Contacts of the helix formed by residues 462 - 477 (chain A) in PDB entry 1CJY
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 ALA 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A LEU* 5.1 6.1 - - + -
405A LEU* 3.7 31.7 - - + +
460A ASN* 3.3 18.4 + - - +
461A GLN* 1.3 75.3 - - - +
463A SER* 1.3 62.8 + - - +
464A TRP 3.2 2.7 - - - -
465A ILE* 3.4 31.2 + - + +
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Residues in contact with SER 463 (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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402A ASN 5.6 0.9 + - - -
405A LEU* 4.9 3.9 - - - -
460A ASN* 2.9 33.6 + - - +
461A GLN 3.2 1.2 - - - -
462A ALA* 1.3 76.8 - - - +
464A TRP* 1.3 67.0 + - - +
465A ILE 3.2 0.2 - - - -
466A HIS* 3.2 19.4 + - - +
467A ARG* 3.2 17.4 + - - +
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Residues in contact with TRP 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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460A ASN 5.0 2.4 + - - -
461A GLN* 3.4 48.4 + - - +
462A ALA 3.2 0.2 - - - -
463A SER* 1.3 80.1 - - - +
465A ILE* 1.3 52.4 + - + +
467A ARG* 3.0 36.7 + - + +
468A MET* 2.7 36.5 + - - +
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Residues in contact with ILE 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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264A LEU* 3.6 26.0 - - + +
265A LEU* 5.3 2.2 - - - -
267A LEU* 3.6 37.2 - - + +
405A LEU* 4.4 14.4 - - + -
461A GLN 5.3 0.7 - - - +
462A ALA* 3.4 25.1 - - + +
464A TRP* 1.3 79.5 - - + +
466A HIS* 1.3 56.6 + - - +
468A MET* 3.2 13.8 + - + +
469A ILE* 2.8 39.6 + - + +
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Residues in contact with HIS 466 (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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291A PHE* 4.9 5.6 - + - -
401A PHE* 4.2 13.3 - + + -
402A ASN* 4.0 33.7 + - + +
405A LEU* 3.5 27.0 - - + +
463A SER* 3.2 14.9 + - - +
465A ILE* 1.3 79.8 - - - +
467A ARG* 1.3 61.0 + - + +
469A ILE* 3.8 5.5 - - - +
470A MET* 3.0 44.6 + - + +
485A ARG* 3.6 28.9 + - - -
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Residues in contact with ARG 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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463A SER* 3.2 11.0 + - - +
464A TRP* 3.0 41.7 + - + +
466A HIS* 1.3 81.1 - - + +
468A MET* 1.3 56.1 + - - +
470A MET* 3.1 5.7 + - - +
471A ALA* 2.7 38.6 + - - +
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Residues in contact with MET 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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267A LEU 3.7 22.4 - - - +
269A PRO* 3.9 35.0 - - + -
272A VAL* 3.9 18.4 - - + -
464A TRP 2.7 20.0 + - - +
465A ILE* 3.6 22.2 - - + +
467A ARG* 1.3 73.7 - - - +
469A ILE* 1.3 61.5 + - + +
471A ALA* 3.6 6.3 - - - +
472A LEU* 3.0 45.3 + - + +
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Residues in contact with ILE 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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267A LEU* 3.8 34.5 - - + -
272A VAL* 4.0 27.1 - - + -
291A PHE* 3.9 13.9 - - + -
294A ILE* 4.3 13.9 - - + -
401A PHE* 4.3 13.2 - - + -
465A ILE* 2.8 26.9 + - + +
466A HIS* 3.8 5.8 - - - +
468A MET* 1.3 80.1 - - + +
470A MET* 1.3 83.2 + - + +
472A LEU* 3.2 2.9 + - - +
473A VAL* 2.9 35.1 + - + +
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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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291A PHE* 3.4 23.6 - - + -
466A HIS* 3.0 34.4 + - + +
467A ARG* 3.7 5.2 - - - +
469A ILE* 1.3 101.4 - - + +
471A ALA* 1.3 62.3 + - - +
473A VAL* 3.4 15.0 + - + +
474A SER* 3.0 25.1 + - - -
479A PHE* 4.7 3.4 - - + -
481A THR* 3.8 28.5 - - + +
485A ARG* 3.1 30.3 - - - +
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Residues in contact with ALA 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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467A ARG 2.7 22.2 + - - +
468A MET* 3.6 7.4 - - - +
470A MET* 1.3 70.9 - - - +
472A LEU* 1.3 69.0 + - + +
474A SER* 3.2 7.6 + - - -
475A ASP* 2.9 27.5 + - - +
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Residues in contact with LEU 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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269A PRO* 3.7 17.3 - - + +
272A VAL* 3.5 34.1 - - + -
273A LYS* 3.9 29.2 - - + +
276A VAL* 4.7 7.2 - - + +
468A MET* 3.0 33.8 + - + +
469A ILE 3.6 4.3 - - - +
471A ALA* 1.3 79.3 - - + +
473A VAL* 1.3 60.7 + - - +
475A ASP* 3.7 7.7 - - + +
476A SER* 2.9 29.0 + - - -
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Residues in contact with VAL 473 (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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276A VAL* 4.7 9.4 - - + -
294A ILE* 3.7 28.0 - - + -
469A ILE* 2.9 18.2 + - + +
470A MET* 3.7 16.8 - - + +
471A ALA 3.2 0.2 - - - -
472A LEU* 1.3 75.0 - - + +
474A SER* 1.3 60.2 + - - +
476A SER* 3.2 5.5 + - - -
477A ALA* 2.9 22.9 + - - -
478A LEU* 3.2 19.5 + - + -
479A PHE* 3.5 47.2 + - + +
481A THR* 4.5 3.8 - - + -
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Residues in contact with SER 474 (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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470A MET 3.0 13.1 + - - -
471A ALA* 3.2 12.5 + - - -
473A VAL* 1.3 77.2 - - - +
475A ASP* 1.3 65.8 + - - +
477A ALA* 3.0 15.5 + - - +
479A PHE 5.1 2.9 - - - -
481A THR* 4.6 13.4 - - - +
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Residues in contact with ASP 475 (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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471A ALA 2.9 20.2 + - - +
472A LEU* 3.7 11.4 - - + +
474A SER* 1.3 79.6 + - - +
476A SER* 1.3 57.8 + - - +
477A ALA* 5.3 0.3 - - - +
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Residues in contact with SER 476 (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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276A VAL* 3.2 30.8 - - - +
280A TRP* 3.3 21.7 + - - -
472A LEU 2.9 18.7 + - - -
473A VAL* 3.2 7.4 + - - -
475A ASP* 1.3 76.2 - - - +
477A ALA* 1.3 70.1 + - - +
478A LEU* 3.2 3.8 + - - +
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Residues in contact with ALA 477 (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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280A TRP* 3.7 5.3 - - + -
283A LYS* 3.5 15.4 + - - -
473A VAL 2.9 7.1 + - - -
474A SER* 3.0 12.8 + - - +
475A ASP 5.3 0.4 - - - +
476A SER* 1.3 81.1 - - - +
478A LEU* 1.3 65.9 + - - +
479A PHE* 3.2 6.0 + - - +
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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