Contacts of the helix formed by residues 450 - 473 (chain C) in PDB entry 4AD7
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 ASP 450 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C VAL* 3.3 25.1 - - - +
241C PRO* 5.4 1.0 - - - +
282C ASN* 3.0 24.3 + - + +
449C PRO* 1.3 71.1 - - - +
451C MET* 1.3 59.7 + - - +
452C THR* 3.0 27.9 + - - -
453C ILE* 3.3 25.5 + - + +
454C ARG* 3.0 27.9 + - - +
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Residues in contact with MET 451 (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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449C PRO* 3.3 45.9 + - + +
450C ASP* 1.3 71.4 + - - +
452C THR* 1.3 60.0 + - - +
454C ARG* 3.2 14.3 + - + +
455C GLN* 2.9 45.4 + - - +
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Residues in contact with THR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C LYS* 4.3 16.8 - - + +
237C VAL* 5.0 1.1 - - - +
240C VAL* 4.3 18.0 - - + +
450C ASP* 3.0 12.4 + - - -
451C MET* 1.3 78.4 - - - +
453C ILE* 1.3 62.8 + - - +
455C GLN* 3.2 17.6 + - - +
456C GLN* 3.0 41.2 + - + +
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Residues in contact with ILE 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C VAL* 3.7 34.5 - - + -
240C VAL* 3.7 18.8 - - + -
282C ASN* 3.2 35.7 - - + +
283C GLN* 4.7 7.2 - - + -
285C ASP* 4.8 1.3 - - + -
286C LEU* 3.8 18.8 - - + -
450C ASP* 3.3 30.9 + - + +
452C THR* 1.3 75.3 - - - +
454C ARG* 1.3 60.0 + - + +
456C GLN* 3.2 7.5 + - - +
457C ILE* 2.9 40.7 + - + +
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Residues in contact with ARG 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ASP* 5.7 4.3 + - - +
449C PRO* 4.1 23.8 - - + -
450C ASP 3.0 20.4 + - - +
451C MET* 3.2 21.1 + - + +
453C ILE* 1.3 77.0 - - - +
455C GLN* 1.3 62.4 + - + +
457C ILE* 3.1 43.6 + - - +
458C MET* 3.0 31.0 + - - +
461C LYS* 5.1 8.1 - - - +
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Residues in contact with GLN 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C MET* 2.9 31.2 + - + +
452C THR* 3.4 16.8 + - - +
454C ARG* 1.3 74.9 - - + +
456C GLN* 1.3 71.1 + - - +
458C MET* 3.0 23.7 + - + +
459C GLN* 2.9 34.0 + - + +
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Residues in contact with GLN 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ASP* 5.4 0.2 - - - +
233C VAL* 3.5 36.1 + - + +
236C LYS* 3.2 42.5 - - + +
237C VAL* 3.7 23.3 - - + -
286C LEU* 4.2 2.7 - - + -
452C THR* 3.0 24.7 + - + +
453C ILE 3.2 7.2 + - - +
455C GLN* 1.3 86.7 + - - +
457C ILE* 1.3 66.5 + - - +
459C GLN* 3.2 15.9 + - - +
460C LEU* 2.9 29.0 + - - +
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Residues in contact with ILE 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ASP* 4.1 25.1 - - + +
286C LEU* 3.6 19.1 - - + -
289C GLU* 3.7 24.6 - - + +
453C ILE* 2.9 29.4 + - + +
454C ARG* 3.2 47.8 - - - +
456C GLN* 1.3 75.4 - - - +
458C MET* 1.3 57.3 + - + +
460C LEU* 3.2 9.3 + - - +
461C LYS* 2.9 39.1 + - - +
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Residues in contact with MET 458 (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 ARG* 3.0 18.3 + - - +
455C GLN* 3.0 25.5 + - + +
457C ILE* 1.3 79.3 - - + +
459C GLN* 1.3 57.9 + - + +
461C LYS* 3.2 14.2 + - + +
462C ILE* 2.9 40.1 + - + +
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Residues in contact with GLN 459 (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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229C VAL* 4.2 15.8 - - + +
233C VAL* 4.6 4.3 - - + -
236C LYS* 5.7 6.6 - - - +
455C GLN* 2.9 24.8 + - + +
456C GLN* 3.2 20.3 + - - +
458C MET* 1.3 76.7 - - - +
460C LEU* 1.3 64.2 + - - +
462C ILE* 3.1 21.9 + - - +
463C MET* 3.0 24.8 + - - +
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Residues in contact with LEU 460 (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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229C VAL* 4.5 5.4 - - + -
230C ALA* 4.8 0.9 - - - -
233C VAL* 3.6 26.0 - - + -
286C LEU* 4.3 20.6 - - + +
289C GLU* 3.8 16.8 - - + +
290C TRP* 3.6 44.4 - - + +
293C LEU* 3.6 29.4 - - + +
456C GLN 2.9 17.2 + - - +
457C ILE* 3.4 7.9 - - - +
459C GLN* 1.3 76.9 - - - +
461C LYS* 1.3 54.4 + - - +
463C MET* 3.9 2.1 - - - +
464C THR* 2.6 38.8 + - - -
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Residues in contact with LYS 461 (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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289C GLU* 3.5 43.1 + - - +
454C ARG* 5.1 8.1 - - - +
457C ILE* 2.9 22.8 + - - +
458C MET* 3.4 16.4 - - + +
460C LEU* 1.3 75.8 - - - +
462C ILE* 1.3 57.6 + - + +
464C THR* 3.4 5.1 - - + -
465C ASN* 2.9 27.9 + - - +
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Residues in contact with ILE 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C MET* 2.9 25.1 + - + +
