Contacts of the helix formed by residues 451 - 462 (chain A) in PDB entry 4JVS
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 TYR 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A ASN* 3.0 30.2 + - - -
405A PHE* 3.9 20.4 - + + -
421A ALA 5.7 0.2 - - - -
422A TYR* 3.4 26.9 - + - -
423A ILE 2.3 37.0 + - - -
424A ALA* 3.5 2.3 - - - -
426A TYR* 3.7 17.7 - + + +
431A ILE* 3.6 30.7 - - + -
435A LEU* 4.4 2.7 - - + -
448A PHE* 3.3 38.0 + + + -
449A ALA 3.1 0.6 - - - -
450A PRO* 1.3 84.4 - - + +
452A GLU* 1.3 59.2 + - - +
453A ALA 3.4 2.7 - - - -
454A PRO* 3.6 6.3 - - + -
455A SER* 2.9 34.4 + - - -
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Residues in contact with GLU 452 (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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435A LEU* 3.4 14.9 - - - +
445A MET* 4.6 5.2 - - - +
447A ARG* 5.7 2.6 + - - +
448A PHE 3.8 18.1 + - - +
449A ALA* 3.4 18.0 + - + +
451A TYR* 1.3 78.1 - - - +
453A ALA* 1.3 57.9 + - - +
455A SER* 3.7 4.1 + - - -
456A THR* 3.0 31.7 + - - -
20B SER* 4.8 11.7 - - - +
42B SER* 4.8 3.1 + - - -
70B GLN* 3.4 29.8 + - + +
72B ARG* 2.9 35.0 + - - -
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Residues in contact with ALA 453 (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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408A PHE 6.0 0.2 - - - +
409A LYS* 5.0 6.3 - - - +
449A ALA 4.6 2.7 + - - +
452A GLU* 1.3 76.4 - - - +
454A PRO* 1.3 67.9 - - + +
455A SER 3.2 0.7 - - - -
456A THR* 3.2 5.7 + - - -
457A ASP* 2.8 40.3 + - - +
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Residues in contact with PRO 454 (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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405A PHE* 3.8 28.9 - - + +
408A PHE* 4.0 23.9 - - + +
409A LYS* 3.6 38.4 - - + +
422A TYR* 5.1 0.2 - - + -
450A PRO 3.6 15.3 - - - +
451A TYR* 3.6 14.1 - - + +
453A ALA* 1.3 93.4 - - + +
455A SER* 1.3 55.8 + - - +
457A ASP* 3.2 1.6 + - - +
458A TYR* 2.8 31.5 + - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 3.8 14.3 - - - -
435A LEU* 3.6 19.3 - - - +
451A TYR* 2.9 21.1 + - - -
452A GLU* 3.7 4.8 + - - -
454A PRO* 1.3 77.0 - - - +
456A THR* 1.3 65.7 + - - +
458A TYR* 3.2 3.6 + - - +
459A CYS* 3.0 25.9 + - - -
467A TRP* 3.9 7.8 + - - +
471A GLN* 2.8 29.3 + - - -
72B ARG* 4.9 2.3 + - - -
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Residues in contact with THR 456 (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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452A GLU* 3.0 18.3 + - - -
453A ALA* 3.7 5.8 - - - -
455A SER* 1.3 79.8 + - - +
457A ASP* 1.3 64.7 + - - +
459A CYS* 3.2 9.5 + - - +
460A ARG* 3.2 42.8 + - - +
471A GLN* 5.6 0.6 + - - +
70B GLN* 5.0 5.7 - - - +
71B GLU* 4.0 39.7 + - + +
72B ARG* 5.5 4.5 + - - -
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Residues in contact with ASP 457 (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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408A PHE* 3.6 33.9 - - + +
453A ALA* 2.8 26.1 + - - +
454A PRO 3.5 4.3 - - - +
456A THR* 1.3 78.0 - - - +
458A TYR* 1.3 61.4 + - - +
460A ARG* 2.6 43.5 + - - +
461A HIS* 3.2 26.0 + - - +
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Residues in contact with TYR 458 (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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404A PHE* 3.3 50.2 - + + -
405A PHE* 3.9 12.1 - + + -
408A PHE* 3.8 24.8 - + + -
454A PRO 2.8 17.0 + - - +
455A SER 3.5 5.4 - - - +
457A ASP* 1.3 76.3 - - - +
459A CYS* 1.3 57.2 + - - +
460A ARG 2.9 0.7 + - - -
461A HIS 3.2 1.9 + - - -
462A PHE* 2.8 50.7 + + - -
465A SER* 3.2 35.3 - - - -
466A PRO* 5.1 3.3 - - - +
467A TRP* 3.7 26.6 - + + +
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Residues in contact with CYS 459 (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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455A SER 3.0 17.8 + - - -
456A THR* 3.2 10.0 + - - +
458A TYR* 1.3 76.4 - - - +
460A ARG* 1.3 57.6 + - - +
462A PHE 4.0 8.3 - - - -
463A PRO* 3.2 27.7 - - - +
467A TRP* 3.5 29.6 - - - -
468A ALA* 4.2 15.5 - - + -
471A GLN* 3.9 16.8 - - - -
472A ARG* 5.6 1.0 + - - +
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Residues in contact with ARG 460 (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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456A THR* 3.2 30.2 + - - +
457A ASP* 2.6 39.8 + - - +
458A TYR 2.9 1.2 + - - -
459A CYS* 1.3 76.5 - - - +
461A HIS* 1.3 78.4 + - - +
463A PRO* 3.4 13.2 - - - +
71B GLU* 3.9 23.3 + - - +
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Residues in contact with HIS 461 (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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408A PHE* 3.8 23.7 - + + -
457A ASP* 3.2 15.0 + - + +
458A TYR 3.2 2.9 + - - +
460A ARG* 1.3 91.0 - - + +
462A PHE* 1.3 90.3 + + + +
463A PRO* 3.4 6.3 - - - +
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Residues in contact with PHE 462 (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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408A PHE* 4.1 14.8 - + - -
458A TYR* 2.8 48.3 + + + +
459A CYS* 3.7 3.7 - - - +
461A HIS* 1.3 101.3 - + + +
463A PRO* 1.3 57.4 - - - +
464A ASP 3.1 5.2 - - - -
465A SER* 2.3 51.2 + - - +
468A ALA* 3.6 2.6 - - - +
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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