Contacts of the helix formed by residues 461 - 473 (chain C) in PDB entry 2X7O
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 CYS 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299C VAL* 5.4 6.7 - - + -
417C ILE* 3.9 26.5 - - + -
458C TRP 4.1 1.9 + - - +
460C SER* 1.4 81.5 + - - +
462C GLU* 1.4 64.3 + - - +
463C ALA* 4.5 5.6 - - + +
464C LEU* 3.7 37.7 - - - -
465C ARG* 3.1 31.3 + - - +
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Residues in contact with GLU 462 (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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461C CYS* 1.4 71.2 - - - +
463C ALA* 1.4 59.6 + - - +
465C ARG* 3.2 34.1 + - - +
466C VAL* 3.0 45.2 + - + +
495C LEU* 4.3 12.3 - - + -
498C GLN* 3.7 32.2 + - - +
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Residues in contact with ALA 463 (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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299C VAL* 3.9 26.2 - - + -
302C MET* 3.7 19.7 - - + +
303C ILE* 4.2 13.9 - - + -
461C CYS* 3.5 3.4 - - + +
462C GLU* 1.4 77.3 - - - +
464C LEU* 1.3 62.9 + - + +
466C VAL* 3.7 1.7 + - - +
467C MET* 3.4 29.3 + - - +
495C LEU* 4.0 14.2 - - + +
499C GLU* 5.0 2.7 - - - +
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Residues in contact with LEU 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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299C VAL* 5.8 0.7 - - + -
302C MET* 3.8 21.8 - - + -
412C ALA* 3.5 32.5 - - + +
415C CYS* 3.8 17.9 - - + -
417C ILE* 3.9 11.7 - - + -
457C ARG* 4.6 4.3 - - - +
458C TRP* 3.3 59.6 - - + +
461C CYS* 3.7 27.1 + - - +
462C GLU 3.4 0.4 - - - -
463C ALA* 1.3 77.3 - - + +
465C ARG* 1.3 60.7 + - - +
466C VAL 3.6 0.2 - - - -
467C MET* 3.9 4.9 + - - +
468C ALA* 3.4 22.2 + - - +
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Residues in contact with ARG 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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458C TRP 3.6 5.6 + - - +
459C GLN* 3.5 46.1 + - - +
460C SER 3.6 6.1 + - - -
461C CYS 3.1 42.2 + - - +
462C GLU* 3.2 35.5 + - - +
464C LEU* 1.3 78.3 - - - +
466C VAL* 1.4 62.0 + - + +
468C ALA* 3.5 7.3 + - - +
469C LYS* 3.2 21.1 + - - +
472C ARG* 5.4 0.7 + - - -
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Residues in contact with VAL 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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462C GLU* 3.0 34.1 + - + +
463C ALA 3.7 2.7 + - - +
465C ARG* 1.4 72.2 - - - +
467C MET* 1.4 64.7 + - - +
469C LYS* 3.2 13.9 + - + +
470C ILE* 3.2 38.8 + - + +
491C THR* 5.3 7.4 - - - +
492C LEU* 5.0 2.7 - - + -
495C LEU* 3.8 36.1 - - + -
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Residues in contact with MET 467 (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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302C MET* 3.8 18.2 - - + -
303C ILE* 6.2 0.2 - - - -
306C ALA* 3.9 22.2 - - + -
408C PHE* 3.5 60.0 - - + +
411C ILE* 4.8 6.1 - - + -
412C ALA* 4.3 20.9 - - + +
463C ALA 3.4 18.9 + - - +
464C LEU* 4.1 5.6 - - - +
465C ARG 3.4 0.2 - - - -
466C VAL* 1.4 74.6 - - - +
468C ALA* 1.4 56.6 + - - +
470C ILE* 3.5 8.3 + - - +
471C MET* 3.1 35.0 + - - +
492C LEU* 4.4 14.1 - - + -
495C LEU* 5.3 3.4 - - + -
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Residues in contact with ALA 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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454C ILE* 4.6 15.4 - - + +
458C TRP* 4.3 14.6 - - + -
459C GLN* 4.9 7.0 - - - +
464C LEU 3.4 16.3 + - - +
465C ARG* 3.7 8.7 - - - +
466C VAL 3.3 0.8 - - - -
467C MET* 1.4 75.8 - - - +
469C LYS* 1.4 62.8 + - - +
471C MET* 3.6 14.7 + - + +
472C ARG* 3.4 39.7 + - - +
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Residues in contact with LYS 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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465C ARG 3.2 12.1 + - - +
466C VAL* 3.2 16.2 + - + +
468C ALA* 1.4 75.9 - - - +
470C ILE* 1.4 62.8 + - + +
472C ARG* 3.8 18.3 + - - +
473C GLU* 3.2 45.9 + - + +
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Residues in contact with ILE 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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408C PHE* 4.6 10.5 - - + -
466C VAL* 3.2 30.4 + - + +
467C MET* 3.8 10.5 - - - +
469C LYS* 1.4 75.2 - - + +
471C MET* 1.4 57.5 + - - +
473C GLU* 3.0 19.5 + - - +
474C CYS* 3.0 30.9 + - - -
483C LEU* 3.9 26.0 - - + -
488C ILE* 3.9 21.3 - - + -
491C THR* 4.1 17.0 - - + +
492C LEU* 3.9 28.5 - - + -
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Residues in contact with MET 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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405C GLY* 3.6 22.7 - - - +
408C PHE* 4.0 16.2 - - + +
409C TRP* 3.6 44.4 - - + -
454C ILE* 4.4 11.7 - - + -
458C TRP* 3.6 23.6 - - + -
467C MET* 3.1 30.1 + - - +
468C ALA* 3.7 7.9 - - - +
470C ILE* 1.4 76.1 - - - +
472C ARG* 1.4 57.3 + - + +
474C CYS* 3.3 6.5 + - - +
475C TRP* 3.1 52.3 + - + -
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Residues in contact with ARG 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ILE* 4.0 27.3 - - + +
459C GLN* 5.2 7.1 + - - +
465C ARG 5.4 1.0 + - - -
468C ALA* 3.4 32.7 + - - +
469C LYS* 4.2 16.8 + - - +
471C MET* 1.4 78.5 - - - +
473C GLU* 1.3 60.4 + - + +
474C CYS 3.3 1.6 + - - -
475C TRP* 3.7 20.0 + - + +
476C TYR* 3.8 19.1 + - - -
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Residues in contact with GLU 473 (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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469C LYS* 3.2 38.7 + - + +
470C ILE* 3.0 12.6 + - - +
472C ARG* 1.3 76.1 - - + +
474C CYS* 1.3 57.9 + - - +
475C TRP 3.7 0.2 - - - -
476C TYR* 3.3 44.1 + - + +
482C ARG* 3.5 0.5 - - - -
483C LEU* 3.5 47.4 + - + +
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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