Contacts of the helix formed by residues 381 - 393 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C LYS* 3.0 41.5 + - - +
326C SER* 3.1 19.0 + - - +
379C LYS 3.7 1.2 + - - -
380C VAL* 1.3 86.8 - - - +
382C GLU* 1.3 66.6 + - - +
383C GLU* 3.3 12.9 - - - +
384C LEU* 3.4 11.0 + - + +
385C LYS* 3.6 4.0 + - - -
414C LYS* 3.3 19.5 + - - -
416C TYR* 3.1 25.2 + - - +
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Residues in contact with GLU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C VAL 3.5 2.9 + - - +
381C ASP* 1.3 71.5 - - - +
383C GLU* 1.3 65.6 + - - +
385C LYS* 2.8 51.7 + - - +
386C GLU* 2.9 13.8 + - - +
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Residues in contact with GLU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C ASP* 3.3 22.0 - - - +
382C GLU* 1.3 77.2 + - - +
384C LEU* 1.3 59.3 + - + +
386C GLU* 3.4 3.9 + - - -
387C LEU* 2.9 28.1 + - - +
407C LEU* 3.6 26.3 - - + +
410C LYS* 4.0 37.2 - - + +
411C LEU* 3.9 18.8 - - + -
414C LYS* 3.6 23.8 + - - -
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C SER* 3.1 48.2 - - - +
329C PHE* 3.3 28.0 - - + -
330C LEU* 4.0 23.3 - - + +
333C ILE* 4.1 1.2 - - - +
380C VAL* 4.1 2.7 - - + -
381C ASP* 3.4 10.6 + - + +
382C GLU 3.1 0.4 - - - -
383C GLU* 1.3 76.5 - - + +
385C LYS* 1.3 61.2 + - - +
387C LEU* 3.3 8.7 - - + +
388C TYR 2.9 22.3 + - - -
411C LEU* 3.5 26.2 - - + -
416C TYR* 3.2 27.4 - - + +
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Residues in contact with LYS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C PHE* 4.3 1.3 - - - -
377C TYR* 3.2 57.8 + - + +
378C GLY 4.7 2.9 + - - -
380C VAL* 2.4 50.8 + - + +
381C ASP 3.8 3.8 - - - +
382C GLU* 2.8 34.7 + - - +
384C LEU* 1.3 72.9 - - - +
386C GLU* 1.3 61.4 + - - +
388C TYR* 3.3 8.8 + - - +
389C ASP* 3.0 25.8 + - - +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C GLU 2.9 10.5 + - - +
383C GLU* 3.6 10.0 - - - +
385C LYS* 1.3 74.7 - - - +
387C LEU* 1.3 64.8 + - - +
389C ASP* 2.9 10.6 + - + +
390C ILE* 2.9 39.8 + - + +
403C GLN* 5.3 5.9 + - - +
407C LEU* 3.6 25.0 - - + +
410C LYS* 3.7 15.1 + - - -
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Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C LEU* 4.0 21.3 - - + -
333C ILE* 3.8 26.0 - - + -
383C GLU 2.9 15.3 + - - +
384C LEU* 3.3 11.0 - - - +
386C GLU* 1.3 74.8 - - - +
388C TYR* 1.3 57.3 - - - +
390C ILE* 3.1 4.6 + - - +
391C ILE* 2.9 60.2 + - + +
404C LEU* 4.0 14.6 - - + -
407C LEU* 3.6 20.8 - - + +
408C LEU* 6.0 2.2 - - + -
411C LEU* 4.4 15.0 - - + -
424C LEU* 4.3 15.5 - - + -
428C ILE* 5.2 0.2 - - + -
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Residues in contact with TYR 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C PHE* 3.5 27.1 - + + -
333C ILE* 4.3 10.8 - - + -
367C LEU* 3.5 30.7 - - + +
368C GLN* 5.4 5.4 + - - +
371C ILE* 3.3 31.0 - - + +
377C TYR* 4.9 6.5 - - - -
384C LEU 2.9 14.5 + - - +
385C LYS* 3.4 11.0 - - - +
387C LEU* 1.3 75.5 - - - +
389C ASP* 1.3 59.4 + - - +
391C ILE* 5.2 0.9 - - - -
392C GLU* 2.9 48.2 + - + +
393C VAL* 3.1 30.6 + - + +
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Residues in contact with ASP 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C LYS 3.0 11.4 + - - +
386C GLU* 2.9 13.3 + - + +
388C TYR* 1.3 77.2 - - + +
390C ILE* 1.3 71.4 + - - +
393C VAL* 3.0 36.9 + - + +
394C ASN* 2.7 45.0 + - - +
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Residues in contact with ILE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386C GLU* 2.9 32.6 + - + +
387C LEU* 3.1 10.5 + - - +
389C ASP* 1.3 90.2 - - - +
391C ILE* 1.3 64.9 + - + +
394C ASN 3.5 6.2 - - - +
395C PHE* 3.5 26.2 - - - -
400C VAL* 4.1 12.1 - - + +
403C GLN* 3.2 55.6 - - + +
404C LEU* 4.4 12.3 - - + -
407C LEU* 4.9 4.3 - - + -
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Residues in contact with ILE 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ILE* 4.7 8.1 - - + -
387C LEU* 2.9 44.6 + - + +
390C ILE* 1.3 87.3 - - + +
392C GLU* 1.3 72.3 + - + +
393C VAL 3.8 0.2 - - - -
395C PHE* 3.7 20.1 - - + +
400C VAL* 6.2 0.2 - - + -
404C LEU* 4.6 3.1 - - + -
424C LEU* 4.1 8.1 - - + -
427C VAL* 4.6 9.2 - - + -
428C ILE* 3.5 40.6 - - + -
431C ARG* 3.4 35.2 - - + +
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Residues in contact with GLU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ILE* 4.9 2.9 - - + +
339C GLU* 4.7 0.3 - - - +
363C ARG* 2.7 46.0 + - - +
364C LYS* 5.8 4.3 - - - +
367C LEU* 4.0 9.7 - - + +
388C TYR* 2.9 48.7 + - + +
391C ILE* 1.3 86.9 - - + +
393C VAL* 1.3 64.1 + - - +
395C PHE* 5.3 0.6 - - - +
431C ARG* 2.9 23.1 + - - +
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Residues in contact with VAL 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C TYR* 3.1 37.6 + - + +
389C ASP* 3.0 25.5 + - + +
392C GLU* 1.3 80.8 - - - +
394C ASN* 1.3 84.9 + - - +
395C PHE* 3.7 3.3 + - - +
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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