459C GLN* 3.1 27.1 + - - +
461C LYS* 1.3 73.4 - - + +
463C MET* 1.3 67.6 + - - +
465C ASN* 3.0 10.9 + - + +
466C ARG* 2.9 49.7 + - + +
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Residues in contact with MET 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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222C SER* 5.3 0.4 - - - -
225C GLN* 3.5 34.8 - - + +
226C GLY* 3.7 14.6 - - - -
229C VAL* 3.5 33.2 - - + -
293C LEU* 3.7 22.7 - - + -
459C GLN 3.0 14.9 + - - +
460C LEU 4.1 0.4 - - - +
462C ILE* 1.3 77.0 - - - +
464C THR* 1.3 63.1 + - - +
466C ARG* 3.2 37.5 + - - +
467C LEU* 2.9 51.0 + - + +
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Residues in contact with THR 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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289C GLU* 4.1 3.9 + - - +
292C ASN* 3.9 22.2 - - + +
293C LEU* 3.3 22.2 + - - +
296C SER* 4.1 11.7 - - - +
460C LEU 2.6 23.7 + - - -
461C LYS* 3.4 9.3 - - - -
463C MET* 1.3 76.3 - - - +
465C ASN* 1.3 56.5 + - - +
467C LEU* 3.2 2.6 + - - +
468C ARG* 2.9 69.2 + - + +
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Residues in contact with ASN 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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461C LYS 2.9 14.0 + - - +
462C ILE* 3.0 12.6 + - - +
464C THR* 1.3 76.6 - - - +
466C ARG* 1.3 64.8 + - - +
468C ARG* 3.3 8.1 + - - +
469C SER* 2.9 28.5 + - - -
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Residues in contact with ARG 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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222C SER* 4.4 4.6 + - - +
225C GLN* 4.0 20.0 + - - +
229C VAL* 5.6 0.2 - - - +
462C ILE* 2.9 37.9 + - + +
463C MET* 3.2 44.4 + - - +
465C ASN* 1.3 78.0 - - - +
467C LEU* 1.3 59.7 + - + +
469C SER* 3.5 5.3 + - - -
470C ALA* 2.9 30.4 + - - +
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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
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222C SER* 3.3 39.5 - - - +
223C PHE* 5.0 0.4 - - - -
226C GLY* 4.8 0.4 - - - -
293C LEU* 5.1 0.4 - - + -
296C SER* 3.5 37.4 - - - +
297C MET* 3.5 29.2 - - + +
300C ILE* 4.0 16.3 - - + +
463C MET* 2.9 43.7 + - + +
464C THR 3.2 3.8 + - - +
466C ARG* 1.3 76.2 - - - +
468C ARG* 1.3 61.7 + - - +
470C ALA* 3.9 4.5 - - - +
471C TYR* 2.9 31.4 + - - +
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Residues in contact with ARG 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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289C GLU* 5.4 0.8 + - - -
292C ASN* 3.7 32.3 + - - +
296C SER* 4.7 8.4 - - - -
299C LEU* 6.4 3.6 - - + -
464C THR* 2.9 40.9 + - + +
465C ASN* 3.9 7.4 - - - +
467C LEU* 1.3 75.2 - - - +
469C SER* 1.3 57.7 + - - +
471C TYR* 3.7 5.6 - - - +
472C ASN* 2.9 43.5 + - - +
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Residues in contact with SER 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 ASN* 2.9 23.8 + - - -
466C ARG* 3.6 6.3 - - - -
468C ARG* 1.3 77.9 - - - +
470C ALA* 1.3 57.7 + - - +
472C ASN* 3.1 5.9 + - - +
473C GLY 2.9 22.5 + - - -
474C ASN* 3.0 43.2 + - - +
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Residues in contact with ALA 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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215C ARG* 6.1 1.4 - - - +
218C VAL* 4.5 26.1 - - + +
222C SER* 3.6 24.7 - - - +
300C ILE* 4.3 7.7 - - + +
303C LYS* 5.5 1.7 - - - +
466C ARG 2.9 18.3 + - - +
467C LEU 3.9 3.1 - - - +
468C ARG 3.4 0.2 - - - -
469C SER* 1.3 76.2 - - - +
471C TYR* 1.3 59.9 + - - +
473C GLY* 2.9 18.8 + - - -
474C ASN 4.6 8.1 - - - +
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Residues in contact with TYR 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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296C SER 6.1 0.4 - - - +
299C LEU* 3.1 62.5 - - + +
300C ILE* 3.7 12.5 - - + +
302C ASP* 4.2 14.6 + - + +
303C LYS* 3.7 50.7 + - + +
467C LEU 2.9 20.1 + - - +
468C ARG* 3.7 6.1 - - - +
470C ALA* 1.3 77.6 - - - +
472C ASN* 1.3 73.3 + - - +
473C GLY* 3.2 1.2 + - - -
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Residues in contact with ASN 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ARG* 2.9 30.2 + - - +
469C SER* 3.1 4.9 + - - +
471C TYR* 1.3 86.9 - - - +
473C GLY* 1.3 61.9 + - - +
474C ASN* 3.4 24.5 - - - +
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Residues in contact with GLY 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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218C VAL* 6.3 1.1 - - - -
469C SER 2.9 2.4 + - - -
470C ALA* 2.9 14.6 + - - -
471C TYR 3.1 1.9 + - - -
472C ASN* 1.3 80.6 - - - +
474C ASN* 1.3 63.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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