Contacts of the helix formed by residues 594 - 612 (chain A) in PDB entry 2XIJ
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 SER 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A PHE* 3.6 19.2 - - - -
592A GLY 3.3 2.3 + - - -
593A GLU* 1.3 81.6 - - - +
595A LYS* 1.3 59.9 + - - +
596A GLU* 3.2 15.8 + - - +
597A ILE* 3.3 28.1 + - - +
598A THR* 3.0 31.6 + - - -
1749A EDO 3.2 18.3 + - - -
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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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594A SER* 1.3 72.6 - - - +
596A GLU* 1.3 57.4 + - - +
598A THR* 3.4 6.4 + - - -
599A SER* 2.9 31.6 + - - -
1749A EDO 3.0 31.6 + - - +
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Residues in contact with GLU 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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591A PHE* 4.3 5.5 - - - -
594A SER* 3.2 8.7 + - - +
595A LYS* 1.3 76.0 - - - +
597A ILE* 1.3 66.9 + - + +
599A SER* 3.4 6.0 + - - -
600A ALA* 3.0 24.0 + - + +
727A ARG* 2.8 45.2 + - - -
729A PRO* 3.5 23.3 - - + +
730A LYS* 4.1 6.8 + - - +
1749A EDO 3.2 11.3 + - - +
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Residues in contact with ILE 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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587A TYR* 4.4 7.0 - - + -
588A ARG* 4.2 19.1 - - + +
591A PHE* 3.7 30.5 - - + -
592A GLY 4.8 2.7 - - - +
594A SER* 3.3 27.9 + - - +
596A GLU* 1.3 76.0 - - - +
598A THR* 1.3 60.2 + - - +
600A ALA* 3.3 5.8 + - - +
601A ILE* 2.9 41.5 + - + +
641A LEU* 3.6 25.6 - - + -
729A PRO* 3.8 26.0 - - + -
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Residues in contact with THR 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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588A ARG* 5.8 2.0 + - - +
593A GLU* 6.0 1.0 - - - +
594A SER 3.0 19.5 + - - -
595A LYS* 3.7 7.1 - - - -
597A ILE* 1.3 78.1 - - - +
599A SER* 1.3 63.8 + - - +
601A ILE* 3.4 9.7 + - + +
602A LYS* 3.1 23.6 + - + +
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Residues in contact with SER 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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595A LYS 2.9 18.2 + - - -
596A GLU* 3.7 6.5 - - - -
598A THR* 1.3 78.5 - - - +
600A ALA* 1.3 56.5 + - - +
602A LYS* 3.3 8.6 + - - +
603A ARG* 3.0 33.8 + - - +
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Residues in contact with ALA 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A GLU 3.0 17.0 + - - +
597A ILE* 3.3 5.8 + - - +
599A SER* 1.3 76.7 - - - +
601A ILE* 1.3 62.5 + - - +
603A ARG* 3.4 4.4 + - - +
604A VAL* 3.1 28.6 + - + +
641A LEU* 4.3 23.8 - - + -
729A PRO* 4.4 6.5 - - + +
732A ALA* 5.3 1.6 - - + -
733A VAL* 3.8 29.6 - - + +
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Residues in contact with ILE 601 (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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588A ARG* 3.5 41.5 - - - +
597A ILE* 2.9 33.6 + - + +
598A THR* 3.8 8.3 - - - +
599A SER 3.3 0.2 - - - -
600A ALA* 1.3 76.8 - - - +
602A LYS* 1.3 57.3 + - - +
604A VAL* 3.3 2.8 + - - +
605A HIS* 2.8 33.1 + - + +
640A ASP 4.4 2.2 - - - +
641A LEU* 3.9 34.3 - - + +
642A GLY* 6.3 0.2 - - - -
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Residues in contact with LYS 602 (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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598A THR* 3.1 16.3 + - + +
599A SER* 3.6 10.5 - - - +
600A ALA 3.3 0.2 - - - -
601A ILE* 1.3 74.5 - - - +
603A ARG* 1.3 61.2 + - - +
605A HIS* 3.1 8.6 + - + +
606A LYS* 2.8 51.7 + - + +
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Residues in contact with ARG 603 (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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599A SER* 3.0 21.0 + - - +
600A ALA* 3.5 12.3 - - - +
602A LYS* 1.3 77.6 - - - +
604A VAL* 1.3 61.5 + - - +
606A LYS* 3.3 11.2 + - - +
