Contacts of the helix formed by residues 482 - 495 (chain A) in PDB entry 2XOA
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 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A ALA* 4.4 10.0 - - - +
479A GLN 2.9 12.5 + - - -
480A GLU 3.3 2.2 + - - -
481A GLU* 1.3 79.0 - - - +
483A MET* 1.3 66.0 + - - +
484A LEU* 3.2 3.7 + - - -
485A SER* 3.4 13.0 + - - -
486A LEU* 3.2 20.3 + - - +
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Residues in contact with MET 483 (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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404A ILE* 3.8 20.9 - - + -
407A THR* 4.1 28.5 - - - -
408A ALA* 3.8 26.7 - - + -
478A PHE* 3.1 52.5 + - + +
481A GLU 3.5 20.6 - - - +
482A GLY* 1.3 79.9 - - - +
484A LEU* 1.3 56.8 + - - +
486A LEU* 3.3 14.8 - - + +
487A VAL* 2.9 38.7 + - + +
529A LEU* 4.5 9.4 - - + -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PHE 4.8 0.6 + - - -
479A GLN* 3.6 32.7 - - + +
482A GLY* 3.2 1.4 - - - -
483A MET* 1.3 77.5 - - - +
485A SER* 1.3 57.9 + - - +
487A VAL* 3.3 2.7 + - - +
488A LEU* 2.9 33.7 + - + +
526A LEU* 3.4 30.3 - - + -
529A LEU* 3.9 18.6 - - + +
530A ILE* 3.5 32.5 - - + -
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLY* 3.4 14.7 + - - -
484A LEU* 1.3 77.8 - - - +
486A LEU* 1.3 53.4 + - - +
488A LEU* 3.2 7.9 + - - +
489A ASN* 2.6 47.2 + - - +
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Residues in contact with LEU 486 (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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408A ALA* 4.4 15.9 - - + +
411A TYR* 3.2 44.2 - - + -
412A ASN* 3.8 24.2 - - - +
415A ILE* 3.8 20.0 - - + -
482A GLY 3.2 10.9 + - - +
483A MET* 3.3 26.5 - - + +
484A LEU 3.1 0.2 - - - -
485A SER* 1.3 79.3 - - - +
487A VAL* 1.3 63.4 + - + +
489A ASN* 3.1 17.3 + - - +
490A CYS* 3.3 16.5 + - - -
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TYR* 4.5 13.2 - - + -
483A MET* 2.9 19.9 + - + +
484A LEU* 3.7 4.9 - - - +
486A LEU* 1.3 75.6 - - + +
488A LEU* 1.3 62.8 + - - +
490A CYS* 3.1 6.7 + - - +
491A ILE* 3.1 27.6 + - + +
522A LEU* 3.7 41.1 - - + +
525A LEU* 3.6 26.2 - - + -
526A LEU* 4.3 15.7 - - + +
529A LEU* 4.2 7.0 - - + -
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Residues in contact with LEU 488 (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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484A LEU* 2.9 15.5 + - + +
485A SER* 3.2 12.1 + - - +
487A VAL* 1.3 77.3 - - - +
489A ASN* 1.3 58.9 + - - +
491A ILE* 3.3 12.2 + - + +
492A ASP* 2.8 54.5 + - - +
526A LEU* 3.4 44.2 - - + -
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Residues in contact with ASN 489 (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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415A ILE* 3.7 18.6 - - + +
485A SER* 2.6 30.8 + - - +
486A LEU* 3.1 9.9 + - - +
488A LEU* 1.3 72.3 + - - +
490A CYS* 1.3 65.9 + - - +
492A ASP* 4.0 9.3 + - - +
493A ARG* 3.1 49.0 + - - +
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Residues in contact with CYS 490 (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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411A TYR* 4.1 22.2 - - - -
414A PHE* 4.1 20.2 - - + -
415A ILE* 3.8 24.5 - - - -
418A LEU* 5.3 0.4 - - - -
486A LEU 3.5 13.5 - - - -
487A VAL 3.1 8.1 + - - +
489A ASN* 1.3 74.4 - - - +
491A ILE* 1.3 65.8 + - - +
493A ARG* 3.3 5.2 + - - +
494A LEU* 3.0 27.9 + - - +
522A LEU* 3.6 29.2 - - + -
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Residues in contact with ILE 491 (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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487A VAL* 3.1 21.6 + - + +
488A LEU* 3.3 12.3 + - + +
490A CYS* 1.3 76.8 - - - +
492A ASP* 1.3 69.0 + - - +
494A LEU* 3.3 3.7 + - - +
495A ASN* 3.0 42.8 + - - +
519A VAL* 5.0 4.3 - - + +
522A LEU* 3.6 37.5 - - + -
523A TYR* 3.6 39.3 - - + +
526A LEU* 4.1 17.9 - - + -
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Residues in contact with ASP 492 (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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488A LEU* 2.8 43.6 + - - +
489A ASN* 4.1 10.8 + - - +
491A ILE* 1.3 76.8 - - - +
493A ARG* 1.3 64.4 + - + +
495A ASN* 3.2 14.4 + - - +
496A VAL* 3.3 16.0 + - - +
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Residues in contact with ARG 493 (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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415A ILE* 3.7 29.5 - - - +
418A LEU* 4.0 22.9 - - + +
419A ASP* 2.8 40.0 + - - +
489A ASN* 3.1 48.6 + - - +
490A CYS 3.9 2.2 - - - +
492A ASP* 1.3 79.0 - - + +
494A LEU* 1.3 60.8 + - - +
496A VAL* 3.5 23.8 - - + +
497A TYR* 3.8 10.6 - - - -
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 3.9 22.9 - - + -
418A LEU* 4.2 17.9 - - + -
436A LEU* 6.1 1.1 - - + -
490A CYS 3.0 16.0 + - - +
491A ILE 4.1 2.2 - - - +
493A ARG* 1.3 76.0 - - - +
495A ASN* 1.3 58.0 + - - +
496A VAL 3.2 1.3 - - - -
497A TYR* 3.3 15.3 + - + +
515A TRP* 3.1 54.7 + - + +
518A ILE* 3.9 18.4 - - + -
519A VAL* 4.4 17.7 - - + -
522A LEU* 3.7 30.1 - - + -
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Residues in contact with ASN 495 (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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491A ILE* 3.0 28.5 + - - +
492A ASP* 3.2 6.5 + - - +
494A LEU* 1.3 75.8 - - - +
496A VAL* 1.3 64.1 + - - +
497A TYR 3.0 10.8 + - - +
515A TRP* 4.4 10.0 - - - -
519A VAL* 4.2 14.6 - - - +
523A TYR* 3.0 31.5 + - - -
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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