Contacts of the helix formed by residues 463 - 472 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ATP 3.2 26.9 + - - -
440C VAL* 4.7 3.8 - - - -
441C LEU* 3.6 9.9 - - - +
461C GLY 3.1 4.0 - - - -
462C ALA* 1.3 78.8 - - - +
464C LYS* 1.3 61.3 + - - +
466C SER* 3.5 6.2 + - - -
467C LEU* 3.1 24.3 + - - +
619C LEU* 3.6 12.0 - - - +
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Residues in contact with LYS 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ATP 2.7 47.9 + - - +
456C VAL* 3.8 19.5 - - + +
457C ALA* 3.7 12.1 - - - +
458C GLY* 2.7 42.4 + - - +
459C SER 2.8 12.9 + - - -
462C ALA* 4.7 0.9 - - + -
463C GLY* 1.3 74.8 - - - +
465C THR* 1.3 65.1 + - - +
467C LEU* 3.4 13.0 + - - +
468C LEU* 3.4 17.7 + - - +
603C VAL* 3.9 34.1 - - + +
604C THR 5.4 1.3 - - - +
619C LEU* 3.9 15.9 - - + -
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Residues in contact with THR 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ATP 3.1 20.1 + - - +
8C MG 2.2 30.4 - - - -
464C LYS* 1.3 74.4 - - - +
466C SER* 1.3 51.8 + - - +
468C LEU* 3.0 11.3 + - + +
469C MET* 2.8 57.4 + - + +
490C PHE* 5.4 1.6 - - + -
493C GLN* 3.2 2.2 + - - +
572C ASP* 2.5 29.1 + - - +
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Residues in contact with SER 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ATP 2.5 28.4 + - - -
401C TRP* 3.0 31.0 + - - -
440C VAL* 3.5 18.8 - - - +
441C LEU* 4.0 3.1 - - - -
463C GLY 3.6 6.5 - - - -
465C THR* 1.3 76.1 - - - +
467C LEU* 1.3 56.9 + - - +
469C MET* 3.2 9.4 + - - +
470C MET* 2.8 24.6 + - - +
475C LEU* 3.3 17.6 - - - +
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Residues in contact with LEU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C MET* 3.9 33.2 - - + -
441C LEU* 3.7 15.6 - - + +
444C ILE* 3.9 20.0 - - + -
446C PHE* 4.0 10.1 - - + -
454C LEU* 5.5 0.4 - - + -
456C VAL* 4.3 22.7 - - + -
463C GLY 3.1 13.8 + - - +
464C LYS 3.5 8.1 - - - +
466C SER* 1.3 75.7 - - - +
468C LEU* 1.3 69.1 + - + +
470C MET* 3.3 9.7 + - + +
471C ILE* 3.1 30.5 + - + +
601C ILE* 5.4 1.6 - - + -
617C LEU* 4.0 22.9 - - + -
619C LEU* 4.6 4.3 - - + -
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Residues in contact with LEU 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C VAL* 5.4 0.2 - - + -
464C LYS 3.4 10.0 + - - +
465C THR* 3.0 8.6 + - + +
467C LEU* 1.3 86.8 - - + +
469C MET* 1.3 57.2 + - - +
471C ILE* 3.2 11.9 + - + +
472C MET* 3.0 41.7 + - + +
490C PHE* 4.5 5.2 - - + -
570C LEU* 4.0 26.6 - - + +
571C LEU 4.6 2.0 - - - +
572C ASP* 3.6 44.0 - - + +
601C ILE* 3.9 28.3 - - + -
603C VAL* 3.9 15.0 - - + -
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Residues in contact with MET 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ATP 5.6 3.1 - - - +
401C TRP* 3.6 34.3 - - + -
465C THR* 2.8 37.7 + - + +
466C SER 3.2 8.9 + - - +
468C LEU* 1.3 73.8 - - - +
470C MET* 1.3 55.3 + - - +
472C MET* 3.4 12.5 + - + +
473C GLY 3.2 5.9 + - - -
474C GLU* 2.9 49.7 + - + +
475C LEU 3.2 2.1 + - - -
490C PHE* 3.8 33.7 - - + -
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Residues in contact with MET 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C MET* 3.6 24.2 - - + -
397C VAL* 3.4 30.3 - - + -
399C ALA* 3.6 28.7 - - + -
441C LEU* 3.7 22.0 - - + -
444C ILE* 5.2 1.1 - - + -
466C SER 2.8 16.3 + - - +
467C LEU* 3.6 6.3 - - + +
468C LEU 3.2 0.2 - - - -
469C MET* 1.3 73.9 - - - +
471C ILE* 1.3 64.7 + - - +
472C MET 3.2 0.4 - - - -
473C GLY* 3.1 11.6 + - - -
475C LEU* 3.2 28.1 - - + +
477C PRO* 4.2 9.2 - - + +
482C ILE* 3.8 18.5 - - + +
484C HIS* 5.2 1.4 - - - -
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Residues in contact with ILE 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C VAL* 4.5 9.0 - - + -
394C MET* 3.6 22.9 - - + -
446C PHE* 4.7 2.0 - - + -
467C LEU* 3.1 24.8 + - + +
468C LEU* 3.2 11.2 + - + +
470C MET* 1.3 75.4 - - - +
472C MET* 1.3 58.8 + - - +
473C GLY 3.2 1.1 + - - -
482C ILE* 5.7 0.7 - - - -
484C HIS* 3.3 36.5 + - + +
488C ILE* 3.7 8.1 - - + +
568C LEU* 3.7 26.9 - - + -
570C LEU* 3.9 16.8 - - + -
601C ILE* 3.7 29.6 - - + -
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Residues in contact with MET 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C LEU* 3.0 31.6 + - + +
469C MET* 3.9 19.1 - - + +
470C MET 3.2 0.4 - - - -
471C ILE* 1.3 74.9 - - - +
473C GLY* 1.3 60.6 + - - +
474C GLU* 3.3 13.4 + - + +
488C ILE* 4.0 17.3 - - + -
490C PHE* 3.6 62.8 - - + -
570C LEU* 3.7 16.8 - - + -
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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