Contacts of the helix formed by residues 463 - 472 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E ATP 3.1 24.8 + - - -
440E VAL 4.6 7.9 - - - -
441E LEU* 3.8 4.8 - - - +
461E GLY 3.2 3.0 - - - -
462E ALA* 1.3 79.7 - - - +
464E LYS* 1.3 60.7 + - - +
465E THR 3.5 1.8 - - - -
466E SER* 3.7 6.1 - - - -
467E LEU* 3.0 29.3 + - - +
619E LEU* 3.8 7.4 - - - +
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Residues in contact with LYS 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ATP 2.7 52.7 + - - +
456E VAL* 4.0 13.6 - - + +
457E ALA* 3.6 11.7 - - - +
458E GLY* 2.9 42.0 + - - +
459E SER 3.1 8.9 + - - -
462E ALA* 4.7 1.8 - - + -
463E GLY* 1.3 76.8 - - - +
465E THR* 1.3 62.1 + - - +
467E LEU* 3.2 18.2 + - - +
468E LEU* 3.4 12.1 + - - +
603E VAL* 3.7 40.2 - - + +
604E THR 5.7 1.6 - - - -
619E LEU* 3.9 14.1 - - + -
646E GLY 5.8 1.3 - - - -
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Residues in contact with THR 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ATP 2.9 24.9 + - - +
10E MG 2.1 27.6 - - - -
464E LYS* 1.3 75.3 - - - +
466E SER* 1.3 58.1 + - - +
468E LEU* 3.0 10.6 + - + +
469E MET* 2.9 50.1 + - + +
490E PHE* 5.4 0.7 - - + -
493E GLN* 3.2 1.9 + - - +
572E ASP* 2.6 29.1 + - - +
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Residues in contact with SER 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ATP 2.6 31.7 + - - -
401E TRP* 3.0 24.9 + - - +
440E VAL* 3.4 23.8 - - - +
441E LEU* 3.9 4.9 - - - -
463E GLY* 3.7 6.1 - - - -
464E LYS 3.3 0.2 - - - -
465E THR* 1.3 75.7 - - - +
467E LEU* 1.3 57.4 + - - +
469E MET* 3.2 12.1 + - - +
470E MET* 3.0 24.1 + - - +
475E LEU* 3.4 13.8 - - - +
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Residues in contact with LEU 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E MET* 3.8 32.5 - - + -
441E LEU* 3.6 17.0 - - + +
444E ILE* 4.3 9.2 - - + -
446E PHE* 4.1 14.6 - - + -
454E LEU* 5.3 1.3 - - + -
456E VAL* 4.3 22.7 - - + -
463E GLY 3.0 14.2 + - - +
464E LYS* 3.4 10.1 - - - +
465E THR 3.1 0.2 - - - -
466E SER* 1.3 75.9 - - - +
468E LEU* 1.3 65.2 + - + +
470E MET* 3.4 12.4 + - + +
471E ILE* 3.3 29.3 + - + +
601E ILE* 5.4 1.1 - - + -
617E LEU* 3.9 26.0 - - + -
619E LEU* 4.5 2.9 - - + -
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Residues in contact with LEU 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456E VAL* 5.6 0.7 - - + -
464E LYS 3.4 8.9 + - - +
465E THR* 3.0 8.2 + - + +
467E LEU* 1.3 83.8 - - + +
469E MET* 1.3 57.6 + - - +
471E ILE* 3.2 10.4 + - + +
472E MET* 3.0 42.7 + - + +
490E PHE* 4.4 6.7 - - + -
570E LEU* 3.6 26.7 - - + +
571E LEU 4.5 2.5 - - - +
572E ASP* 3.7 42.6 - - + +
601E ILE* 3.9 31.4 - - + +
603E VAL* 3.9 16.4 - - + -
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Residues in contact with MET 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ATP 5.6 4.0 - - - +
401E TRP* 3.7 33.4 - - + -
465E THR* 2.9 40.5 + - + +
466E SER* 3.2 8.7 + - - +
468E LEU* 1.3 76.8 - - - +
470E MET* 1.3 56.2 + - - +
472E MET* 3.4 13.7 + - + +
473E GLY 3.0 6.4 + - - -
474E GLU* 2.9 48.2 + - + +
475E LEU* 4.0 2.0 - - + -
490E PHE* 3.9 27.1 - - + -
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Residues in contact with MET 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E MET* 3.7 25.8 - - + -
397E VAL* 3.6 28.5 - - + -
399E ALA* 3.7 29.6 - - - -
441E LEU* 3.7 22.2 - - + -
444E ILE* 5.6 1.3 - - + -
466E SER 3.0 12.5 + - - +
467E LEU* 3.6 9.0 - - + +
468E LEU 3.2 0.2 - - - -
469E MET* 1.3 72.8 - - - +
471E ILE* 1.3 66.7 + - - +
473E GLY* 3.2 12.3 + - - -
475E LEU* 3.3 29.4 - - + +
477E PRO* 4.4 6.2 - - + +
482E ILE* 3.8 18.3 - - + +
484E HIS* 4.9 2.8 - - - -
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Residues in contact with ILE 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392E VAL* 4.7 9.0 - - + -
394E MET* 3.6 24.9 - - + -
446E PHE* 4.7 1.8 - - + -
467E LEU* 3.3 25.5 + - + +
468E LEU* 3.2 12.4 + - + +
470E MET* 1.3 76.9 - - - +
472E MET* 1.3 61.0 + - - +
473E GLY* 3.5 0.7 + - - -
482E ILE* 5.4 0.4 - - - -
484E HIS* 2.8 43.7 + - + +
488E ILE* 3.7 6.0 - - + +
568E LEU* 3.6 27.4 - - + -
570E LEU* 4.0 13.0 - - + -
601E ILE* 3.7 28.5 - - + -
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Residues in contact with MET 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468E LEU* 3.0 31.9 + - + +
469E MET* 3.4 28.2 + - + +
470E MET 3.2 0.2 - - - -
471E ILE* 1.3 76.1 - - - +
473E GLY* 1.3 59.0 + - - +
474E GLU* 3.4 13.6 + - + +
488E ILE* 4.0 17.7 - - + +
490E PHE* 3.6 55.9 - - + -
570E LEU* 3.7 13.2 - - + -
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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