Contacts of the helix formed by residues 464 - 476 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B PHE* 3.2 43.2 - + - -
282B PRO* 4.8 7.9 - - + -
298B GLN* 5.7 0.4 - - - -
299B THR* 4.3 7.1 - - + +
459B GLU* 5.3 0.8 + - - -
462B SER* 3.5 31.2 + - - -
463B GLU* 1.3 91.9 + - - +
465B PRO* 1.3 67.1 - - + +
466B LEU* 4.1 5.4 - - + +
467B ALA* 3.8 14.9 - - + +
468B ASN* 2.6 45.3 + - - +
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Residues in contact with PRO 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B PRO* 3.4 31.0 - - + +
281B ILE* 5.2 1.8 - - + -
282B PRO* 4.0 19.3 - - + -
298B GLN* 5.8 2.5 - - - +
435B HIS* 6.3 1.1 - - - +
436B PRO* 4.1 27.4 - - + +
464B HIS* 1.3 87.9 - - + +
466B LEU* 1.3 55.3 + - + +
468B ASN* 3.5 9.6 + - + +
469B ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 6.0 9.0 - - + -
436B PRO* 4.9 9.2 - - + +
459B GLU* 4.9 7.4 - - - +
464B HIS* 3.1 5.1 - - + -
465B PRO* 1.3 78.7 - - + +
467B ALA* 1.3 61.7 + - - +
469B ALA* 2.8 26.5 + - + +
470B ILE* 3.0 24.1 + - + +
506B ILE* 6.5 0.4 - - + -
535B SER* 5.3 2.5 - - - +
537B MET* 5.4 14.1 - - + -
551B VAL* 3.5 44.0 - - + -
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B GLU* 3.3 37.2 + - - +
462B SER 3.3 26.5 - - - +
464B HIS* 3.2 21.3 + - + +
466B LEU* 1.3 79.3 - - - +
468B ASN* 1.3 58.3 + - - +
470B ILE 3.2 1.9 + - - -
471B VAL* 3.0 34.3 + - - +
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Residues in contact with ASN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B GLU 5.3 0.5 - - - +
460B HIS 5.7 0.3 - - - +
462B SER 4.5 5.2 - - - +
463B GLU* 4.8 4.6 - - - +
464B HIS 2.6 39.1 + - - +
465B PRO* 3.7 9.0 - - + +
467B ALA* 1.3 72.0 - - - +
469B ALA* 1.3 59.7 + - - +
471B VAL* 3.4 14.1 - - + +
472B HIS* 2.8 33.6 + - - +
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Residues in contact with ALA 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B PRO* 4.1 19.3 - - + +
437B LYS* 4.5 1.3 - - - +
438B LEU* 4.0 18.7 + - - +
465B PRO 2.9 14.6 + - - +
466B LEU* 2.8 18.3 + - + +
468B ASN* 1.3 77.9 - - - +
470B ILE* 1.3 60.4 + - + +
472B HIS* 3.9 3.6 - - - +
473B ALA* 3.0 28.8 + - - +
551B VAL* 4.8 5.2 - - + -
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B LEU* 3.7 33.0 - - + -
452B LEU* 3.8 15.4 - - + +
455B ALA* 3.9 12.6 - - + +
456B ALA* 3.6 26.5 - - - +
459B GLU* 3.9 14.8 - - + +
466B LEU* 3.0 30.8 + - + +
467B ALA 3.2 4.2 + - - +
469B ALA* 1.3 75.2 - - - +
471B VAL* 1.3 65.5 + - - +
472B HIS 3.0 1.3 - - - -
473B ALA* 3.3 4.0 + - - +
474B ALA* 3.0 23.2 + - - +
549B LEU* 4.3 15.3 - - + -
551B VAL* 4.4 5.6 - - + -
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B ALA* 3.3 19.3 - - - +
459B GLU* 3.3 7.0 - - + +
460B HIS* 3.2 48.2 - - + +
467B ALA 3.0 15.5 + - - +
468B ASN* 3.4 24.0 - - + +
470B ILE* 1.3 76.1 - - - +
472B HIS* 1.3 61.9 + - + +
474B ALA* 3.3 2.9 - - - +
475B LYS* 3.0 34.4 + - + +
481B LEU* 6.2 0.2 - - - +
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Residues in contact with HIS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ASN 2.8 22.8 + - - +
469B ALA* 3.9 4.2 - - - +
471B VAL* 1.3 76.2 - - + +
473B ALA* 1.3 65.1 + - - +
474B ALA 2.8 5.3 + - - -
475B LYS* 2.9 21.8 + - + +
476B GLU* 2.9 44.6 + - + +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B LYS* 6.4 0.2 - - + -
438B LEU* 3.5 38.6 - - + +
452B LEU* 4.0 12.5 - - + +
469B ALA 3.0 20.0 + - - +
470B ILE 3.9 4.3 - - - +
472B HIS* 1.3 76.4 - - - +
474B ALA* 1.3 62.2 + - - +
476B GLU* 3.9 16.0 + - - +
477B LYS* 4.1 8.8 + - - +
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Residues in contact with ALA 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LEU* 4.2 15.5 - - + +
453B ALA* 5.5 2.5 - - - -
456B ALA* 3.5 21.3 - - + -
470B ILE 3.0 12.5 + - - +
471B VAL* 3.3 11.0 - - - +
472B HIS 2.8 0.6 + - - -
473B ALA* 1.3 77.5 - - - +
475B LYS* 1.3 57.3 + - - +
477B LYS* 2.8 6.5 + - - +
478B GLY* 2.4 44.9 + - - +
480B SER 5.9 1.3 - - - +
481B LEU* 5.8 6.7 - - + -
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Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B HIS* 5.2 15.2 + - - -
471B VAL* 3.0 19.7 + - + +
472B HIS* 2.9 21.3 + - + +
474B ALA* 1.3 74.5 - - - +
476B GLU* 1.3 53.6 + - - +
477B LYS 2.8 11.6 + - - -
478B GLY* 2.9 15.5 + - - +
481B LEU* 5.1 20.9 - - + -
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Residues in contact with GLU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B LYS* 5.8 3.9 - - - -
472B HIS* 2.9 50.6 + - + +
473B ALA* 4.1 10.2 - - - +
474B ALA 3.0 0.4 + - - -
475B LYS* 1.3 73.8 - - - +
477B LYS* 1.3 58.7 + - + +
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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
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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