Contacts of the helix formed by residues 463 - 472 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ATP 3.2 27.2 + - - -
440A VAL 4.6 4.0 - - - -
441A LEU* 3.6 11.7 - - - +
461A GLY 3.2 3.4 - - - -
462A ALA* 1.3 79.1 - - - +
464A LYS* 1.3 60.0 + - - +
466A SER* 3.5 6.8 - - - -
467A LEU* 2.9 30.0 + - - +
619A LEU* 3.8 5.1 - - - +
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Residues in contact with LYS 464 (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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2A ATP 2.8 48.7 + - - +
456A VAL* 4.0 14.5 - - + +
457A ALA* 3.7 12.8 - - - +
458A GLY* 2.8 41.4 + - - +
459A SER 3.0 10.1 + - - -
462A ALA* 4.7 1.6 - - + -
463A GLY* 1.3 76.0 - - - +
465A THR* 1.3 67.7 + - - +
467A LEU* 3.3 14.0 + - - +
468A LEU* 3.4 16.5 + - - +
603A VAL* 3.7 38.2 - - + +
604A THR 5.3 1.8 - - - +
619A LEU* 4.1 11.7 - - + -
647A CYS 5.6 0.2 + - - -
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Residues in contact with THR 465 (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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2A ATP 3.1 24.4 + - - +
7A MG 2.2 25.8 - - - -
464A LYS* 1.3 74.6 - - - +
466A SER* 1.3 58.6 + - - +
468A LEU* 3.0 11.5 + - + +
469A MET* 2.8 50.6 + - + +
493A GLN* 3.2 2.6 + - - +
572A ASP* 2.5 29.3 + - - +
603A VAL* 4.8 0.4 - - - +
662D LEU* 4.9 8.1 - - + -
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ATP 2.7 26.8 + - - -
401A TRP* 2.9 26.4 + - - -
440A VAL* 3.3 23.2 - - - +
441A LEU* 3.9 4.5 - - - -
463A GLY* 3.5 7.2 - - - -
464A LYS 3.2 0.4 - - - -
465A THR* 1.3 77.2 - - - +
467A LEU* 1.3 56.4 + - - +
469A MET* 3.2 11.3 + - - +
470A MET 2.9 24.1 + - - -
475A LEU* 3.4 15.0 - - - +
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Residues in contact with LEU 467 (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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394A MET* 3.7 34.1 - - + -
441A LEU* 3.7 16.1 - - + +
444A ILE* 4.1 9.6 - - + -
446A PHE* 4.1 14.1 - - + -
454A LEU* 5.3 1.1 - - + -
456A VAL* 4.2 24.0 - - + -
463A GLY 2.9 13.4 + - - +
464A LYS* 3.4 10.5 - - - +
466A SER* 1.3 76.3 - - - +
468A LEU* 1.3 65.3 + - + +
470A MET* 3.3 12.8 + - + +
471A ILE* 3.1 33.0 + - + +
601A ILE* 5.3 1.3 - - + -
617A LEU* 3.9 25.1 - - + -
619A LEU* 4.6 2.5 - - + -
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Residues in contact with LEU 468 (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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456A VAL* 5.6 0.4 - - + -
464A LYS 3.4 10.0 + - - +
465A THR* 3.0 8.8 + - + +
467A LEU* 1.3 85.3 - - + +
469A MET* 1.3 55.8 - - - +
471A ILE* 3.2 13.5 + - + +
472A MET* 3.0 42.0 + - + +
490A PHE* 4.2 9.0 - - + -
570A LEU* 3.9 20.9 - - + +
571A LEU 4.5 2.7 - - - -
572A ASP* 3.6 44.6 - - + +
601A ILE* 3.9 30.3 - - + +
603A VAL* 3.9 15.3 - - + -
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Residues in contact with MET 469 (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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2A ATP 5.7 2.2 - - - +
401A TRP* 3.7 33.9 - - + -
465A THR* 2.8 31.5 + - + +
466A SER 3.4 8.5 - - - +
468A LEU* 1.3 74.5 - - - +
470A MET* 1.3 58.6 + - - +
472A MET* 3.3 12.1 + - + -
473A GLY 2.9 7.6 + - - -
474A GLU* 2.9 40.6 + - + +
475A LEU* 4.0 2.0 - - + -
490A PHE* 3.9 25.8 - - + -
662D LEU* 3.6 30.7 - - + -
665D THR* 4.1 17.3 - - + +
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Residues in contact with MET 470 (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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394A MET* 3.7 24.7 - - + -
397A VAL* 3.4 29.8 - - + -
399A ALA* 3.6 30.5 - - - -
441A LEU* 3.5 24.7 - - + -
444A ILE* 5.2 1.1 - - + -
466A SER 2.9 11.5 + - - +
467A LEU* 3.4 9.4 - - + +
468A LEU 3.2 0.2 - - - -
469A MET* 1.3 74.5 - - - +
471A ILE* 1.3 64.8 + - - +
473A GLY* 3.1 12.6 + - - -
475A LEU* 3.3 25.5 - - + +
477A PRO* 4.5 5.8 - - + -
482A ILE* 3.7 21.5 - - + +
484A HIS* 5.1 1.4 - - - -
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Residues in contact with ILE 471 (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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392A VAL* 4.8 9.0 - - + -
394A MET* 3.7 22.4 - - + -
446A PHE* 4.9 1.8 - - + -
467A LEU* 3.1 28.3 + - + +
468A LEU* 3.5 12.3 - - + +
470A MET* 1.3 75.4 - - - +
472A MET* 1.3 61.1 + - - +
473A GLY 3.5 1.0 + - - -
482A ILE* 5.3 0.7 - - - -
484A HIS* 3.2 43.8 + - + +
488A ILE* 3.6 9.9 - - + +
568A LEU* 3.6 29.4 - - + -
570A LEU* 4.1 9.0 - - + -
601A ILE* 3.7 29.2 - - + -
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Residues in contact with MET 472 (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 LEU* 3.0 31.3 + - + +
469A MET* 3.7 18.6 - - - +
470A MET 3.2 0.6 - - - -
471A ILE* 1.3 75.6 - - - +
473A GLY* 1.3 59.4 + - - +
474A GLU* 3.4 5.9 + - + -
488A ILE* 4.0 9.6 - - + -
490A PHE* 3.6 58.1 - - + -
570A LEU* 3.7 18.6 - - + -
581D LEU* 3.7 10.9 - - - +
665D THR* 4.0 3.1 - - - -
669D PHE* 3.6 49.2 - - + -
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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