Contacts of the helix formed by residues 579 - 590 (chain A) in PDB entry 1XMI
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 ASP 579 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578A LEU* 1.3 75.3 - - - +
580A VAL* 1.3 64.0 + - - +
581A LEU* 3.3 13.2 + - - +
582A THR* 2.6 25.0 + - - -
583A GLU* 3.1 21.4 + - - +
661A ILE* 3.7 19.7 + - + +
664A GLU* 3.2 21.8 - - - +
665A THR* 3.4 27.9 + - - +
668A ARG* 3.2 24.4 - - - -
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Residues in contact with VAL 580 (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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579A ASP* 1.3 74.5 - - - +
581A LEU* 1.3 62.0 + - + +
583A GLU* 3.3 12.7 + - - +
584A LYS* 3.0 55.9 + - + +
606A LYS* 5.0 14.1 - - - +
661A ILE* 5.4 0.6 - - - +
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Residues in contact with LEU 581 (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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579A ASP* 3.3 10.3 + - - +
580A VAL* 1.3 83.3 - - + +
582A THR* 1.3 61.7 + - - +
584A LYS* 3.4 19.3 + - + +
585A GLU* 3.1 30.9 + - + +
668A ARG* 3.7 32.5 - - - +
669A PHE* 4.9 15.5 - - + -
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Residues in contact with THR 582 (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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525A GLN* 4.1 13.5 - - - +
555A ARG* 4.5 1.1 - - - -
578A LEU* 3.9 10.1 - - + -
579A ASP* 2.6 30.3 + - - -
581A LEU* 1.3 74.1 - - - +
583A GLU* 1.3 60.2 + - - +
585A GLU* 3.3 4.2 + - - +
586A ILE* 2.9 51.8 + - + +
664A GLU* 3.9 17.7 + - - +
667A ARG* 4.4 5.5 + - - +
668A ARG* 3.3 23.1 + - - +
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Residues in contact with GLU 583 (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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575A PHE* 3.3 47.1 - - + +
578A LEU* 4.4 7.1 - - + +
579A ASP 3.1 14.4 + - - +
580A VAL* 3.4 17.3 - - - +
582A THR* 1.3 75.8 - - - +
584A LYS* 1.3 59.0 + - + +
586A ILE* 4.3 0.3 - - - +
587A PHE* 2.9 33.4 + - - +
604A THR* 5.1 0.2 + - - -
606A LYS* 3.3 42.1 + - - +
609A HIS* 3.2 25.6 - - + +
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Residues in contact with LYS 584 (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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580A VAL* 3.0 39.7 + - + +
581A LEU* 3.6 21.4 - - + +
582A THR 3.3 0.2 - - - -
583A GLU* 1.3 78.0 - - + +
585A GLU* 1.3 63.2 + - + +
587A PHE* 3.8 7.6 - - - +
588A GLU* 3.2 22.7 + - - +
608A GLU* 5.9 10.5 - - + -
609A HIS* 5.3 3.6 - - - +
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Residues in contact with GLU 585 (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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525A GLN* 2.9 26.8 + - - +
581A LEU* 3.1 17.4 + - + +
582A THR* 3.3 1.0 + - - +
584A LYS* 1.3 79.8 - - + +
586A ILE* 1.3 57.2 + - - +
588A GLU* 3.4 5.5 + - - +
589A SER* 2.9 32.3 + - - -
668A ARG* 2.7 47.2 + - - -
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Residues in contact with ILE 586 (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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523A ALA 4.0 11.2 - - - +
524A CYS* 3.8 12.1 - - - +
525A GLN* 3.9 15.5 - - + +
555A ARG* 3.6 34.5 - - + -
558A LEU* 3.6 31.4 - - + -
575A PHE* 3.8 11.2 - - + -
578A LEU* 4.2 7.2 - - + -
582A THR* 2.9 31.5 + - + +
585A GLU* 1.3 73.2 - - - +
587A PHE* 1.3 60.4 + - - +
589A SER* 3.4 4.0 - - - -
590A CYS* 2.7 44.8 + - + +
591A VAL 3.6 0.2 + - - -
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Residues in contact with PHE 587 (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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453A LEU* 4.0 9.6 - - + -
575A PHE* 4.0 13.3 - + + -
583A GLU 2.9 19.4 + - - +
584A LYS* 3.8 6.5 - - - +
586A ILE* 1.3 76.5 - - - +
588A GLU* 1.3 63.1 + - - +
591A VAL* 3.2 27.6 + - + +
592A CYS* 2.9 48.9 + - - -
602A LEU* 3.7 27.1 - - + -
608A GLU* 4.5 2.7 - - + -
609A HIS* 3.5 50.0 - + + +
612A LYS* 3.9 23.6 - - + -
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Residues in contact with GLU 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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584A LYS 3.2 15.5 + - - +
585A GLU* 3.7 5.2 - - - +
586A ILE 3.2 0.2 - - - -
587A PHE* 1.3 84.1 - - + +
589A SER* 1.3 59.0 + - - +
592A CYS* 3.3 21.0 - - - +
593A LYS* 3.0 60.0 + - - +
612A LYS* 3.3 32.4 + - - -
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Residues in contact with SER 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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522A LYS 5.4 0.7 - - - -
523A ALA* 2.7 38.6 + - - +
525A GLN* 5.4 2.1 + - - +
585A GLU 2.9 22.2 + - - -
586A ILE* 3.4 3.3 - - - +
588A GLU* 1.3 75.4 - - - +
590A CYS* 1.3 57.9 + - - +
593A LYS* 3.5 12.5 - - - +
594A LEU* 3.1 25.3 + - - +
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Residues in contact with CYS 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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523A ALA* 4.2 7.9 - - + +
524A CYS* 3.9 18.2 - - - -
558A LEU* 4.1 10.3 - - + -
562A VAL* 3.5 38.8 - - - -
586A ILE* 2.7 32.9 + - + +
589A SER* 1.3 73.2 + - - +
591A VAL* 1.3 63.2 + - + +
592A CYS 3.4 0.4 - - - -
594A LEU* 3.4 9.6 + - - +
595A MET* 3.0 36.3 + - - +
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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