607A PHE* 3.1 17.3 + - - +
733A VAL* 3.4 26.5 - - + +
736A LEU* 3.6 27.8 - - + +
737A ASP* 2.5 32.7 + - - +
740A GLU* 2.9 32.5 + - - +
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Residues in contact with VAL 604 (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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600A ALA* 3.1 16.3 + - + +
601A ILE 3.3 3.8 + - - +
602A LYS 3.2 0.2 - - - -
603A ARG* 1.3 72.8 - - + +
605A HIS* 1.3 66.0 + - - +
607A PHE* 3.2 5.8 + - - +
608A MET* 3.1 21.0 + - + +
614A ARG* 5.5 0.9 - - + -
615A PRO* 3.8 16.8 - - + -
641A LEU* 3.4 20.4 - - + +
642A GLY* 3.4 33.4 - - - +
643A PHE* 4.2 22.0 - - + -
732A ALA* 5.8 2.5 - - + +
733A VAL* 6.4 1.3 - - + -
736A LEU* 4.1 15.0 - - + -
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Residues in contact with HIS 605 (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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601A ILE* 2.8 26.8 + - + +
602A LYS* 3.1 10.1 + - + +
604A VAL* 1.3 74.0 - - - +
606A LYS* 1.3 56.9 + - + +
608A MET* 3.2 29.7 + - + +
609A GLU* 3.0 52.3 + - + +
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Residues in contact with LYS 606 (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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602A LYS* 2.8 44.1 + - + +
603A ARG* 3.8 11.2 - - - +
604A VAL 3.3 0.2 - - - -
605A HIS* 1.3 71.2 - - + +
607A PHE* 1.3 61.0 + - - +
609A GLU* 3.5 18.1 + - - +
610A ARG* 3.0 31.7 + - - +
740A GLU* 5.9 0.4 - - - +
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Residues in contact with PHE 607 (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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603A ARG 3.1 10.2 + - - +
604A VAL* 3.3 9.2 - - - +
606A LYS* 1.3 77.5 - - - +
608A MET* 1.3 51.7 + - - +
610A ARG* 3.3 16.8 + - - +
611A GLU* 2.7 60.4 + - + +
613A ARG 3.4 16.4 - - - -
614A ARG 3.8 2.0 - - - -
615A PRO* 3.4 31.6 - - + -
667A HIS* 3.8 22.4 - + - -
736A LEU* 3.5 24.7 - - + -
739A ILE* 3.8 15.5 - - + -
740A GLU* 3.6 22.6 + - + +
743A LEU* 3.8 20.0 - - + -
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Residues in contact with MET 608 (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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604A VAL* 3.1 12.3 + - + +
605A HIS* 3.5 32.5 - - + +
607A PHE* 1.3 76.1 - - - +
609A GLU* 1.3 86.0 + - + +
612A GLY* 2.7 33.4 + - - -
613A ARG* 3.3 31.9 - - - +
614A ARG* 4.4 14.6 - - + +
1747A SO4 5.7 0.4 - - - +
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Residues in contact with GLU 609 (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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605A HIS* 3.0 38.6 + - - +
606A LYS* 3.7 23.4 - - - +
608A MET* 1.3 91.1 - - + +
610A ARG* 1.3 61.4 + - - +
612A GLY* 4.3 2.3 + - - -
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Residues in contact with ARG 610 (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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606A LYS 3.0 18.2 + - - +
607A PHE* 3.7 16.1 - - - +
609A GLU* 1.3 78.2 - - - +
611A GLU* 1.3 94.5 + - - +
612A GLY 3.8 0.3 + - - -
740A GLU* 3.1 49.2 + - - +
743A LEU* 4.1 7.7 - - - +
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Residues in contact with GLU 611 (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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607A PHE* 2.7 52.9 + - + +
610A ARG* 1.3 107.0 + - - +
612A GLY* 1.3 61.1 + - - +
613A ARG* 3.4 16.5 + - + +
667A HIS* 5.4 2.1 + - - +
743A LEU* 3.5 25.9 - - + +
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Residues in contact with GLY 612 (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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608A MET* 2.7 23.1 + - - -
609A GLU 4.3 2.3 + - - -
610A ARG 3.6 1.8 - - - -
611A GLU* 1.3 71.1 - - - +
613A ARG* 1.3 59.9 + - - +
1747A SO4 4.9 2.6 + - - -
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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