Contacts of the helix formed by residues 381 - 393 (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 ASP 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B LYS* 2.7 50.0 + - - +
326B SER* 2.9 21.3 + - - +
379B LYS 3.6 0.8 + - - -
380B VAL* 1.3 86.7 - - - +
382B GLU* 1.3 64.8 + - - +
383B GLU* 3.5 11.4 - - - +
384B LEU* 3.4 10.8 + - + +
385B LYS* 3.8 1.7 + - - +
414B LYS* 3.7 13.7 + - - +
416B TYR* 3.0 27.5 + - - +
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Residues in contact with GLU 382 (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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380B VAL 3.5 2.6 + - - +
381B ASP* 1.3 70.9 - - - +
383B GLU* 1.3 64.1 + - - +
385B LYS* 2.8 58.9 + - - +
386B GLU* 3.0 14.6 + - + +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ASP* 3.5 13.3 - - - +
382B GLU* 1.3 85.9 + - - +
384B LEU* 1.3 57.7 + - + +
386B GLU* 3.3 7.4 + - - +
387B LEU* 2.9 27.6 + - - +
407B LEU* 3.6 26.7 - - + +
410B LYS* 3.9 40.0 - - + +
411B LEU* 3.9 19.5 - - + -
414B LYS* 3.6 25.4 + - - -
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Residues in contact with LEU 384 (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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326B SER* 3.1 48.9 - - - +
329B PHE* 3.4 25.4 - - + -
330B LEU* 3.9 24.5 - - + +
333B ILE* 4.0 1.8 - - + +
380B VAL* 4.0 1.3 - - + -
381B ASP* 3.4 10.4 + - + +
382B GLU 3.1 0.8 - - - -
383B GLU* 1.3 74.7 - - + +
385B LYS* 1.3 60.1 + - - +
387B LEU* 3.3 8.8 + - + +
388B TYR 2.9 23.4 + - - -
411B LEU* 3.5 35.0 - - + -
416B TYR* 3.6 18.8 - - + +
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Residues in contact with LYS 385 (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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329B PHE* 4.2 4.0 - - - -
377B TYR* 3.3 61.3 + - + +
378B GLY* 4.1 8.3 + - - -
380B VAL* 3.3 33.6 + - + -
381B ASP 3.8 4.5 - - - +
382B GLU* 2.8 40.0 + - - +
384B LEU* 1.3 76.1 - - - +
386B GLU* 1.3 62.9 + - - +
388B TYR* 3.3 6.7 + - - +
389B ASP* 3.0 20.8 + - - +
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Residues in contact with GLU 386 (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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382B GLU* 3.0 13.6 + - + +
383B GLU* 3.4 9.7 - - - +
384B LEU 3.2 0.2 - - - -
385B LYS* 1.3 75.3 - - - +
387B LEU* 1.3 59.6 + - - +
389B ASP* 2.9 23.7 + - + +
390B ILE* 2.9 36.2 + - + +
403B GLN* 5.5 4.2 - - - +
407B LEU* 3.3 26.7 - - + +
410B LYS* 4.1 11.4 + - - -
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Residues in contact with LEU 387 (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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330B LEU* 4.0 21.8 - - + -
333B ILE* 3.9 21.3 - - + -
383B GLU 2.9 13.9 + - - +
384B LEU* 3.4 10.1 - - - +
386B GLU* 1.3 74.2 - - - +
388B TYR* 1.3 62.7 + - - +
390B ILE* 3.0 4.8 + - - +
391B ILE* 3.0 52.5 + - + +
404B LEU* 3.8 22.4 - - + -
407B LEU* 3.7 15.4 - - + +
408B LEU* 6.1 2.0 - - + -
411B LEU* 4.5 13.2 - - + -
424B LEU* 4.1 24.2 - - + -
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Residues in contact with TYR 388 (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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329B PHE* 3.6 26.2 - + + -
333B ILE* 4.2 8.7 - - + +
367B LEU* 3.6 24.8 - - + +
368B GLN* 5.1 6.2 + - - -
371B ILE* 3.3 30.5 - - + +
377B TYR* 5.2 4.5 - - - -
384B LEU 2.9 14.2 + - - +
385B LYS* 3.5 9.6 - - - +
387B LEU* 1.3 74.8 - - - +
389B ASP* 1.3 62.5 + - + +
391B ILE* 5.1 0.7 - - - -
392B GLU* 2.9 55.4 + - + +
393B VAL* 3.2 24.5 + - + +
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Residues in contact with ASP 389 (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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385B LYS 3.0 12.2 + - - +
386B GLU* 2.9 13.7 + - + +
388B TYR* 1.3 76.6 - - + +
390B ILE* 1.3 71.3 + - - +
393B VAL* 3.0 40.3 + - + +
394B ASN* 2.9 42.3 + - - +
403B GLN* 5.5 0.2 + - - -
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Residues in contact with ILE 390 (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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386B GLU* 2.9 37.9 + - + +
387B LEU* 3.0 10.7 + - - +
389B ASP* 1.3 86.3 - - - +
391B ILE* 1.3 63.8 + - + +
394B ASN 3.5 5.6 - - - +
395B PHE* 3.4 27.7 - - - -
396B ASP 4.7 0.2 + - - -
400B VAL* 4.0 20.4 - - + +
403B GLN* 3.3 59.0 - - + +
404B LEU* 4.4 9.4 - - + -
407B LEU* 4.8 5.6 - - + -
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Residues in contact with ILE 391 (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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333B ILE* 4.8 5.2 - - + -
387B LEU* 3.0 41.5 + - + +
388B TYR* 5.1 0.2 - - - -
390B ILE* 1.3 92.2 - - + +
392B GLU* 1.3 79.5 - - + +
393B VAL 3.7 0.2 - - - -
395B PHE* 3.6 25.2 - - + +
400B VAL* 5.4 2.5 - - + -
404B LEU* 4.7 1.8 - - + -
424B LEU* 4.2 8.1 - - + -
427B VAL* 4.5 12.1 - - + -
428B ILE* 3.5 33.9 - - + -
431B ARG* 3.7 27.8 + - + +
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 4.7 3.9 - - + +
363B ARG* 2.8 38.6 + - - +
364B LYS* 6.0 1.4 - - - -
367B LEU* 4.2 8.3 - - + +
388B TYR* 2.9 52.5 + - + +
391B ILE* 1.3 89.9 - - + +
393B VAL* 1.3 66.4 + - - +
395B PHE* 5.6 0.2 - - - -
427B VAL* 4.6 0.5 - - - +
431B ARG* 3.4 25.1 + - - -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B TYR* 3.5 30.1 - - + +
389B ASP* 3.0 35.2 + - + +
392B GLU* 1.3 81.8 - - - +
394B ASN* 1.3 79.5 - - - +
395B PHE* 3.7 3.0 + - - +
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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