Contacts of the helix formed by residues 541 - 549 (chain A) in PDB entry 2XT6
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 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A GLU* 4.7 1.8 - - - -
506A PHE* 3.1 18.8 + - - -
508A LEU* 3.8 24.9 - - - +
537A MET* 3.9 3.4 - - - -
539A HIS 3.0 2.4 + - - -
540A ARG* 1.3 73.0 - - - +
542A ARG* 1.3 62.5 + - - +
543A LEU 3.5 2.5 - - - -
544A ASN* 3.1 21.0 + - - +
545A VAL* 3.1 15.3 + - - +
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Residues in contact with ARG 542 (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 MET* 3.3 40.8 + - + +
538A PRO 3.9 3.2 + - - +
539A HIS 3.0 18.6 + - - +
540A ARG 3.4 1.8 - - - -
541A GLY* 1.3 76.2 - - - +
543A LEU* 1.4 58.2 + - - +
545A VAL* 3.3 4.7 + - - +
546A LEU* 3.0 28.0 + - - +
577A LYS 4.0 5.1 + - - -
578A TYR* 3.3 46.0 + - + +
579A HIS 4.0 2.6 - - - -
580A LEU 3.1 24.2 + - - -
599A LEU* 3.4 24.4 - - + +
600A THR 2.8 27.9 + - - -
602A ASN* 2.6 23.3 + - - +
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Residues in contact with LEU 543 (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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492A PHE* 3.7 19.0 - - + -
496A LEU* 4.2 12.6 - - + -
541A GLY 3.5 0.8 - - - -
542A ARG* 1.4 73.1 - - + +
544A ASN* 1.3 60.2 + - - +
546A LEU* 3.2 26.6 + - + +
547A ALA* 3.0 28.8 + - - +
557A ILE* 4.2 12.2 - - + +
558A PHE* 4.3 6.5 - - + -
561A PHE* 3.6 32.1 - - + -
577A LYS* 4.1 25.8 - - + +
578A TYR* 3.4 39.7 + - + +
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Residues in contact with ASN 544 (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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489A ALA* 3.1 30.5 + - - +
492A PHE* 3.7 21.5 - - + -
493A GLU* 3.2 26.0 + - - +
496A LEU* 6.2 0.2 - - - +
508A LEU* 4.1 8.8 - - + +
515A ILE* 3.7 18.5 - - + +
541A GLY 3.1 16.0 + - - +
543A LEU* 1.3 79.2 - - - +
545A VAL* 1.3 50.1 + - - +
547A ALA* 3.4 0.4 + - - -
548A ASN* 2.7 63.6 + - - +
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Residues in contact with VAL 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU* 5.8 0.7 - - + -
514A VAL* 5.8 2.0 - - + -
515A ILE* 3.8 17.7 - - + -
518A MET* 3.7 33.9 - - + -
535A ILE* 4.4 6.7 - - + -
537A MET* 3.8 28.5 - - + -
541A GLY 3.1 12.4 + - - +
542A ARG 3.5 8.3 - - - +
544A ASN* 1.3 73.3 - - - +
546A LEU* 1.4 51.6 + - - +
549A ILE* 2.8 24.6 + - + +
550A VAL* 2.8 40.3 + - + -
599A LEU* 5.1 4.0 - - + -
642A LEU* 5.3 0.9 - - + -
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Residues in contact with LEU 546 (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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542A ARG* 3.0 18.3 + - + +
543A LEU* 3.2 35.6 + - + +
545A VAL* 1.4 76.4 - - - +
547A ALA* 1.3 55.8 + - - +
550A VAL* 3.6 7.7 - - + +
551A GLY 3.0 8.8 + - - -
552A LYS* 2.9 31.8 + - + +
557A ILE* 3.9 24.7 - - + -
577A LYS* 4.5 10.5 - - + +
580A LEU 5.4 2.9 - - - +
582A ALA* 3.7 31.4 - - + -
599A LEU* 3.7 21.1 - - + -
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Residues in contact with ALA 547 (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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492A PHE* 3.9 10.3 - - + -
543A LEU 3.0 16.6 + - - +
544A ASN 3.9 2.5 - - - +
546A LEU* 1.3 77.3 - - - +
548A ASN* 1.3 66.4 + - - +
549A ILE 3.5 0.2 - - - -
551A GLY* 3.4 21.0 - - - -
552A LYS 3.8 10.9 - - - +
554A TYR* 3.9 22.9 - - + -
557A ILE* 3.7 13.9 - - + +
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Residues in contact with ASN 548 (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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485A LYS* 3.1 27.4 + - - +
488A ALA* 3.4 40.4 + - + +
489A ALA 4.2 0.6 - - - +
492A PHE* 4.1 6.7 - - - +
515A ILE* 3.8 18.4 - - + -
519A ASP* 4.7 1.0 - - - +
544A ASN* 2.7 42.5 + - - +
547A ALA* 1.3 83.1 - - - +
549A ILE* 1.3 66.6 + - - +
551A GLY* 4.7 1.1 - - - -
554A TYR* 4.7 7.2 + - - -
586A TYR* 5.8 0.7 - - - -
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Residues in contact with ILE 549 (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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515A ILE* 3.5 48.2 - - + +
518A MET* 4.0 10.5 - - + -
519A ASP* 3.7 24.7 - - + +
522A ILE* 3.4 29.4 - - + -
535A ILE* 3.9 18.6 - - + -
545A VAL* 2.8 23.5 + - + +
547A ALA 3.5 0.2 - - - -
548A ASN* 1.3 88.5 - - - +
550A VAL* 1.4 61.8 + - - +
551A GLY* 3.2 1.8 - - - -
585A THR 5.4 0.5 - - - +
586A TYR* 4.3 19.4 - - + +
597A VAL* 4.3 9.1 - - + +
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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