Contacts of the helix formed by residues 454 - 466 (chain B) in PDB entry 1U0E
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 SER 454 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B GLN* 6.1 0.2 - - - -
452B GLY 3.4 4.2 + - - -
453B LYS* 1.3 74.4 - - - +
455B PRO* 1.3 68.4 - - - +
456B GLU* 3.7 5.9 + - - +
457B ASP* 3.2 33.1 + - - +
458B LEU* 2.8 28.3 + - - +
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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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449B GLN* 5.9 2.7 - - - +
453B LYS 4.5 1.1 - - - +
454B SER* 1.3 86.1 - - - +
456B GLU* 1.3 77.8 + - + +
458B LEU* 3.6 6.4 - - + +
459B GLU* 3.2 23.2 + - - +
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Residues in contact with GLU 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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454B SER* 3.3 6.2 + - - +
455B PRO* 1.3 87.2 - - + +
457B ASP* 1.3 68.4 + - - +
459B GLU* 3.4 5.6 + - - +
460B LYS* 3.0 45.7 + - + +
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Residues in contact with ASP 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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453B LYS* 4.4 16.4 + - + +
454B SER* 3.2 26.8 + - - +
456B GLU* 1.3 75.4 - - - +
458B LEU* 1.3 66.8 + - - +
460B LYS* 3.3 11.0 + - - +
461B LEU* 2.9 34.5 + - + +
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Residues in contact with LEU 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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445B ARG* 3.4 46.0 - - + +
448B LEU* 3.7 31.8 - - + +
449B GLN* 3.5 43.5 - - + +
453B LYS* 4.1 11.3 - - + +
454B SER 2.8 22.4 + - - +
455B PRO* 3.6 7.6 - - + +
457B ASP* 1.3 73.7 - - - +
459B GLU* 1.3 62.1 + - - +
461B LEU* 4.9 0.7 - - - -
462B LEU* 2.9 37.3 + - + +
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Residues in contact with GLU 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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445B ARG* 3.5 28.1 + - - -
455B PRO 3.2 14.4 + - - +
456B GLU* 4.0 5.4 - - - +
457B ASP 3.3 0.2 - - - -
458B LEU* 1.3 79.9 - - - +
460B LYS* 1.3 62.4 + - + +
462B LEU* 4.0 13.1 - - - +
463B PRO* 3.5 17.2 - - - +
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Residues in contact with LYS 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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367A GLY* 5.7 1.6 - - - -
456B GLU* 3.0 37.0 + - + +
457B ASP* 3.7 11.7 - - - +
458B LEU 3.2 0.2 - - - -
459B GLU* 1.3 79.0 - - + +
461B LEU* 1.3 64.4 + - + +
463B PRO* 3.6 6.2 - - - +
464B HIS* 3.4 19.1 + - - -
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Residues in contact with LEU 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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92A THR* 3.3 45.3 - - + +
512A TRP* 4.5 16.2 - - + -
448B LEU* 4.1 19.3 - - + -
453B LYS* 3.7 34.8 - - + +
457B ASP* 2.9 23.1 + - + +
458B LEU 4.0 1.8 - - - +
460B LYS* 1.3 81.7 - - + +
462B LEU* 1.3 67.8 + - - +
463B PRO 3.4 0.2 - - - -
464B HIS* 3.0 22.0 + - + +
465B LYS* 3.4 9.6 + - + +
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Residues in contact with LEU 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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441B PRO* 3.6 23.1 - - + +
444B ALA* 3.8 9.6 - - + -
445B ARG* 3.5 49.4 - - + +
448B LEU* 3.8 10.3 - - + -
458B LEU* 2.9 19.5 + - + +
459B GLU* 4.0 21.1 - - - +
461B LEU* 1.3 76.5 - - - +
463B PRO* 1.3 71.4 - - + +
465B LYS* 3.0 14.5 + - - +
466B VAL* 3.3 19.4 + - + +
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Residues in contact with PRO 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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362A TYR* 3.6 11.4 + - - -
363A ILE* 3.6 40.4 - - + +
367A GLY* 4.3 17.7 - - - +
459B GLU 3.5 13.2 - - - +
460B LYS 3.6 9.0 - - - +
461B LEU 3.5 3.4 - - - -
462B LEU* 1.3 96.3 - - + +
464B HIS* 1.3 61.5 + - + +
465B LYS 3.3 0.5 + - - -
466B VAL* 3.4 16.0 + - + +
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Residues in contact with HIS 464 (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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91A TYR* 4.3 10.1 - + - -
92A THR* 3.6 31.4 - - + +
363A ILE* 3.4 45.4 - - + +
364A THR 3.9 10.1 + - - -
365A LYS 5.7 0.8 + - - -
367A GLY* 5.2 1.8 - - - -
507A ASN* 5.6 1.6 - - + -
510A ASP* 4.4 5.2 + - - -
512A TRP* 3.5 30.9 - - + +
396B GLN* 3.1 22.9 + - - +
460B LYS 3.4 25.3 + - - -
461B LEU* 3.0 10.9 + - + +
463B PRO* 1.3 77.7 - - + +
465B LYS* 1.3 58.2 + - + +
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Residues in contact with LYS 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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512A TRP* 3.8 37.2 - - + -
515A GLU* 4.1 15.8 + - - +
396B GLN* 4.8 0.2 - - - +
439B LYS* 3.6 17.1 + - - +
444B ALA* 3.8 25.3 + - + +
447B GLU* 3.2 31.0 + - - +
448B LEU* 3.6 28.7 - - + +
461B LEU* 3.6 15.7 - - + +
462B LEU* 3.0 10.1 + - - +
464B HIS* 1.3 78.5 - - + +
466B VAL* 1.3 64.3 + - - +
467B PHE* 3.4 18.6 - - - -
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TYR* 2.7 27.9 + - - +
396B GLN* 2.9 15.8 + - - -
439B LYS 3.4 13.0 - - - +
440B LEU* 4.9 0.2 - - - -
441B PRO* 3.7 44.2 - - + -
444B ALA* 4.3 4.9 - - + -
462B LEU* 3.4 18.4 - - + +
463B PRO* 3.4 12.4 + - + +
465B LYS* 1.3 79.0 - - - +
467B PHE* 1.3 68.5 + - - +
468B GLU* 4.4 6.5 - - + +
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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