +
595A LYS* 2.8 28.2 + - - +
607A ILE* 4.0 28.0 - - + +
608A ASP 5.8 0.9 - - - +
609A PRO* 5.8 6.1 - - + -
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Residues in contact with LEU 592 (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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342A MET* 3.6 23.3 - - + +
553A THR* 4.1 18.4 - - + +
554A PHE* 3.8 20.5 - - + -
588A LYS* 3.1 54.4 + - + +
589A GLU* 2.9 12.6 + - - +
591A LEU* 1.3 74.8 - - + +
593A ALA* 1.3 61.0 + - - +
595A LYS* 3.2 11.4 + - + +
596A TRP* 2.9 26.3 + - - +
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Residues in contact with ALA 593 (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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554A PHE* 4.0 25.3 - - + -
556A LEU* 4.8 1.3 - - + +
558A TYR* 3.5 37.9 - - + -
562A LEU* 5.4 0.2 - - - +
589A GLU 2.9 12.0 + - - +
590A LEU* 3.4 8.5 - - - +
592A LEU* 1.3 74.5 - - - +
594A GLU* 1.3 60.4 + - - +
596A TRP* 3.1 4.3 + - - +
597A ALA* 2.9 29.6 + - - +
604A PHE* 4.2 5.1 - - + -
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Residues in contact with GLU 594 (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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590A LEU 2.8 12.6 + - - +
591A LEU* 3.3 28.7 - - - +
593A ALA* 1.3 78.7 - - - +
595A LYS* 1.3 61.0 + - - +
597A ALA* 3.5 2.6 + - - +
598A LYS* 3.2 21.9 + - + +
604A PHE* 3.8 32.3 - - + +
605A PRO 4.8 0.2 - - - +
606A LYS* 3.7 6.1 - - - -
607A ILE* 2.8 43.2 + - + +
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Residues in contact with LYS 595 (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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342A MET* 3.4 24.9 - - + +
591A LEU 2.8 12.6 + - - +
592A LEU* 3.5 15.4 - - + +
593A ALA 3.1 0.2 - - - -
594A GLU* 1.3 77.7 + - - +
596A TRP* 1.3 65.4 + - - +
598A LYS* 3.4 5.6 + - + +
599A MET* 3.0 33.0 + - + +
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Residues in contact with TRP 596 (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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342A MET* 4.0 22.5 + - + -
344A ALA 5.1 2.2 + - - -
346A TRP* 3.9 20.3 - + + +
358A LYS* 5.7 8.1 - - + -
554A PHE* 3.5 33.7 - + + -
558A TYR* 5.3 0.9 - - + -
559A PRO* 3.4 51.1 - - + -
562A LEU* 4.2 12.8 - - + -
592A LEU 2.9 6.8 + - - +
593A ALA 3.1 8.5 + - - +
595A LYS* 1.3 75.6 - - - +
597A ALA* 1.3 77.4 + - - +
599A MET* 3.0 14.7 + - + +
600A ASN* 2.9 55.8 + - - +
602A LEU* 3.7 30.5 - - + -
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Residues in contact with ALA 597 (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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562A LEU* 4.5 7.6 - - + -
593A ALA 2.9 16.1 + - - +
594A GLU 3.6 4.5 - - - +
596A TRP* 1.3 86.0 - - - +
598A LYS* 1.3 63.1 + - - +
600A ASN* 3.0 3.3 + - - -
601A LYS 2.9 5.0 + - - -
602A LEU* 2.9 46.3 + - - +
604A PHE* 3.5 28.0 - - + -
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Residues in contact with LYS 598 (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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594A GLU* 3.2 14.8 + - + +
595A LYS* 3.8 6.1 - - - +
597A ALA* 1.3 78.1 - - - +
599A MET* 1.3 64.9 + - - +
601A LYS* 2.9 15.7 + - - +
602A LEU 4.9 1.8 - - - +
604A PHE* 5.6 0.4 - - - +
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Residues in contact with MET 599 (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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342A MET* 3.3 49.6 - - + +
343A PHE* 3.8 33.0 - - + -
595A LYS* 3.0 32.6 + - + +
596A TRP* 3.0 13.6 + - - +
598A LYS* 1.3 77.7 - - - +
600A ASN* 1.3 62.3 + - - +
601A LYS* 3.7 0.5 + - - +
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Residues in contact with ASN 600 (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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358A LYS* 3.7 35.7 - - + +
596A TRP* 2.9 55.8 + - + +
597A ALA 3.0 3.1 + - - +
599A MET* 1.3 82.0 + - - +
601A LYS* 1.3 73.1 + - - +
602A LEU* 3.3 24.1 + - + +
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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