Contacts of the helix formed by residues 532 - 539 (chain A) in PDB entry 1XR2
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 GLY 532 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A THR* 1.3 78.1 - - - +
533A PRO* 1.3 72.5 - - - +
536A ILE* 3.2 17.8 + - - +
559A ILE* 3.6 0.4 - - - -
576A ILE* 3.7 16.3 - - - +
577A ASP 2.7 15.9 + - - -
578A GLU* 3.0 24.2 - - - +
603A PHE* 5.4 0.2 - - - -
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Residues in contact with PRO 533 (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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532A GLY* 1.3 82.0 - - - +
534A VAL* 1.3 66.4 + - - +
536A ILE* 3.4 2.0 + - - +
537A MET* 3.0 24.9 + - - +
552A ALA* 3.5 23.1 - - - +
555A ILE* 4.0 13.4 - - + +
556A ALA* 3.6 18.8 - - + +
559A ILE* 3.3 15.2 - - + -
576A ILE* 5.2 1.1 - - + -
578A GLU* 3.4 7.9 - - - +
602A ALA* 3.7 31.0 - - + +
603A PHE* 4.7 3.6 - - - -
606A ALA* 4.0 13.5 - - + -
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A PRO* 1.3 72.5 - - - +
535A THR* 1.3 55.9 + - - +
537A MET* 3.5 7.8 + - - +
538A SER* 2.9 27.9 + - - -
552A ALA* 5.0 0.4 - - + -
578A GLU* 2.8 27.8 + - + +
580A ALA* 3.7 15.5 - - + +
581A PHE* 4.7 1.8 - - + +
584A LYS* 4.1 14.8 - - + +
595A TYR* 3.7 22.4 - - - +
598A TRP* 4.3 13.7 - - + -
599A ALA* 4.2 20.6 - - + +
602A ALA* 4.1 23.6 - - + -
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Residues in contact with THR 535 (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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468A MET* 4.7 0.9 - - - -
469A VAL* 3.8 3.1 - - + +
531A THR* 3.8 17.0 - - + -
532A GLY 3.6 4.0 - - - -
534A VAL* 1.3 75.2 - - - +
536A ILE* 1.3 65.2 + - - +
538A SER* 3.4 1.0 + - - -
539A TRP* 3.2 46.5 + - + +
578A GLU* 2.4 26.8 + - - -
579A PRO* 3.2 39.9 - - + +
580A ALA* 3.3 15.0 + - + +
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Residues in contact with ILE 536 (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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469A VAL* 4.0 21.5 - - + +
472A PHE* 4.2 25.1 - - + -
473A ALA* 5.6 2.7 - - + -
476A LEU* 4.4 6.5 - - + -
479A ILE* 4.5 17.9 - - + -
500A ILE* 5.0 1.1 - - + -
531A THR* 3.8 31.2 - - + +
532A GLY 3.2 8.0 + - - +
533A PRO 3.4 6.3 + - - +
535A THR* 1.3 77.4 - - - +
537A MET* 1.3 60.1 + - - +
539A TRP 3.8 0.2 + - - -
540A SER* 2.6 31.9 + - - +
555A ILE* 3.9 24.5 - - + -
559A ILE* 3.9 17.7 - - + -
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Residues in contact with MET 537 (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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500A ILE* 4.1 9.4 - - - -
533A PRO 3.0 14.3 + - - +
534A VAL* 3.8 9.0 - - - +
536A ILE* 1.3 77.4 - - - +
538A SER* 1.3 57.8 + - - +
540A SER* 2.9 25.8 + - - +
542A TYR* 3.4 30.7 - - + -
548A GLU* 3.7 24.5 - - + +
551A ILE* 4.0 13.7 - - + -
552A ALA* 3.4 34.3 - - + -
555A ILE* 4.0 8.7 - - + -
584A LYS* 4.3 8.3 - - - -
598A TRP* 3.4 27.6 - - + -
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Residues in contact with SER 538 (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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109A ASN* 6.0 1.6 - - - +
534A VAL 2.9 14.6 + - - -
535A THR 3.4 0.7 + - - -
537A MET* 1.3 77.6 - - - +
539A TRP* 1.3 74.7 + - - +
540A SER 3.2 3.7 + - - +
542A TYR* 5.0 1.6 - - - -
580A ALA* 3.2 21.1 - - - +
584A LYS* 3.5 36.6 - - - +
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Residues in contact with TRP 539 (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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467A ASP* 3.1 21.8 - - - -
468A MET* 3.5 33.2 - - + -
469A VAL* 3.3 20.2 - - + -
495A TYR* 3.2 45.0 - + + +
497A PRO* 3.4 20.6 - - - +
498A PRO* 4.3 0.7 - - - -
535A THR* 3.2 32.9 + - + +
537A MET 3.4 0.2 - - - -
538A SER* 1.3 92.1 + - - +
540A SER* 1.3 58.6 + - - +
579A PRO* 4.2 8.1 - - + +
580A ALA* 5.1 2.4 - - - +
583A GLU* 5.0 2.0 + - - -
1200A C2F 3.3 73.1 + + - -
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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