Contacts of the helix formed by residues 452 - 463 (chain B) in PDB entry 4UIS
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 LEU 452 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B ALA* 2.7 39.2 + - + +
450B ASP 3.5 1.0 - - - -
451B TYR* 1.3 87.4 - - + +
453B VAL* 1.3 72.9 + - + +
454B GLN 3.3 1.3 - - - -
455B PRO* 3.2 12.5 - - - +
456B PHE* 3.6 11.5 + - - +
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Residues in contact with VAL 453 (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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405B ASN* 6.4 1.6 - - + -
448B ALA* 3.9 3.6 + - + +
449B THR* 4.1 24.0 + - + +
452B LEU* 1.3 84.8 - - + +
454B GLN* 1.3 67.5 + - - +
456B PHE* 3.0 14.8 + - + +
457B ALA* 2.8 33.4 + - + +
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Residues in contact with GLN 454 (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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404B TRP 5.7 4.8 - - - +
405B ASN* 4.5 26.1 - - + +
406B THR* 3.6 19.9 + - - +
449B THR* 3.8 15.8 + - + +
450B ASP* 4.5 8.6 - - - +
453B VAL* 1.3 82.4 - - - +
455B PRO* 1.3 71.4 - - + +
457B ALA* 3.4 3.5 + - - +
458B ASP* 2.9 42.6 + - - +
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Residues in contact with PRO 455 (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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450B ASP 4.3 4.7 - - - +
451B TYR 3.6 19.7 - - - +
452B LEU 3.2 13.5 - - - +
454B GLN* 1.3 95.8 - - + +
456B PHE* 1.3 55.6 + - - +
458B ASP* 3.3 11.5 + - + +
459B GLN* 2.9 29.5 + - - +
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Residues in contact with PHE 456 (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 3.6 10.5 + - - +
453B VAL* 3.0 17.8 + - + +
455B PRO* 1.3 77.9 - - - +
457B ALA* 1.3 68.9 + - + +
459B GLN* 3.1 8.4 + - + +
460B LEU* 2.9 37.5 + - + +
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Residues in contact with ALA 457 (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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405B ASN* 6.1 2.0 - - - +
453B VAL* 2.8 28.6 + - + +
454B GLN* 4.0 3.6 - - - +
456B PHE* 1.3 81.6 - - + +
458B ASP* 1.3 59.7 + - - +
460B LEU* 3.1 17.4 - - + +
461B ALA* 2.9 29.6 + - - +
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Residues in contact with ASP 458 (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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405B ASN* 5.1 5.4 + - - -
454B GLN* 2.9 42.0 + - - +
455B PRO* 3.3 10.5 - - + +
456B PHE 3.1 0.2 - - - -
457B ALA* 1.3 76.6 - - - +
459B GLN* 1.3 61.1 + - - +
461B ALA* 3.2 5.5 + - - +
462B PHE* 2.9 29.2 + - - +
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Residues in contact with GLN 459 (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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455B PRO 2.9 16.7 + - - +
456B PHE* 3.1 6.6 + - + +
458B ASP* 1.3 72.9 - - - +
460B LEU* 1.3 67.7 + - - +
462B PHE* 3.4 18.6 - - + +
463B HIS* 3.7 16.5 + - + +
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Residues in contact with LEU 460 (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 PHE* 2.9 26.6 + - + +
457B ALA* 3.1 22.4 - - + +
459B GLN* 1.3 76.5 - - - +
461B ALA* 1.3 55.9 + - + +
463B HIS* 2.6 41.1 + - - +
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Residues in contact with ALA 461 (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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457B ALA 2.9 14.5 + - - +
458B ASP* 3.9 4.7 - - - +
460B LEU* 1.3 79.5 - - + +
462B PHE* 1.3 65.3 + - - +
463B HIS 2.8 12.8 - - - +
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Residues in contact with PHE 462 (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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458B ASP 2.9 12.4 + - - +
459B GLN* 3.4 18.2 - - + +
460B LEU 2.9 0.4 + - - -
461B ALA* 1.3 77.5 - - - +
463B HIS* 1.3 87.1 + + - +
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Residues in contact with HIS 463 (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 GLN* 3.7 17.1 + - + +
460B LEU* 2.6 26.6 + - - +
461B ALA* 2.8 16.6 - - - +
462B PHE* 1.3 106.2 - + - +
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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