Contacts of the helix formed by residues 463 - 472 (chain D) in PDB entry 1XMI
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 463 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ATP 3.2 25.7 + - - -
440D VAL* 4.6 4.5 - - - -
441D LEU* 3.7 10.7 - - - +
461D GLY 3.2 3.6 - - - -
462D ALA* 1.3 79.4 - - - +
464D LYS* 1.3 60.2 + - - +
466D SER* 3.3 7.3 + - - -
467D LEU* 2.8 30.3 + - - +
619D LEU* 3.8 5.2 - - - -
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Residues in contact with LYS 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ATP 2.9 48.9 + - - +
456D VAL* 3.9 13.6 - - + +
457D ALA* 3.6 12.8 - - - +
458D GLY 2.8 41.5 + - - +
459D SER 3.2 7.7 + - - -
462D ALA* 4.7 4.0 - - + -
463D GLY* 1.3 73.1 - - - +
465D THR* 1.3 66.8 + - - +
467D LEU* 3.2 14.0 + - - +
468D LEU* 3.3 16.8 + - - +
603D VAL* 3.6 39.3 - - + -
604D THR 5.6 2.5 - - - -
619D LEU* 4.0 11.9 - - + -
647D CYS 5.8 0.2 + - - -
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Residues in contact with THR 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ATP 3.1 17.0 + - - +
9D MG 2.2 30.7 - - - -
464D LYS* 1.3 76.9 - - - +
466D SER* 1.3 57.3 + - - +
468D LEU* 3.1 8.0 + - + +
469D MET* 2.8 52.2 + - + +
490D PHE* 5.3 1.6 - - + -
493D GLN* 3.2 2.1 + - - +
572D ASP* 2.5 30.5 + - - +
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Residues in contact with SER 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ATP 2.8 29.8 + - - -
401D TRP* 2.8 27.7 + - - -
440D VAL* 3.4 22.5 - - - +
441D LEU* 3.9 4.7 - - - -
463D GLY 3.4 6.7 - - - -
464D LYS 3.2 0.4 - - - -
465D THR* 1.3 77.0 - - - +
467D LEU* 1.3 57.0 + - - +
469D MET* 3.3 9.4 + - - +
470D MET* 2.9 24.4 + - - +
475D LEU* 3.3 16.5 - - - +
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Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D MET* 3.8 25.6 - - + -
441D LEU* 3.7 16.8 - - + +
444D ILE* 3.9 23.6 - - + -
446D PHE* 4.1 10.1 - - + -
454D LEU* 5.4 0.9 - - + -
456D VAL* 4.2 22.4 - - + -
463D GLY 2.8 13.8 + - - +
464D LYS* 3.2 10.0 + - - +
466D SER* 1.3 75.8 - - - +
468D LEU* 1.3 65.6 + - + +
470D MET* 3.4 12.3 + - + +
471D ILE* 3.3 26.4 + - + +
601D ILE* 5.4 1.6 - - + -
617D LEU* 3.8 26.5 - - + -
619D LEU* 4.6 2.2 - - + -
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Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D VAL* 5.3 0.4 - - + -
464D LYS 3.6 12.3 - - - +
465D THR* 3.1 7.5 + - + +
467D LEU* 1.3 83.5 - - + +
469D MET* 1.3 64.2 + - - +
471D ILE* 3.1 13.2 + - + +
472D MET* 3.0 36.3 + - + +
490D PHE* 4.1 10.3 - - + -
570D LEU* 4.0 21.4 - - + +
571D LEU 4.5 2.2 - - - +
572D ASP* 3.8 38.4 - - + +
601D ILE* 3.9 28.5 - - + -
603D VAL* 3.9 20.0 - - + -
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Residues in contact with MET 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ATP 5.7 2.0 - - - +
401D TRP* 3.8 33.9 - - + -
465D THR* 2.8 36.4 + - + +
466D SER 3.4 8.5 - - - +
468D LEU* 1.3 73.2 - - - +
470D MET* 1.3 60.0 + - - +
472D MET* 3.2 15.1 + - + +
473D GLY 3.1 4.2 + - - -
474D GLU* 3.0 46.8 + - + +
475D LEU* 4.0 1.8 - - + -
490D PHE* 3.9 31.9 - - + -
492D SER* 5.8 0.4 - - - +
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Residues in contact with MET 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D MET* 3.6 32.5 - - + -
397D VAL* 3.6 26.9 - - + -
399D ALA* 3.8 23.8 - - - -
441D LEU* 3.6 24.7 - - + -
444D ILE* 5.4 1.1 - - + -
466D SER 2.9 12.7 + - - +
467D LEU* 3.5 11.2 - - + +
468D LEU 3.2 0.2 - - - -
469D MET* 1.3 73.9 - - - +
471D ILE* 1.3 64.5 + - - +
473D GLY* 3.0 14.6 + - - -
475D LEU* 3.4 26.1 - - + +
477D PRO* 4.6 6.8 - - + +
482D ILE* 3.7 19.4 - - + +
484D HIS* 5.3 0.9 - - - -
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Residues in contact with ILE 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D VAL* 4.6 9.9 - - + -
394D MET* 3.5 24.0 - - + -
446D PHE* 4.6 4.5 - - + -
467D LEU* 3.3 19.9 + - + +
468D LEU* 3.1 12.9 + - + +
470D MET* 1.3 76.4 - - - +
472D MET* 1.3 60.7 + - - +
473D GLY* 3.2 1.1 + - - -
482D ILE* 5.1 2.9 - - + -
484D HIS* 3.1 37.8 + - + +
488D ILE* 3.5 11.0 - - + +
568D LEU* 3.7 25.8 - - + -
570D LEU* 4.1 11.7 - - + -
601D ILE* 3.8 27.4 - - + -
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Residues in contact with MET 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D LEU* 3.0 30.8 + - + +
469D MET* 3.6 24.0 - - + +
470D MET 3.2 0.2 - - - -
471D ILE* 1.3 75.6 - - - +
473D GLY* 1.3 60.5 + - - +
474D GLU* 3.3 12.6 + - + +
488D ILE* 4.1 17.7 - - + -
490D PHE* 3.7 59.9 - - + -
570D LEU* 3.7 13.9 - - + -
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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