Contacts of the helix formed by residues 445 - 452 (chain B) in PDB entry 4U1D
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 GLN 445 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443B VAL 3.6 2.7 + - - -
444B SER* 1.3 71.6 - - - +
446B SER* 1.3 61.9 + - - +
448B LEU* 4.6 2.0 - - - -
449B TYR* 3.1 76.9 + - + +
466B GLU* 3.4 13.7 + - - -
482B ILE* 3.8 13.3 - - - +
483B ASP 4.2 5.9 - - - +
484B HIS* 4.4 6.9 + - - -
487B ALA* 2.7 44.4 + - + +
488B LYS* 3.8 1.2 + - - +
489B VAL* 4.0 16.4 - - + -
77C LYS* 4.2 19.9 + - - +
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Residues in contact with SER 446 (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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444B SER* 3.2 11.5 + - - -
445B GLN* 1.3 79.5 - - - +
447B GLU* 1.3 61.3 + - - +
449B TYR* 4.4 1.8 - - - +
450B LYS* 3.1 27.8 + - - +
487B ALA* 4.4 6.1 + - - +
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Residues in contact with GLU 447 (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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440B PHE* 5.0 11.1 - - + -
443B VAL* 3.8 17.7 - - + -
444B SER* 3.1 18.3 + - - +
446B SER* 1.3 78.3 - - - +
448B LEU* 1.3 60.3 + - - +
450B LYS* 3.3 13.8 + - - +
451B LEU* 2.9 36.5 + - + +
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Residues in contact with LEU 448 (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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432B VAL* 6.0 0.7 - - + -
433B PHE* 3.7 34.3 - - + -
436B ALA* 4.8 13.5 - - + -
440B PHE* 6.2 0.2 - - + -
443B VAL* 3.8 28.2 - - + +
444B SER 2.9 19.9 + - - +
445B GLN* 4.1 3.1 - - - +
447B GLU* 1.3 73.5 - - - +
449B TYR* 1.3 69.3 + - + +
451B LEU* 3.1 11.5 + - + +
452B ALA* 3.0 20.2 + - + +
469B LEU* 3.9 16.2 - - + -
489B VAL* 3.9 20.0 - - + -
491B PHE* 3.8 19.3 - - + -
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Residues in contact with TYR 449 (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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445B GLN* 3.1 62.7 + - + +
446B SER* 4.4 2.5 - - - +
448B LEU* 1.3 87.8 - - + +
450B LYS* 1.3 55.1 + - - +
452B ALA 3.2 0.9 + - - -
453B THR* 2.5 34.9 + - - -
462B ALA* 3.8 31.4 - - + +
465B ILE* 3.4 33.9 - - + +
466B GLU* 3.2 27.9 + - + +
469B LEU* 4.0 24.9 - - + +
482B ILE* 3.7 9.0 - - - +
489B VAL* 5.0 0.2 - - + -
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Residues in contact with LYS 450 (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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401B LYS* 2.5 37.0 + - - +
446B SER 3.1 20.0 + - - +
447B GLU* 3.7 15.3 - - - +
449B TYR* 1.3 77.1 - - - +
451B LEU* 1.3 52.0 + - - +
453B THR* 3.7 10.1 + - - -
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Residues in contact with LEU 451 (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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397B VAL* 3.5 40.6 - - + +
398B ASP* 4.7 8.1 - - - +
400B VAL* 5.8 0.2 - - - +
401B LYS* 3.5 23.1 - - + +
432B VAL* 4.0 9.9 - - + +
436B ALA* 4.3 16.4 - - + -
439B LYS* 5.6 2.9 - - + -
440B PHE* 4.2 27.1 - - + -
447B GLU* 2.9 24.7 + - + +
448B LEU* 3.1 11.6 + - + +
450B LYS* 1.3 78.5 - - - +
452B ALA* 1.3 56.1 + - - +
453B THR 3.4 0.4 - - - -
454B LEU* 5.6 0.3 - - - +
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Residues in contact with ALA 452 (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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429B MET* 3.3 40.5 - - + +
432B VAL* 3.9 20.6 - - + -
433B PHE* 3.9 19.3 - - + -
448B LEU* 3.0 14.6 + - + +
449B TYR 3.2 4.7 + - - +
451B LEU* 1.3 76.9 - - - +
453B THR* 1.3 59.0 + - - +
454B LEU* 3.3 8.6 + - - +
460B LEU* 5.7 0.2 - - - +
465B ILE* 4.0 7.2 - - + +
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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