Contacts of the helix formed by residues 570 - 584 (chain A) in PDB entry 2XOY
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 THR 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A LEU* 4.9 4.5 - - - +
568A GLY 4.8 4.7 - - - +
569A LEU* 1.3 80.2 - - - +
571A TRP* 1.3 68.7 + - - +
572A LYS* 3.3 13.4 + - - +
573A ASN* 2.7 42.7 + - - +
574A MET* 3.3 12.8 + - - +
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Residues in contact with TRP 571 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A LEU 3.7 8.1 - - - -
540A ASN* 4.6 1.3 - - - -
541A LEU* 3.6 46.2 - - + -
542A GLY 3.6 17.1 + - - -
543A ASP* 4.8 12.3 + - - +
545A CYS* 3.3 29.4 - - - -
546A LEU* 3.9 29.8 - - + +
564A LEU* 5.1 0.7 - - - -
570A THR* 1.3 77.2 - - - +
572A LYS* 1.3 107.4 + - + +
574A MET* 3.3 12.5 + - - +
575A LEU* 3.0 36.0 + - + +
609A PHE* 4.4 8.9 - + + -
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Residues in contact with LYS 572 (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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537A CYS 5.9 2.5 - - - +
538A GLU 6.0 1.6 - - - -
539A LEU 5.1 2.2 - - - -
540A ASN* 4.9 12.4 + - - -
570A THR* 3.1 11.3 + - - +
571A TRP* 1.3 125.5 - - + +
573A ASN* 1.3 63.4 + - - +
575A LEU* 3.4 4.2 + - - +
576A THR* 2.8 29.0 + - - +
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Residues in contact with ASN 573 (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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568A GLY 4.2 2.6 - - - +
569A LEU* 3.5 24.5 - - + +
570A THR* 2.7 39.5 + - - +
572A LYS* 1.3 77.8 - - - +
574A MET* 1.3 62.3 + - - +
576A THR* 3.2 9.4 + - - -
577A GLU* 3.1 31.3 + - + +
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Residues in contact with MET 574 (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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546A LEU* 3.7 29.4 - - + -
560A LEU* 4.1 8.7 - - - -
564A LEU* 4.2 12.1 - - + -
569A LEU* 6.1 0.4 - - + -
570A THR 3.3 8.5 + - - +
571A TRP* 3.6 9.0 - - - +
572A LYS 3.2 0.4 - - - -
573A ASN* 1.3 76.8 - - - +
575A LEU* 1.3 59.8 + - - +
577A GLU* 3.3 13.6 + - - +
578A SER* 2.9 33.3 + - - +
609A PHE* 3.7 13.0 - - + -
613A THR* 3.4 35.0 - - + +
616A TYR* 3.5 51.0 - - + +
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Residues in contact with LEU 575 (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 PHE* 4.2 29.2 - - + +
537A CYS 5.0 6.7 - - - +
539A LEU* 5.3 3.1 - - + +
541A LEU* 4.6 3.4 - - + -
571A TRP* 3.0 35.4 + - + +
572A LYS* 3.7 5.4 - - - +
574A MET* 1.3 76.8 - - - +
576A THR* 1.3 58.4 + - - +
578A SER* 3.2 3.9 + - - -
579A LEU* 2.8 50.8 + - + +
609A PHE* 4.1 27.1 - - + -
612A LEU* 3.8 28.5 - - + -
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Residues in contact with THR 576 (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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572A LYS* 2.8 21.2 + - - +
573A ASN* 3.2 11.3 + - - -
575A LEU* 1.3 77.8 - - - +
577A GLU* 1.3 62.9 + - - +
579A LEU* 3.5 9.5 + - - +
580A VAL* 3.2 29.1 + - + +
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Residues in contact with GLU 577 (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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569A LEU* 5.1 7.8 - - - +
573A ASN* 3.1 24.4 + - + +
574A MET* 3.8 6.6 - - - +
576A THR* 1.3 75.1 - - + +
578A SER* 1.3 64.4 + - - +
580A VAL* 3.0 20.1 + - - +
581A ALA* 3.2 11.7 + - - +
616A TYR* 3.2 38.6 + - + -
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Residues in contact with SER 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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574A MET* 2.9 21.7 + - - +
575A LEU* 3.5 8.3 - - - -
577A GLU* 1.3 75.9 - - - +
579A LEU* 1.3 58.6 + - - +
581A ALA* 3.2 4.9 + - - +
582A LEU* 2.9 27.3 + - - +
587A PHE* 3.8 26.5 - - - -
612A LEU* 3.9 30.8 + - - +
613A THR* 5.1 0.2 - - - -
616A TYR* 4.0 16.2 - - - +
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Residues in contact with LEU 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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536A PHE* 3.9 31.9 - - + -
537A CYS* 3.8 32.3 - - + +
575A LEU* 2.8 43.6 + - + +
576A THR* 4.0 7.6 - - - +
577A GLU 3.3 0.4 - - - -
578A SER* 1.3 71.9 - - - +
580A VAL* 1.3 58.3 + - + +
581A ALA 3.4 0.2 - - - -
582A LEU* 3.7 22.9 - - + +
583A GLN* 3.0 27.9 + - - +
596A GLY* 4.1 13.5 - - - +
612A LEU* 4.0 5.8 - - + -
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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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576A THR* 3.2 22.0 - - + +
577A GLU* 3.0 11.4 + - - +
579A LEU* 1.3 78.2 - - + +
581A ALA* 1.3 60.8 + - - +
583A GLN* 3.6 8.9 + - - +
584A ARG* 3.0 42.0 + - + +
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Residues in contact with ALA 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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577A GLU 3.2 10.1 + - - +
578A SER 3.5 4.5 - - - +
580A VAL* 1.3 75.8 - - - +
582A LEU* 1.3 62.8 + - - +
584A ARG* 3.2 3.3 + - - +
585A GLY 3.2 3.1 + - - -
586A VAL* 2.9 42.6 + - + +
587A PHE* 3.5 40.6 - - + -
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Residues in contact with LEU 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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578A SER 2.9 16.3 + - - +
579A LEU* 3.7 28.0 - - + +
581A ALA* 1.3 75.6 - - - +
583A GLN* 1.3 65.8 - - - +
585A GLY* 2.9 15.9 + - - -
587A PHE* 3.6 25.7 - - - +
588A LEU* 4.5 0.2 - - - -
589A LEU* 3.6 44.6 - - + +
592A TYR 6.0 1.6 - - - +
594A VAL* 3.6 16.4 - - + +
595A THR* 4.3 10.3 - - - -
596A GLY 4.8 0.4 - - - +
612A LEU* 4.1 10.1 - - + -
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Residues in contact with GLN 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 LEU 3.0 15.7 + - - +
580A VAL* 4.0 9.9 - - - +
581A ALA 3.3 0.2 - - - -
582A LEU* 1.3 81.4 - - - +
584A ARG* 1.3 63.9 + - - +
585A GLY 3.5 0.2 + - - -
595A THR* 6.4 2.0 - - - -
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Residues in contact with ARG 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 27.4 - - + +
581A ALA* 3.2 1.4 + - - +
582A LEU 3.1 1.2 - - - -
583A GLN* 1.3 80.6 - - + +
585A GLY* 1.3 60.0 + - - +
586A VAL* 3.6 29.6 + - + +
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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