Contacts of the helix formed by residues 577 - 587 (chain A) in PDB entry 1XBA
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 LYS 577 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A GLY 4.3 0.4 + - - +
576A MET* 1.3 73.1 - - - +
578A GLY* 1.3 66.4 + - - +
579A SER* 3.9 18.5 + - - +
580A GLU* 2.9 42.4 + - + +
581A VAL* 3.0 13.6 + - - +
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Residues in contact with GLY 578 (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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536A VAL* 4.2 23.6 - - - +
537A LYS* 4.9 6.4 - - - +
576A MET 4.1 0.4 + - - -
577A LYS* 1.3 72.9 - - - +
579A SER* 1.3 60.4 + - - +
581A VAL* 3.3 10.3 + - - +
582A THR* 3.1 25.8 + - - -
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Residues in contact with SER 579 (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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577A LYS* 3.9 18.4 + - - +
578A GLY* 1.3 71.6 - - - +
580A GLU* 1.3 65.9 + - - +
582A THR* 3.5 8.8 + - - -
583A ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 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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575A GLY 4.2 4.0 - - - +
576A MET* 3.6 22.8 - - + +
577A LYS* 2.9 54.5 + - + +
579A SER* 1.3 78.0 + - - +
581A VAL* 1.3 60.1 + - - +
583A ALA* 3.4 7.1 + - - +
584A MET* 2.8 29.1 + - - +
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Residues in contact with VAL 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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536A VAL* 5.5 3.8 - - + +
537A LYS* 3.9 25.6 - - + -
573A TYR* 3.6 57.2 - - + -
576A MET* 4.1 11.7 - - + -
577A LYS 3.0 19.1 + - - +
578A GLY* 3.3 8.3 + - - +
580A GLU* 1.3 74.3 - - - +
582A THR* 1.3 57.9 + - - +
584A MET* 3.0 3.1 + - - +
585A LEU* 2.7 54.3 + - + +
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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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536A VAL* 5.1 3.3 - - - +
544A ILE* 4.0 31.8 - - + +
545A ASN* 5.1 7.4 - - - +
578A GLY 3.1 12.7 + - - -
579A SER* 3.6 12.4 - - - -
581A VAL* 1.3 78.1 - - - +
583A ALA* 1.3 65.2 + - - +
585A LEU* 3.2 9.8 + - - +
586A GLU* 2.9 35.4 + - - +
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Residues in contact with ALA 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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579A SER 3.0 17.9 + - - +
580A GLU* 3.6 7.9 - - - +
581A VAL 3.2 0.2 - - - -
582A THR* 1.3 78.1 - - - +
584A MET* 1.4 61.5 + - - +
586A GLU* 3.2 19.0 + - - +
587A LYS* 3.2 30.7 + - - +
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Residues in contact with MET 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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573A TYR* 4.0 23.8 - - + -
576A MET* 3.4 29.2 - - + +
580A GLU 2.8 20.1 + - - +
581A VAL 3.0 3.8 + - - +
583A ALA* 1.4 71.6 - - - +
585A LEU* 1.3 62.5 + - - +
587A LYS* 3.2 16.4 + - - +
589A GLU* 3.1 48.0 + - + +
590A ARG* 3.5 40.4 - - - +
591A MET* 3.7 7.9 - - + +
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Residues in contact with LEU 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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539A TYR 4.8 8.3 - - - +
541A PRO* 5.2 5.6 - - + -
556A TRP* 3.5 33.9 - - + +
573A TYR* 3.6 26.5 - - + +
581A VAL* 2.7 40.5 + - + +
582A THR* 3.7 7.4 - - - +
584A MET* 1.3 73.0 - - + +
586A GLU* 1.3 56.7 + - - +
588A GLY* 3.1 9.2 + - - -
589A GLU 3.6 14.4 - - - +
590A ARG* 3.1 36.9 + - - +
611A TYR* 4.2 15.4 - - + -
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Residues in contact with GLU 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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582A THR* 2.9 24.5 + - - +
583A ALA* 3.4 13.7 - - - +
584A MET 3.1 0.2 - - - -
585A LEU* 1.3 75.1 - - - +
587A LYS* 1.3 55.6 + - + +
588A GLY 3.0 8.6 + - - -
611A TYR* 4.6 20.2 + - + +
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Residues in contact with LYS 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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583A ALA* 3.2 29.9 + - - +
584A MET* 3.2 10.7 + - - +
586A GLU* 1.3 72.8 - - + +
588A GLY* 1.3 60.9 + - - +
589A GLU* 3.3 32.6 + - - +
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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