Contacts of the helix formed by residues 464 - 476 (chain A) in PDB entry 3RFU
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 HIS 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A PHE* 3.2 43.8 - + - -
282A PRO* 4.8 7.2 - - + -
298A GLN* 5.7 0.4 - - - -
299A THR* 4.3 6.5 - - + +
459A GLU* 5.3 0.6 + - - -
462A SER* 3.5 32.1 + - - -
463A GLU* 1.3 91.9 + - - +
465A PRO* 1.3 67.4 - - + +
466A LEU* 3.1 4.7 - - + +
467A ALA* 3.8 15.7 - - + +
468A ASN* 2.6 45.2 + - - +
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Residues in contact with PRO 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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280A PRO* 3.4 30.7 - - + +
281A ILE* 5.2 1.8 - - + -
282A PRO* 4.0 19.3 - - + -
298A GLN* 5.8 2.2 - - - +
435A HIS* 6.3 1.1 - - - +
436A PRO* 4.1 27.1 - - + +
464A HIS* 1.3 87.2 - - + +
466A LEU* 1.3 56.3 + - + +
468A ASN* 3.5 9.9 + - + +
469A ALA* 2.9 26.0 + - - +
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Residues in contact with LEU 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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281A ILE* 6.0 9.0 - - + -
436A PRO* 4.9 9.2 - - + +
459A GLU* 4.9 6.5 - - - +
464A HIS* 3.1 4.9 - - + -
465A PRO* 1.3 79.9 - - - +
467A ALA* 1.3 62.6 + - - +
469A ALA* 2.8 26.5 + - + +
470A ILE* 3.0 23.6 + - + +
506A ILE* 6.5 0.7 - - + -
535A SER* 5.3 2.7 - - - +
537A MET* 5.4 13.5 - - + -
551A VAL* 3.5 44.6 - - + -
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Residues in contact with ALA 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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459A GLU* 3.3 37.3 + - - +
462A SER 3.3 26.7 - - - +
464A HIS* 3.2 21.7 + - + +
466A LEU* 1.3 78.3 - - - +
468A ASN* 1.3 58.9 + - - +
470A ILE 3.2 1.7 + - - -
471A VAL* 3.0 34.3 + - - +
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Residues in contact with ASN 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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459A GLU 5.3 0.5 - - - +
460A HIS 5.7 0.5 - - - +
462A SER 4.5 5.5 - - - +
463A GLU* 4.8 4.7 - - - +
464A HIS 2.6 39.9 + - - +
465A PRO* 3.7 8.2 - - + +
467A ALA* 1.3 70.2 - - - +
469A ALA* 1.3 59.8 + - - +
471A VAL* 3.4 13.3 - - + +
472A HIS* 2.8 34.0 + - - +
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Residues in contact with ALA 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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436A PRO 4.1 19.7 - - - +
437A LYS* 4.5 1.8 - - - +
438A LEU* 4.0 17.4 + - - +
465A PRO 2.9 15.7 + - - +
466A LEU* 2.8 17.8 + - + +
468A ASN* 1.3 77.9 - - - +
470A ILE* 1.3 60.8 + - + +
472A HIS* 3.8 3.9 - - - +
473A ALA* 3.0 28.6 + - - +
551A VAL* 4.8 5.6 - - + -
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Residues in contact with ILE 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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438A LEU* 3.7 33.2 - - + -
452A LEU* 3.8 16.1 - - + +
455A ALA* 3.9 12.1 - - + +
456A ALA* 3.6 26.7 - - - +
459A GLU* 3.9 13.5 - - + +
466A LEU* 3.0 30.4 + - + +
467A ALA 3.2 4.5 + - - +
469A ALA* 1.3 75.3 - - - +
471A VAL* 1.3 64.7 + - - +
472A HIS 3.0 2.0 - - - -
473A ALA* 3.3 4.0 + - - +
474A ALA* 3.0 22.9 + - - +
549A LEU* 4.3 15.5 - - + -
551A VAL* 4.4 5.4 - - + -
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Residues in contact with VAL 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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456A ALA* 3.3 20.2 - - - +
459A GLU* 3.3 6.3 - - + +
460A HIS* 3.2 47.1 - - + +
467A ALA 3.0 16.2 + - - +
468A ASN* 3.4 24.5 - - + +
470A ILE* 1.3 75.5 - - - +
472A HIS* 1.3 63.1 + - + +
474A ALA* 3.3 2.8 - - - +
475A LYS* 3.0 34.3 + - + +
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Residues in contact with HIS 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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468A ASN 2.8 23.0 + - - +
469A ALA* 3.8 4.0 - - - +
471A VAL* 1.3 77.6 - - + +
473A ALA* 1.3 63.7 + - - +
474A ALA 2.8 6.1 + - - -
475A LYS* 2.9 22.3 + - + +
476A GLU* 2.8 44.0 + - + +
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Residues in contact with ALA 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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437A LYS* 6.4 0.2 - - + -
438A LEU* 3.5 38.4 - - + +
452A LEU* 4.0 13.5 - - + +
469A ALA 3.0 20.4 + - - +
470A ILE* 3.3 4.5 + - - +
472A HIS* 1.3 76.4 - - - +
474A ALA* 1.3 62.3 + - - +
476A GLU* 3.9 15.3 + - - +
477A LYS* 4.1 8.5 + - - +
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Residues in contact with ALA 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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452A LEU* 4.2 16.1 - - + +
453A ALA* 5.5 1.8 - - - -
456A ALA* 3.5 21.3 - - + -
470A ILE 3.0 14.0 + - - +
471A VAL 3.3 10.8 - - - +
472A HIS 2.8 0.6 + - - -
473A ALA* 1.3 76.7 - - - +
475A LYS* 1.3 56.9 + - - +
477A LYS* 2.7 6.2 + - - +
478A GLY* 2.4 46.2 + - - +
480A SER 5.9 1.6 - - - +
481A LEU* 5.8 5.4 - - + -
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Residues in contact with LYS 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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460A HIS* 5.2 15.4 + - - -
471A VAL* 3.0 20.5 + - + +
472A HIS* 2.9 20.0 + - + +
474A ALA* 1.3 74.1 - - - +
476A GLU* 1.3 54.7 + - + +
477A LYS 2.8 11.6 + - - -
478A GLY* 2.9 14.2 + - - +
481A LEU* 5.1 21.1 - - + -
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Residues in contact with GLU 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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437A LYS* 5.8 3.7 - - - -
472A HIS* 2.8 52.0 + - + +
473A ALA* 4.1 9.9 - - - +
474A ALA 3.0 0.2 + - - -
475A LYS* 1.3 74.2 - - - +
477A LYS* 1.3 56.3 + - - +
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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